Biomolecules

2024

Jump to: 2022, 2021

15 pages, 2689 KiB

Open AccessArticle

Enhancing Acetate Utilization in Phaeodactylum tricornutum through the Introduction of Acetate Transport Protein

by Pu Song, Ning Ma, Shaokun Dong, Hongjin Qiao, Jumei Zhang, Bo Guan, Shanying Tong and Yancui Zhao

Biomolecules 2024, 14(7), 822; https://doi.org/10.3390/biom14070822 - 9 Jul 2024

Viewed by 868

Abstract

The diatom Phaeodactylum tricornutum, known for its high triacylglycerol (TAG) content and significant levels of n-3 long chain polyunsaturated fatty acids (LC-PUFAs), such as eicosapentaenoic acid (EPA), has a limited ability to utilize exogenous organic matter. This study investigates the enhancement of [...] Read more.

The diatom Phaeodactylum tricornutum, known for its high triacylglycerol (TAG) content and significant levels of n-3 long chain polyunsaturated fatty acids (LC-PUFAs), such as eicosapentaenoic acid (EPA), has a limited ability to utilize exogenous organic matter. This study investigates the enhancement of acetate utilization in P. tricornutum by introducing an exogenous acetate transport protein. The acetate transporter gene ADY2 from Saccharomyces cerevisiae endowed the organism with the capability to assimilate acetate and accelerating its growth. The transformants exhibited superior growth rates at an optimal NaAc concentration of 0.01 M, with a 1.7- to 2.0-fold increase compared to the wild-type. The analysis of pigments and photosynthetic activities demonstrated a decline in photosynthetic efficiency and maximum electron transport rate. This decline is speculated to result from the over-reduction of the electron transport components between photosystems due to acetate utilization. Furthermore, the study assessed the impact of acetate on the crude lipid content and fatty acid composition, revealing an increase in the crude lipid content and alterations in fatty acid profiles, particularly an increase in C16:1n-7 at the expense of EPA and a decrease in the unsaturation index. The findings provide insights into guiding the biomass and biologically active products production of P. tricornutum through metabolic engineering. Full article

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2022

Jump to: 2024, 2021

19 pages, 4372 KiB

Open AccessArticle

Rapid and Highly Efficient Genetic Transformation and Application of Interleukin-17B Expressed in Duckweed as Mucosal Vaccine Adjuvant

by Xiao Tan, Shuang Chen, Yang Fang, Penghui Liu, Zhubin Hu, Yanling Jin, Zhuolin Yi, Kaize He, Xing Li, Leyi Zhao, Hongning Wang and Hai Zhao

Biomolecules 2022, 12(12), 1881; https://doi.org/10.3390/biom12121881 - 15 Dec 2022

Cited by 5 | Viewed by 3218

Abstract

Molecular farming utilizes plants as a platform for producing recombinant biopharmaceuticals. Duckweed, the smallest and fastest growing aquatic plant, is a promising candidate for molecular farming. However, the efficiency of current transformation methods is generally not high in duckweed. Here, we developed a [...] Read more.

Molecular farming utilizes plants as a platform for producing recombinant biopharmaceuticals. Duckweed, the smallest and fastest growing aquatic plant, is a promising candidate for molecular farming. However, the efficiency of current transformation methods is generally not high in duckweed. Here, we developed a fast and efficient transformation procedure in Lemna minor ZH0403, requiring 7–8 weeks from screening calluses to transgenic plants with a stable transformation efficiency of 88% at the DNA level and 86% at the protein level. We then used this transformation system to produce chicken interleukin-17B (chIL-17B). The plant-produced chIL-17B activated the NF-κB pathway, JAK-STAT pathway, and their downstream cytokines in DF-1 cells. Furthermore, we administrated chIL-17B transgenic duckweed orally as an immunoadjuvant with mucosal vaccine against infectious bronchitis virus (IBV) in chickens. Both IBV-specific antibody titer and the concentration of secretory immunoglobulin A (sIgA) were significantly higher in the group fed with chIL-17B transgenic plant. This indicates that the duckweed-produced chIL-17B enhanced the humoral and mucosal immune responses. Moreover, chickens fed with chIL-17B transgenic plant demonstrated the lowest viral loads in different tissues among all groups. Our work suggests that cytokines are a promising adjuvant for mucosal vaccination through the oral route. Our work also demonstrates the potential of duckweed in molecular farming. Full article

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16 pages, 4838 KiB

Open AccessArticle

Development of Artificial System to Induce Chromatin Loosening in Saccharomyces cerevisiae

by Ryota Yamamoto, Genki Sato, Takamitsu Amai, Mitsuyoshi Ueda and Kouichi Kuroda

Biomolecules 2022, 12(8), 1138; https://doi.org/10.3390/biom12081138 - 18 Aug 2022

Cited by 2 | Viewed by 2124

Abstract

In eukaryotic cells, loosening of chromatin causes changes in transcription and DNA replication. The artificial conversion of tightly packed chromatin (heterochromatin) to loosely packed chromatin (euchromatin) enables gene expression and regulates cell differentiation. Although some chemicals convert chromatin structures through histone modifications, they [...] Read more.

