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A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 11967

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Prof. Dr. Zhangli Hu

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Guangdong Technology Research Center for Marine Algal Bioengineering, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
Interests: synthetic biology; natural products; epigenetics; microalgae; chlamydomnas; gene engineering

Special Issue Information

Dear Colleagues,

Natural active compounds are small molecules, including phenylpropanoids, lignans, flavonoids, phenols, terpenoids, tannins and alkaloids, produced naturally by living organisms. Tanshinones, forskolin, taxol and ingenol- angelate, curcumin and resveratrol are the best examples of natural, effective therapeutic products. Natural products have a wide range of applications, including in biomedicine and pharmacotherapy. They also have a variety of biological properties with great potential to cure many serious diseases, including cancer, hepatitis, malaria, asthma, etc. Herbal treatments, which began with total extracts, have evolved into advanced modern techniques that can produce isolated active compounds. Since natural products’ discovery, novel advanced techniques for identification, characterization and application have been developed to address some of the challenges of plant-based therapeutics. With an improved understanding of the biosynthetic and metabolic pathways of natural products, it has become possible to utilize synthetic biology pathways to produce natural products. Several microorganisms, including bacteria, yeast and microalgae, represent ideal platforms for the production of these natural products using synthetic biology approaches. This Special Issue will include original research and reviews related to recent advances in chemical characterization, pharmacological applications and synthetic biology of natural products. Papers may address the construction of engineered microorganisms using synthetic biology approaches, structural elucidation and green preparation of bioactive substances and their role in the treatment of chronic diseases.

Prof. Dr. Zhangli Hu
Guest Editor

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Keywords

natural products
synthetic biology
bioactive components
green manufacturing
therapeutic effect
pharmacology
chronic diseases
medicinal plants
microalgae
engineered microorganisms

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Published Papers (8 papers)

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Research

15 pages, 4523 KiB

Open AccessArticle

Effect of Partial Elimination of Mitochondrial DNA on Genome-Wide Identified AOX Gene Family in Chlamydomonas reinhardtii

by Asadullah Khan, Zuo Jihong, Haolin Luo, Ali Raza, Quaid Hussain and Zhangli Hu

Processes 2024, 12(8), 1654; https://doi.org/10.3390/pr12081654 - 7 Aug 2024

Viewed by 678

Abstract

Using Chlamydomonas as a model organism, we attempted to eliminate mitochondrial DNA (mtDNA) similar to rho⁰ or rho⁻ cells (completely or partially mtDNA-eliminated cells) in yeast. We successfully generated partially mtDNA-eliminated cells named as crm- cells, causing the inactivation of mitochondrial activity. We used three different chemicals to eliminate mtDNA including acriflavine (AF), ethidium bromide (EB) and dideoxycytidine (ddC) which prevents replication, inhibits POLG (DNA polymerase gamma) and terminates the mtDNA chain, respectively. The qPCR method was used to detect the mtDNA copy number and the selected rrnL6 gene for the detection of mitochondria, as well as the selected Chlamydomonas CC-124 strain. A reduction in the mitochondrial copy number led to a higher expression of AOX1, UCP1, PGRL1 and ICL1, which indicates the disturbance of the mitochondria–chloroplast ATP and NADPH balance. We selected AOX genes to further study this family and carried out a genome-wide search to identify AOX genes in green algae (C. reinhardtii). Our results revealed that C. reinhardtii contains four AOX genes, i.e., CrAOX1, CrAOX2, CrAOX3 and CrAOX4, which are distributed on Chr 3, Chr7 and Chr9. All CrAOX genes were predicted to localize in mitochondria using bioinformatics tools. Phylogenetic analysis suggests that these CrAOXs are subdivided into four groups and genes existing in the same group could perform identical functions. Collinearity analysis describes the strong evolutionary relationships of AOXs between the unicellular green algae Chlamydomonas reinhardtii and the multicellular green algae Volvox carteri. GO (gene ontology) annotation analysis predicted that CrAOXs played an integral part in carrying out alternate oxidative and respirative activities. Three putative miRNAs, cre-miR1162-3p, cre-miR1171 and cre-miR914, targeting the CrAOX2 gene were identified. Our studies have laid a foundation for the further use of partially mtDNA-eliminated cells and elucidating the functional characteristics of the AOX gene family. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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16 pages, 680 KiB

