Subject: Life Sciences, Microbiology Keywords: membrane remodeling; membrane biosynthesis; membrane curvature; phospholipids; inner membrane; lipid biosynthesis
Online: 25 August 2020 (10:03:25 CEST)
Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering an abnormal accumulation of membrane structures inside the cells (or membrane proliferation) share two major common features: 1) they promote the formation of highly curved membrane domains and 2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, and inspire new applications, either for academia (high-yield membrane protein production and nanovesicle production) or industry (biofuel production and vaccine preparation).
HYPOTHESIS | doi:10.20944/preprints202004.0186.v5
Online: 11 October 2022 (07:11:27 CEST)
Steroid and hopanoid biomarkers can be found in ancient rocks and may give a glimpse of what life was present at that time. Sterols and hopanoids are produced by two related enzymes, though the evolutionary history of this protein family is complicated by losses and horizontal gene transfers, and appears to be widely misinterpreted. Here, I have added sequences from additional species, and re-analysis of the phylogeny of SHC and OSC indicates a single origin of both enzymes among eukaryotes. This pattern is best explained by endosymbiotic acquisition of both enzymes from a bacterial ancestor, followed by widespread loss of SHC, and two subsequent HGT events to ferns and ascomycetes. Thus, the last common ancestor of eukaryotes would have been bifunctional for both sterol and hopanoid production. Later enzymatic innovations allowed diversification of sterols in eukaryotes. Contrary to previous interpretations, the last eukaryotic common ancestor (LECA) potentially would have been able to produce hopanoids as a substitute for sterols in anaerobic conditions. Without invoking any other metabolic demand, the LECA could have been a facultative aerobe, living in unstable conditions with respect to oxygen level.
REVIEW | doi:10.20944/preprints202211.0548.v1
Subject: Life Sciences, Molecular Biology Keywords: millet; fermentation; microbiome; metagenomics; vitamins; biosynthesis
Online: 29 November 2022 (09:42:36 CET)
Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics and the purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analysis conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipeline with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were significant differences in the relative abundances of bacteria involved in the spontaneous fermentation of millet namely, Lactobacillaceae, Leuconostocaceae, and Clostridiaceae in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristic of fermented millet. The datasets were collected with fermentations mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as vitamins suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.
ARTICLE | doi:10.20944/preprints201903.0015.v1
Subject: Biology, Plant Sciences Keywords: plant; sesquiterpenes; biosynthesis; graph grammars; database;
Online: 1 March 2019 (14:30:16 CET)
Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases. Here, we investigate to what extent metabolic pathways can be reconstructed just from knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β-caryophyllene, α-humulene, and β-farnesene. We also introduce a graph database to integrate simulation results with experimental biological evidence for selected predicted sesquiterpenes biosynthesis.
ARTICLE | doi:10.20944/preprints201811.0371.v1
Subject: Chemistry, Medicinal Chemistry Keywords: biosynthesis; nanoparticles; plant extracts; Citrus reticulata
Online: 16 November 2018 (04:33:22 CET)
Biosynthesis of nanoparticles for delivery of therapeutic agents has introduced new opportunities in upgrading medical treatment. Plant extracts contains different capping and reducing agents naturally thus provided simpler and less expensive way to synthesize AgNPs. In present work, Citrus reticulata mediated stabilised AgNPs was synthesized. Optimum concentration of reactants was achieved by varying the amount of extracts (1-11 ml) and AgNO3 concentration (0.5-3 mM). Surface Plasmon peak of Citrus reticulata mediated AgNPs was determined by UV-visible spectrophotometer and functional groups of capping agents were examined by FTIR analysis. Surface Plasmon peaks of Citrus reticulata fresh peel, seed, and juice extracts were observed at 420 nm. But in dry peel extract, absorption peak of AgNPs appeared at 410 nm. Colour of different extracts was changed after the reduction of AgNO3 to AgNPs by reducing agents present in the extracts. FTIR analysis showed band peaks at 3316 cm-1 correspond to amide (N-H and O-H) stretching vibrations while alkanes peaks was observed at 1638 cm-1 which showed C=C stretching aromatic ring (flavonoids). Furthermore, Citrus reticulata fresh peel mediated AgNPs showed impressive stability up-to 112 days. In conclusion, Citrus reticulata fresh peel extract provided an excellent source of reducing agents for synthesizing stabilized AgNPs.
REVIEW | doi:10.20944/preprints202206.0193.v1
Subject: Chemistry, Organic Chemistry Keywords: aminosugar; antibiotic; biosynthesis; glycosylation; lemonomycin; total synthesis
Online: 14 June 2022 (04:55:21 CEST)
Lemonomycin (1) was first isolated from the fermentation broth of Streptomyces candidus in 1964. The complete chemical structure was not elucidated until 2000 with extensive spectroscopic analysis. Lemonomycin is currently known as the only glycosylated tetrahydroisoquinoline antibiotic. Its potent antibacterial activity against Staphylococcus aureus and Bacillus subtilis and complex architecture make it an ideal target for total synthesis. In this short review, we summarize the research status of lemonomycin for biological activity, biosynthesis and chemical synthesis. The unique deoxy aminosugar-lemonose was proposed to play a crucial role in biological activity, as shown in other antibiotics, such as arimetamycin A, nocathiacin I, glycothiohexide α, and thiazamycins. Given the self-resistance of the original bacterial host, the integration of biosynthesis and chemical synthesis to pursue efficient synthesis and further derivatization is in high demand for the development of novel antibiotics to combat antibiotic-resistant infections.