In eukaryotic cells, loosening of chromatin causes changes in transcription and DNA replication. The artificial conversion of tightly packed chromatin (heterochromatin) to loosely packed chromatin (euchromatin) enables gene expression and regulates cell differentiation. Although some chemicals convert chromatin structures through histone modifications, they lack sequence specificity. This study attempted to establish a novel technology for inducing chromatin loosening in target regions of Saccharomyces cerevisiae. We focused on histone acetylation, which is one of the mechanisms of euchromatin induction. The sequence-recognizing ability of the dead Cas9 (dCas9) and guide RNA (gRNA) complex was used to promote histone acetylation at a targeted genomic locus. We constructed a plasmid to produce a fusion protein consisting of dCas9 and histone acetyltransferase Gcn5 and a plasmid to express gRNA recognizing the upstream region of heterochromatic URA3. Confocal microscopy revealed that the fusion proteins were localized in the nucleus. The yeast strain producing the fusion protein and gRNA grew well in the uracil-deficient medium, while the strain harboring empty plasmids or the strain containing the mutations that cause loss of nucleosomal histone acetylation activity of Gcn5 did not. This suggests that the heterochromatin was loosened as much as euchromatin through nucleosomal histone acetylation. The amount of euchromatic DNA at the target locus increased, indicating that chromatin loosening was induced by our system. Nucleosomal histone acetylation in heterochromatic loci by our developed system is a promising method for inducing euchromatic state in a target locus. Full article

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13 pages, 1829 KiB

Open AccessArticle

Leptolyngbya sp. NIVA-CYA 255, a Promising Candidate for Poly(3-hydroxybutyrate) Production under Mixotrophic Deficiency Conditions

by Alexander Kettner, Matthias Noll and Carola Griehl

Biomolecules 2022, 12(4), 504; https://doi.org/10.3390/biom12040504 - 26 Mar 2022

Cited by 6 | Viewed by 2710

Abstract

Cyanobacteria are a promising source for the sustainable production of biodegradable bioplastics such as poly(3-hydroxybutyrate) (PHB). The auto-phototrophic biomass formation is based on light and CO₂, which is an advantage compared to heterotrophic PHB-producing systems. So far, only a handful of [...] Read more.

Cyanobacteria are a promising source for the sustainable production of biodegradable bioplastics such as poly(3-hydroxybutyrate) (PHB). The auto-phototrophic biomass formation is based on light and CO₂, which is an advantage compared to heterotrophic PHB-producing systems. So far, only a handful of cyanobacterial species suitable for the high-yield synthesis of PHB have been reported. In the present study, the PHB formation, biomass, and elemental composition of Leptolyngbya sp. NIVA-CYA 255 were investigated. Therefore, a three-stage cultivation process was applied, consisting of a growth stage; an N-, P-, and NP-depleted phototrophic stage; and a subsequent mixotrophic deficiency stage, initiated by sodium acetate supplementation. The extracted cyanobacterial PHB was confirmed by FTIR- and GC-MS analyses. Furthermore, the fluorescent dyes LipidGreen2 and Nile red were used for fluorescence-based monitoring and the visualization of PHB. LipidGreen2 was well suited for PHB quantification, while the application of Nile red was limited by fluorescence emission crosstalk with phycocyanin. The highest PHB yields were detected in NP- (325 mg g⁻¹) and N-deficiency (213 mg g⁻¹). The glycogen pool was reduced in all cultures during mixotrophy, while lipid composition was not affected. The highest glycogen yield was formed under N-deficiency (217 mg g⁻¹). Due to the high carbon storage capacity and PHB formation, Leptolyngbya sp. NIVA-CYA 255 is a promising candidate for PHB production. Further work will focus on upscaling to a technical scale and monitoring the formation by LipidGreen2-based fluorometry. Full article

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51 pages, 5141 KiB

Open AccessEditor’s ChoiceArticle

IMGT^®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies

by Marie-Paule Lefranc and Gérard Lefranc

Biomolecules 2022, 12(3), 381; https://doi.org/10.3390/biom12030381 - 28 Feb 2022

Cited by 7 | Viewed by 3528

Abstract

IMGT^®, the international ImMunoGeneTics information system^®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the [...] Read more.