Open AccessArticle

Isolation and Characterization of Bacillus Subtilis BSP1 from Soil: Antimicrobial Activity and Optimization of Fermentation Conditions

by Heba Hellany, Jean Claude Assaf, Sara Barada, Dalia el-Badan, Rana El Hajj, Sonia Abou Najem, Antoine G. Abou Fayad and Mahmoud I. Khalil

Processes 2024, 12(8), 1621; https://doi.org/10.3390/pr12081621 - 2 Aug 2024

Viewed by 966

Abstract

This study focused on the isolation, characterization, and evaluation of the antimicrobial and antioxidant activities of a crude extract from Bacillus subtilis isolated from rhizosphere soil. Through biochemical and physiological assessments, followed by whole genome sequencing, the isolate was confirmed as Bacillus subtilis BSP1. We examined the antimicrobial activity of B. subtilis BSP1 metabolites against various pathogenic bacteria and fungi. To enhance its antibacterial efficacy, we optimized the fermentation medium to maximize the secretion of antibacterial agents. Our findings demonstrated that the crude extract exhibited notable antimicrobial properties against various pathogenic bacterial and fungal isolates. The antioxidant test revealed a dose-dependent increase in the extract’s DPPH scavenging activity and reducing power, with an impressive 98.9% DPPH scavenging activity at 30 mg/mL. Importantly, safety assessments indicated a lack of hemolytic activity on human red blood cells, with only 1.3% hemolysis at 100 mg/mL, suggesting its potential suitability for practical applications. In summary, Bacillus subtilis BSP1, isolated from soil, appears to be a promising candidate for antibiotic production. Its significant antimicrobial and antioxidant properties, combined with its safety profile, highlight its potential applications in medicine, agriculture, and biotechnology. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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11 pages, 1710 KiB

Open AccessArticle

Synergistic Effects of Plastid Terminal Oxidases 1 and 2 in Astaxanthin Regulation under Stress Conditions

by Jun Chen, Jiangxin Wang, Hui Li, Ming Xiao, Yihong Zheng, Jiancheng Li, Jinxia Wu and Guanqin Huang

Processes 2024, 12(4), 804; https://doi.org/10.3390/pr12040804 - 17 Apr 2024

Viewed by 887

Abstract

Plastid terminal oxidases (PTOXs) are essential for maintaining photosynthetic efficiency and cellular redox homeostasis. Astaxanthin, a carotenoid pigment with antioxidant properties, is synthesized and accumulates in response to oxidative stress induced by high-light intensity or nutrient limitation. It suggests that PTOX may impact astaxanthin biosynthesis under environmental stress conditions due to its involvement in ROS regulation. The ptox1 gene is thought to have a conserved role in safeguarding the photosynthetic apparatus from over-reduction and participating in energy dissipation. On the other hand, the ptox2 gene seems to be involved in the evolution of astaxanthin synthesis and adaptive responses to diverse environmental stressors. Efficient gene silencing strains were developed in Chlamydomonas reinhardtii CC849 for ptox1 and ptox2. The study found that the ptox2 gene correlates highly with resistance to intense light stress. Furthermore, the ptox2 gene showed increased activity under high salt stress conditions, indicating its importance in stress coping mechanisms. The quantification of astaxanthin in the gene-silenced strains revealed that ptox1 acts as a positive regulator, while ptox2 functions as a negative regulator of astaxanthin accumulation. Understanding the coordination between ptox1 and ptox2 could clarify the synergistic actions of these genes in maintaining photosynthetic performance and redox balance under fluctuating environmental conditions. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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14 pages, 2600 KiB

Open AccessArticle

MYB Transcriptional Factors Affects Upstream and Downstream MEP Pathway and Triterpenoid Biosynthesis in Chlamydomonas reinhardtii

by Muhammad Anwar, Jingkai Wang, Jiancheng Li, Muhammad Mohsin Altaf and Zhangli Hu

