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SynBio, Volume 2, Issue 3 (September 2024) – 6 articles

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18 pages, 652 KiB

Open AccessReview

Can Methylococcus capsulatus Revolutionize Methane Capture and Utilization for Sustainable Energy Production?

by Adenike A. Akinsemolu and Helen N. Onyeaka

SynBio 2024, 2(3), 311-328; https://doi.org/10.3390/synbio2030019 - 4 Sep 2024

Viewed by 1544

Abstract

Methane is the second largest contributor to global warming after carbon dioxide. Once it is released into the atmosphere, methane lingers for over 10 years, during which it traps heat, contributes to the formation of ground-level ozone, and affects air quality adversely. Conversely, methane has some benefits that could be harnessed to address its impact on the environment while utilizing it for good. Methane’s significant role in global warming and potential for energy production and other beneficial applications necessitate the adoption of innovative solutions to remediate the gas from the atmosphere and harness some of its benefits. This article explores Methylococcus capsulatus, a methanotrophic bacterium, and its potential for revolutionizing sustainable methane capture and utilization. With its unique metabolic abilities, M. capsulatus efficiently oxidizes methane, making it a promising candidate for biotechnological applications. We review current research in its current and potential applications in methane capture and utilization, emphasizing key characteristics, implementation challenges, benefits, and limitations in methane capture and conversion. We also highlight the importance of interdisciplinary collaborations and technological advancements in synthetic biology to maximize its energy production potential. Our article analyzes M. capsulatus’ role in addressing methane-related environmental concerns and advancing sustainable energy solutions. Full article

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13 pages, 2984 KiB

Open AccessArticle

The Crystal Structure of Thermal Green Protein Q66E (TGP-E) and Yellow Thermostable Protein (YTP-E) E148D

by Matthew R. Anderson, Caitlin M. Padgett, Victoria O. Ogbeifun and Natasha M. DeVore

SynBio 2024, 2(3), 298-310; https://doi.org/10.3390/synbio2030018 - 23 Aug 2024

Viewed by 1149

Abstract

Thermal green protein Q66E (TGP-E) has previously shown increased thermal stability compared to thermal green protein (TGP), a thermal stable fluorescent protein produced through consensus and surface protein engineering. In this paper, we describe the protein crystal structure of TGP-E to 2.0 Å. This structure reveals alterations in the hydrogen bond network near the chromophore that may result in the observed increase in thermal stability. We compare the very stable TGP-E protein to the structure of a yellow mutant version of this protein YTP-E E148D. The structure of this mutant protein reveals the rationale for the observed low quantum yield and directions for future protein engineering efforts. Full article

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13 pages, 4077 KiB

Open AccessArticle

The Natural Evolution of RNA Viruses Provides Important Clues about the Origin of SARS-CoV-2 Variants

by Hiroshi Arakawa

SynBio 2024, 2(3), 285-297; https://doi.org/10.3390/synbio2030017 - 16 Aug 2024

Viewed by 15639

Abstract

Despite the recent pandemic, the origin of its causative agent, SARS-CoV-2, remains controversial. This study identifies several prototype SARS-CoV-2 variants (proto-variants) that are descendants of the Wuhan variant. A thorough evaluation of the evolutionary histories of the genomes of these proto-variants reveals that most mutations in proto-variants were biased toward mutations that change the amino acid sequence. While these nonsynonymous substitutions (N mutations) were common in SARS-CoV-2 proto-variants, nucleotide changes that do not result in an amino acid change, termed synonymous substitutions (S mutations), dominate the mutations found in other RNA viruses. The N mutation bias in the SARS-CoV2 proto-variants was found in the spike gene as well as several other genes. The analysis of the ratio of N to S mutations in general RNA viruses revealed that the probability that an RNA virus spontaneously evolves a proto-variant is between 1.5 × 10⁻⁹ and 2.7 × 10⁻²⁶ under natural conditions. These results suggest that SARS-CoV-2 variants did not emerge via a canonical route. Full article

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18 pages, 1805 KiB

Open AccessReview

Tropical Fruit Virus Resistance in the Era of Next-Generation Plant Breeding

by Marcella Silva Vieira, Rafael Lara Rezende Cabral, Luíza Favaratto, Laiane Silva Maciel, André da Silva Xavier, Francisco Murilo Zerbini and Patricia M. B. Fernandes