IMGT^®, the international ImMunoGeneTics information system^®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT^® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT^® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT^® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT^®Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies. Full article

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15 pages, 3080 KiB

Open AccessArticle

Enzymatic Synthesis of Maltitol and Its Inhibitory Effect on the Growth of Streptococcus mutans DMST 18777

by Patinya Haewpetch, Prakarn Rudeekulthamrong and Jarunee Kaulpiboon

Biomolecules 2022, 12(2), 167; https://doi.org/10.3390/biom12020167 - 20 Jan 2022

Cited by 4 | Viewed by 2529

Abstract

This study aimed to synthesize maltitol using recombinant CGTase from Bacillus circulans A11 with β-cyclodextrin (β-CD) and sorbitol as a glucosyl donor and acceptor, respectively, and assess its antibacterial activity. Optimal conditions for producing the highest yield, 25.0% (w/w), [...] Read more.

This study aimed to synthesize maltitol using recombinant CGTase from Bacillus circulans A11 with β-cyclodextrin (β-CD) and sorbitol as a glucosyl donor and acceptor, respectively, and assess its antibacterial activity. Optimal conditions for producing the highest yield, 25.0% (w/w), were incubation of 1% (w/v) β-CD and sorbitol with 400 U/mL of CGTase in 20 mM phosphate buffer at pH 6.0 and 50 °C for 72 h. Subsequently, maltitol underwent large-scale production and was purified by HPLC. By mass spectrometry, the molecular weight of the synthesized maltitol was 379.08 daltons, corresponding exactly to that of standard maltitol. The relative sweetness of synthesized and standard maltitol was ~90% of that of sucrose. Spot assay on the agar plate showed that maltitol inhibited the growth of Streptococcus mutans DMST 18777 cells. In addition, the MIC and MBC values of synthesized and standard maltitol against S. mutans were also determined as 20 and 40 mg/mL, respectively. These results show that the synthesized maltitol can be produced at high yields and has the potential to be used as an anticariogenic agent in products such as toothpaste. Full article

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14 pages, 3421 KiB

Open AccessArticle

Whole-Cell Display of Phosphotransferase in Escherichia coli for High-Efficiency Extracellular ATP Production

by Shuai Zhao, Guoli Yang, Xiaochen Xie, Guangbo Yan, Fei Wang, Wanping Chen and Lixin Ma

Biomolecules 2022, 12(1), 139; https://doi.org/10.3390/biom12010139 - 15 Jan 2022

Cited by 7 | Viewed by 2939

Abstract

Adenosine triphosphate (ATP), as a universal energy currency, takes a central role in many biochemical reactions with potential for the synthesis of numerous high-value products. However, the high cost of ATP limits industrial ATP-dependent enzyme-catalyzed reactions. Here, we investigated the effect of cell-surface [...] Read more.

Adenosine triphosphate (ATP), as a universal energy currency, takes a central role in many biochemical reactions with potential for the synthesis of numerous high-value products. However, the high cost of ATP limits industrial ATP-dependent enzyme-catalyzed reactions. Here, we investigated the effect of cell-surface display of phosphotransferase on ATP regeneration in recombinant Escherichia coli. By N-terminal fusion of the super-folder green fluorescent protein (sfGFP), we successfully displayed the phosphotransferase of Pseudomonas brassicacearum (PAP-Pb) on the surface of E. coli cells. The catalytic activity of sfGFP-PAP-Pb intact cells was 2.12 and 1.47 times higher than that of PAP-Pb intact cells, when the substrate was AMP and ADP, respectively. The conversion of ATP from AMP or ADP were up to 97.5% and 80.1% respectively when catalyzed by the surface-displayed enzyme at 37 °C for only 20 min. The whole-cell catalyst was very stable, and the enzyme activity of the whole cell was maintained above 40% after 40 rounds of recovery. Under this condition, 49.01 mg/mL (96.66 mM) ATP was accumulated for multi-rounds reaction. This ATP regeneration system has the characteristics of low cost, long lifetime, flexible compatibility, and great robustness. Full article

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29 pages, 1962 KiB

Open AccessEditor’s ChoiceReview

Anti-Planktonic and Anti-Biofilm Properties of Pentacyclic Triterpenes—Asiatic Acid and Ursolic Acid as Promising Antibacterial Future Pharmaceuticals

by Zuzanna Sycz, Dorota Tichaczek-Goska and Dorota Wojnicz

Biomolecules 2022, 12(1), 98; https://doi.org/10.3390/biom12010098 - 7 Jan 2022

Cited by 38 | Viewed by 3686

Abstract

Due to the ever-increasing number of multidrug-resistant bacteria, research concerning plant-derived compounds with antimicrobial mechanisms of action has been conducted. Pentacyclic triterpenes, which have a broad spectrum of medicinal properties, are one of such groups. Asiatic acid (AA) and ursolic acid (UA), which [...] Read more.