Processes 2024, 12(3), 487; https://doi.org/10.3390/pr12030487 - 28 Feb 2024

Cited by 1 | Viewed by 1416

Abstract

Terpenoids are enormous and different types of naturally occurring metabolites playing an important role in industrial applications. Cost-effective and sustainable production of terpenoids at commercial scale is the big challenge because of its low abundance from their natural sources. Metabolic and genetic engineering in microorganisms provide the ideal platform for heterologous overexpression protein systems. The photosynthetic green alga Chlamydomonas reinhardtii is considered as a model host for the production of economic and sustainable terpenoids, but the regulation mechanism of their metabolisms is still unclear. In this study, we have investigated the genetic and metabolic synthetic engineering strategy of MYB transcriptional factors (MYB TFs) in terpenoids’ synthesis from C. reinhardtii for the first time. We heterologous overexpressed MYB TFs, specifically SmMYB36 from Salvia miltiorrhiza in C. reinhardtii. MYB upregulated the key genes involved in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Expression of the SQS gene, which is involved in the downstream triterpenoid synthesis pathway, highly accumulated in MYB-overexpression lines of C. reinhardtii. The contents of squalene increased about 90.20 μg/g in MYB-overexpressed lines. Our results propose the rerouting of the carbon flux toward the biosynthesis of triterpenoids upon overexpression of MYB TFs in C. reinhardtii. Our study suggests imperative novel understandings into the regulation mechanisms of C. reinhardtii triterpenoid metabolism through MYB TFs in photosynthetic green microalgae C. reinhardtii. The role of MYB TFs is investigated for the first time in C. reinhardtii, and provides a prodigious potential for recognizing important transcriptional regulators of the MEP pathway as goals for prospective metabolic and genetic manipulation investigation for increased production of triterpenoids. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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14 pages, 2423 KiB

Open AccessArticle

Underutilized Fig (Ficus carica L.) Cultivars from Puglia Region, Southeastern Italy, for an Innovative Product: Dried Fig Disks

by Giuseppe Ferrara, Andrea Magarelli, Andrea Mazzeo, Antonio Coletta, Pasquale Crupi, Francesco Loperfido, Giuseppe Maggi and Pasquale Venerito

Processes 2023, 11(5), 1485; https://doi.org/10.3390/pr11051485 - 14 May 2023

Cited by 4 | Viewed by 1651

Abstract

Fig fruits have recently received more attention by consumers for their quality as either fresh or dried fruits and, consequently, growers are becoming more interested in the cultivation of this species. Figs are mainly consumed as processed fruits (dried, marmalade, jam, etc.), but limited attention has been paid to new possible processing applications of several local cultivars grown in Mediterranean countries. This study aimed to investigate both the morpho-pomological characteristics and consumer sensory ratings (two groups: students and technicians) for four fig cultivars processed as a new type of product, ‘dried fig disks’. The results showed that three out of the four cultivars (Processotto Nero, Natalese Nera, and Verde di Natale) had good pomological characteristics such as fruit weight and skin color, as well as easy peeling, yield, ripening time, and TSS. The same cultivars received positive hedonic scores for appearance (>5 on a 10-point hedonic scale), flavor (4–6 on a 10-point hedonic scale) and taste (6–7 on a 10-point hedonic scale). The overall score was positive for Processotto Nero, Natalese Nera, and Verde di Natale (>5 on a 10-point hedonic scale), whereas one cultivar, Comunione, was less appreciated (<5 on a 10-point hedonic scale). The flavor–sensory attributes most appreciated were black-red fruit, cooked, grassy, and floral; fig off-flavors were perceived as rancid only by students and to a limited extent. Consumer overall acceptance toward dried fig disks was mainly driven by the acceptability of appearance of the new product, together with pleasant flavor and taste. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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13 pages, 2291 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Involvement of Alternative Splicing in the Nitrogen Starvation Response of Chlamydomonas reinhardtii

by Xingcai Yang, Xiangyu Li, Jialin Zhao, Mingshi Xie, Xinyi Li, Bin Jia and Ying Huang

Processes 2022, 10(12), 2719; https://doi.org/10.3390/pr10122719 - 16 Dec 2022

Cited by 2 | Viewed by 1758

Abstract

Alternative splicing (AS) is a regulatory mechanism of post-transcriptional regulation that plays an important role in plant response to abiotic stresses. However, corresponding research involving the mechanism of AS in the nitrogen starvation response of C. reinhardtii is rare. This study performed a comprehensive and systematic analysis of AS events in C. reinhardtii at nine time points (0 h, 10 m, 30 m, 1 h, 6 h, 8 h, 24 h, and 48 h) under nitrogen starvation. It used STAR and rMATS tools to identify and quantify the probability of the AS event happening through the transcriptome high-throughput sequencing data. A total of 5806 AS events in 3500 genes were identified, and the retained intron and skipped exon were considered the main AS types. The genes related to the AS event in nitrogen starvation were mainly involved in spliceosome and transporter and enriched in the citrate cycle and fatty acid degradation pathways. These results suggested that AS may play an important role in the nitrogen starvation response in C. reinhardtii, and provided insights into post-transcriptional regulation under nitrogen starvation. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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12 pages, 2200 KiB