SynBio 2024, 2(3), 267-284; https://doi.org/10.3390/synbio2030016 - 8 Jul 2024

Cited by 1 | Viewed by 1335

Abstract

Plant viral diseases constitute a major contributor to agricultural production losses, significantly impacting the economies of exporting countries by more than USD 30 billion annually. Understanding and researching the biology and genomics of viruses is crucial for developing virus-resistant genetically edited or genetically modified plants. Genetic modifications can be targeted to specific regions within genes of target plants which are important or essential for the virus to establish a systemic infection, thus fostering resistance or enabling plants to effectively respond to invading agents while preserving their yield. This review provides an overview of viral incidence and diversity in tropical fruit crops and aims to examine the current state of the knowledge on recent research efforts aimed at reducing or eliminating the damage caused by viral diseases, with emphasis on genetically edited products that have reached the market in recent years. Full article

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13 pages, 1105 KiB

Open AccessArticle

Efficient Stereoselective Biotransformation of Prochiral Carbonyls by Endophytic Fungi from Handroanthus impetiginosus

by Valmore Henrique Pereira dos Santos, Monielly Vasconcellos Pereira de Souza, Maurício Moraes Victor, Valéria Belli Riatto and Eliane Oliveira Silva

SynBio 2024, 2(3), 254-266; https://doi.org/10.3390/synbio2030015 - 5 Jul 2024

Viewed by 700

Abstract

Endophytic microorganisms are promising sources for new biocatalysts as they must deal with their host plants’ chemicals by developing adaptative strategies, such as enzymatic pathways. As part of our efforts in selecting endophytic strains as biocatalysts, this study describes the screening of endophytic fungi isolated from Handroanthus impetiginosus leaves for selective bioreduction of Acetophenone. The bioreductions were monitored by chiral gas chromatography and conducted to the selection of the endophyte Talaromyces sp. H4 as capable of reducing acetophenone to (S)-1-phenylethanol in excellent conversion and enantiomeric excess rates. The influence of seven parameters on the stereoselective bioreduction of acetophenone by Talaromyces sp. H4 was studied: reaction time, inoculum charge, shaking, pH, temperature, substrate concentration, and co-solvent. The optimal conditions were then used to reduce substituted acetophenones and Acetophenone scale-up, which furnished (S)-1-Phenylethanol in 73% yield and 96% ee. The results highlight the endophytic fungus Talaromyces sp. H4 as an excellent biocatalyst for stereoselective reduction of prochiral carbonyls. Full article

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14 pages, 3025 KiB

Open AccessArticle

Metformin Lowers Plasma Triacylglycerol Levels in Mice with Impaired Carnitine Biosynthesis and Fatty Liver

by Bodil Bjørndal, Tra-My Thi Le, Elin Strand, Lise Madsen and Rolf K. Berge

SynBio 2024, 2(3), 240-253; https://doi.org/10.3390/synbio2030014 - 3 Jul 2024

Viewed by 4044

Abstract

The antidiabetic drug metformin has a wide range of metabolic effects and may also reduce the risk of obesity-related diseases. The aim of the current study was to investigate if metformin could counteract meldonium-induced fatty liver. Four groups of male C57BL/6J mice were fed a low-fat control diet, or low-fat diets supplemented with metformin, meldonium, or metformin and meldonium for three weeks. Meldonium treatment led to 5.2-fold higher hepatic triacylglycerol (TAG) levels compared to control, and metformin lowered the meldonium-induced lipid accumulation insignificantly by 21%. Mice treated with metformin and meldonium demonstrated significantly lower weight gain, visceral adipose tissue weight and plasma levels of TAG compared to meldonium alone. The hepatic mRNA level of carnitine palmitoyl transferase 1 was increased 2-fold with combined meldonium and metformin treatment compared to meldonium treatment (p < 0.001). Increased hepatic expression of genes involved in fatty acid oxidation and lipid transport was observed in the combination group compared to control, and increased gene expression of the mitochondrial uncoupling protein UCP2 was observed compared to the meldonium group. In addition, the product of fatty acid oxidation, acetylcarnitine, increased in plasma in metformin-treated mice. Altogether, metformin treatment influenced hepatic lipid metabolism and lowered plasma TAG in meldonium-induced fatty liver in mice. Full article

(This article belongs to the Special Issue Feature Paper Collection in Synthetic Biology)

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