Due to the ever-increasing number of multidrug-resistant bacteria, research concerning plant-derived compounds with antimicrobial mechanisms of action has been conducted. Pentacyclic triterpenes, which have a broad spectrum of medicinal properties, are one of such groups. Asiatic acid (AA) and ursolic acid (UA), which belong to this group, exhibit diverse biological activities that include antioxidant, anti-inflammatory, diuretic, and immunostimulatory. Some of these articles usually contain only a short section describing the antibacterial effects of AA or UA. Therefore, our review article aims to provide the reader with a broader understanding of the activity of these acids against pathogenic bacteria. The bacteria in the human body can live in the planktonic form and create a biofilm structure. Therefore, we found it valuable to present the action of AA and UA on both planktonic and biofilm cultures. The article also presents mechanisms of the biological activity of these substances against microorganisms. Full article

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2021

Jump to: 2024, 2022

22 pages, 4983 KiB

Open AccessEditor’s ChoiceArticle

Quantitative Morphological Analysis of Filamentous Microorganisms in Cocultures and Monocultures: Aspergillus terreus and Streptomyces rimosus Warfare in Bioreactors

by Anna Ścigaczewska, Tomasz Boruta and Marcin Bizukojć

Biomolecules 2021, 11(11), 1740; https://doi.org/10.3390/biom11111740 - 22 Nov 2021

Cited by 4 | Viewed by 1993

Abstract

The aim of this study was to quantitatively characterize the morphology of the filamentous microorganisms Aspergillus terreus ATCC 20542 and Streptomyces rimosus ATCC 10970, cocultivated in stirred tank bioreactors, and to characterize their mutual influence with the use of quantitative image analysis. Three [...] Read more.

The aim of this study was to quantitatively characterize the morphology of the filamentous microorganisms Aspergillus terreus ATCC 20542 and Streptomyces rimosus ATCC 10970, cocultivated in stirred tank bioreactors, and to characterize their mutual influence with the use of quantitative image analysis. Three distinct coculture initiation strategies were applied: preculture versus preculture, spores versus spores and preculture versus preculture with time delay for one of the species. Bioreactor cocultures were accompanied by parallel monoculture controls. The results recorded for the mono- and cocultures were compared in order to investigate the effect of cocultivation on the morphological evolution of A. terreus and S. rimosus. Morphology-related observations were also confronted with the analysis of secondary metabolism. The morphology of the two studied filamentous species strictly depended on the applied coculture initiation strategy. In the cocultures initiated by the simultaneous inoculation, S. rimosus gained domination or advance over A. terreus. The latter microorganism dominated only in these experiments in which S. rimosus was introduced with a delay. Full article

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12 pages, 3565 KiB

Open AccessArticle

Pyrazines Biosynthesis by Bacillus Strains Isolated from Natto Fermented Soybean

by Grzegorz Kłosowski, Dawid Mikulski and Katarzyna Pielech-Przybylska

Biomolecules 2021, 11(11), 1736; https://doi.org/10.3390/biom11111736 - 22 Nov 2021

Cited by 27 | Viewed by 3060

Abstract

Pyrazines are organic compounds with a varied, intense aroma of roasted nuts, occasionally with hints of baked potatoes, almonds, and others. As a result, they are used in the food industry as food flavorings. Biosynthesis of pyrazines using microorganisms in environmentally friendly conditions [...] Read more.

Pyrazines are organic compounds with a varied, intense aroma of roasted nuts, occasionally with hints of baked potatoes, almonds, and others. As a result, they are used in the food industry as food flavorings. Biosynthesis of pyrazines using microorganisms in environmentally friendly conditions is an alternative to chemical synthesis. However, screening is required to isolate efficient producer strains for efficient biosynthesis of this compound. The study’s goal was to assess the ability of Bacillus subtilis cultures isolated from natto (fermented soybeans) to biosynthesize a broad range of alkylpyrazines. B. subtilis isolated cultures were found to be capable of producing 2-methylpyrazine, 2,3-dimethylpyrazine, 2,5-dimethylpyrazine, 2,6-dimethylpyrazine, 2,3,5-trimethylpyrazine, and 2,3,5,6-tetramethylpyrazine. As a result of the screening, two cultures of B. subtilis capable of producing alkylpyrazines were isolated. At a total concentration of 3261 µg/L, the BcP4 strain primarily produced 2-methylpyrazine (690 µg/L), 2,3-dimethylpyrazine (680 µg/L), and 2,6-dimethylpyrazine (1891 µg/L). At a total concentration of 558 mg/L, the BcP21 strain produced 2,5-dimethylpyrazine (4.5 mg/L), 2,3,5-trimethylpyrazine (52.6 mg/L), and 2,3,5,6-tetramethylpyrazine (501.1 mg/L). The results show that different B. subtilis strains are predisposed to produce different alkylpyrazines. Full article

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