Open AccessFeature PaperArticle

Expression Analysis of BIRC3 as One Target Gene of Transcription Factor NF-κB for Esophageal Cancer

by Qiulan Luo, Hui Zhu, Yun Li, Qinghan Wu, Junjun Sun and Fei Zhou

Processes 2022, 10(9), 1673; https://doi.org/10.3390/pr10091673 - 23 Aug 2022

Cited by 2 | Viewed by 2226

Abstract

Esophageal cancer (ESCA) is one of the highest lethal malignancy tumors worldwide. Baculoviral IAP repeat-containing protein 3 (BIRC3) is the main inhibitor of apoptosis in many malignancies. The aim of this study was to clarify how BIRC3 acts in ESCA cells. Through TNMplot and GEPIA2 analysis, BIRC3 was found abundantly expressed in ESCA cells. The quantitative RT-PCR assay confirmed BIRC3 was pronouncedly induced in all used ESCA cell lines. In addition, proinflammatory cytokines TNFα and IL-1β were shown to have promotion effects on BIRC3 expression in ESCA cells. These promotive effects were blocked when the function of NF-κB was inhibited by bay 11-7082, which indicates the expression of the BIRC3 gene was regulated via the NF-κB transcription pathway in ESCA. Moreover, bioinformatics analysis showed that the BIRC3 gene had many NF-κB binding cis-elements. Chromatin immunoprecipitation was then performed and it was found that NF-κB directly interacts with cis-elements of the BIRC3 gene. In conclusion, our data proved that the high expression level of BIRC3 maintained the survival of ESCA cells. BIRC3 was up-regulated by proinflammatory cytokine TNFα and IL-1β through the NF-κB signaling pathway, and this may be helpful for esophageal cancer prevention and therapy. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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13 pages, 2823 KiB

Open AccessArticle

Metabolomic Profile and Antibacterial Bioactivity of Akebia trifoliata (Thunb.) Koidz Pericarp Extract

by Jing Chen, Zhimin Sun, Jianhua Chen and Mingbao Luan

Processes 2022, 10(7), 1394; https://doi.org/10.3390/pr10071394 - 17 Jul 2022

Cited by 2 | Viewed by 1502

Abstract

Akebia trifoliata (A. trifoliata) is a significant medicinal and edible fruit crop and has some important bioactivities. However, there are few studies on the bacteriostatic activity of A. trifoliata, and the underlying mechanism of A. trifoliata for antibacterial activity is still unknown. Therefore, the bacteriostatic activity and antibacterial mechanism of A. trifoliata were investigated by a combination of chemical assays, using the UHPLC-TOF-MS/MS technique. The results indicated that alkaloids, triterpenoids, and flavonoids are the major secondary bioactive compounds in A. trifoliata that play a crucial role in antibacterial activity. We found that EEPA exhibited both bacteriostatic and bactericidal effects against all Gram-positive and Gram-negative bacteria tested, with IZDs ranging from 13.80 ± 0.79 to 17.00 ± 0.58 mm. Significant differences in terms of sensitivity between Gram-positive and Gram-negative bacteria were not observed. In contrast, both antibiotics (kanamycin sulfate and ampicillin sodium salt) exhibited much better antimicrobial activity against Gram-positive bacteria than Gram-negative bacteria. In addition, the primary antimicrobial mechanism was that EEPA increased cellular content leakage, altered the cell morphology, and destroyed the internal cell structure. Meanwhile, MA, UA, and OA, as the common triterpenoid components existing in plants, were used to analyze the relationships between the structures and the antimicrobial activities among homologous compounds, to determine the key functional group that plays an antibacterial role in MA, UA, and OA. As result, it was found that both the hydroxide and methyl groups present are important for their antibacterial activity. These findings suggested that EEPA exerted significant antimicrobial activity against S. aureus, E. coli, B. subtilis, and P. aeruginosa and might be a potential natural antibacterial. Full article

(This article belongs to the Special Issue Advances in Chemical Characterization, Pharmacological Applications and Synthetic Biology of Natural Products)

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