ARTICLE | doi:10.20944/preprints202206.0188.v1
Subject: Chemistry, Other Keywords: Stigmatellin; Myxobacteria; Biosynthesis; Natural Products; Secondary Metabolites
Online: 13 June 2022 (12:58:42 CEST)
Myxobacteria generate natural products with unique chemical structures, which not only feature remarkable biological functions but also demonstrate unprecedented biosynthetic assembly strategies. The stigmatellins have been previously described as potent inhibitors of the mitochondrial and photosynthetic respiratory chain and originate from an unusual polyketide synthase assembly line. While previous biosynthetic investigations were focused on the formation of the 5,7-dimethoxy-8-hydroxychromone ring, side chain decoration of the hydrophobic alkenyl chain in position 2 was investigated less thoroughly. We report here the full structure elucidation as well as cytotoxic and antimicrobial activities of three new stigmatellins isolated from the myxobacterium Vitiosangium cumulatum MCy10943T with side chain decorations distinct from previously characterized members of this compound family. These findings provide further implications considering the side chain decoration of these aromatic myxobacterial polyketides and their underlying biosynthesis.
ARTICLE | doi:10.20944/preprints202206.0012.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Endopolygalacturonase; biocatalysts; biosynthesis; heteropolysaccharide; inducer; submerged fermentation
Online: 1 June 2022 (09:58:48 CEST)
Endopolygalacturonase (EndoPGase) is one of the crucial pectinases belonging to the class of carbohydrase. The catalytic action of EndoPGase captivate the attention for production of this extremely valuable catalyst of industrial sector. The main focus was to ascertain a potential bacterial candidate for endoPGase production. The isolated bacterial strain was further identified by 16S rDNA gene sequencing. A genomic library was constructed by using Lambda ZAP II vector system to investigate the pectinolytic potential of the expressed genes. The parameters for enzyme biosynthesis were optimized by single as well as multiple factor approach at a time. The results of our investigation led to the identification of a potent strain of Bacillus subtilis NR2. The strain was found active for pectic enzyme activity under shaking- flask fermentation at pH 5.0 and 50 °C temperature of incubation. Among all monomeric and polymeric substrates, citrus pectin followed by wheat bran was considered the best enzyme inducers at 1 % concentration. Moreover, an increasing trend in enzyme activity was observed with the increasing inducer concentration. The combined effect of three variables (pH, substrates, and substrate concentration) was explored by response surface methodology involving Box Benken Design (BBD). The study concluded that the soil isolated B. subtilis can be utilized for commercial scale pectinase enzyme production.
Subject: Biology, Plant Sciences Keywords: L. tulipifera; tepal; carotenoid biosynthesis; LtuPTOX; functional analysis
Online: 17 September 2019 (12:06:02 CEST)
Flower color and color patterns are important traits for ornamental species; for this reason, a comprehensive understanding of the genetic mechanisms underlying these characters is extremely significant for plant breeders. The tulip tree (Liriodendron tulipifera Linn.) is well known for its flowers, odd leaves and tree form. However, the genetic mechanism underlying its flower color remains unknown. In this study, a putative LtuPTOX gene was identified based on multiple databases of differential transcript expression at various developmental stages and the complete genome sequence of Liriodendron. Then, the full-length cDNA of LtuPTOX was derived from tepals and leaves using RACE approaches. Furthermore, the gene structure and a phylogenetic analysis of PTOX as well as AOXs, highly similar homologs in the AOX family, were used to distinguish between the two subfamilies of genes. In addition, transient transformation and qPCR methods were used to determine the subcellular localization and tissue expression pattern of the LtuPTOX gene. Moreover, the expression of LtuPTOX as well as pigment contents was investigated to illustrate the function of this gene during the formation of orange bands on petals. The results showed that the LtuPTOX gene encodes a 358-aa protein that contains a complete AOX domain (PF01768.17). Accordingly, Liriodendron PTOX and AOX genes were identified as only paralogs since they were rather similar in the sequence. LtuPTOX showed chloroplast localization, and expressed in the colored organs such as petals and leaves. In addition, increasing pattern of LtuPTOX transcripts lead to carotenoids accumulation on the orange-band in the development period of flower bud. Taken together, our results provide that LtuPTOX is involved in petal carotenoid metabolism and orange band formation in L. tulipifera. Meanwhile, the identification of this potentially involved gene will lay a foundation for further uncovering the mechanism of flower color formation in L. tulipifera.
ARTICLE | doi:10.20944/preprints202301.0085.v1
Subject: Life Sciences, Virology Keywords: Biothermodynamics; Biosynthesis; Driving force; Life; Virus; Pathogen-host interaction
Online: 5 January 2023 (01:26:04 CET)
Viroids represent the simplest, but are also among the most interesting life-like forms. They represent a great problem in agriculture. Moreover, pathogens similar to viroids, such as the hepatitis Delta virus represent a risk for human health. Viroids encode no proteins, but are still able to hijack their host cells’ metabolism to perform multiplication. This paper attempts to reply three questions about viroids. First, how can viroids hijack their host cells’ metabolism, even though they encode no proteins to achieve this? Second, what advantages do viroids have from their simplicity? Third, what can viroids, as the simplest life-like forms, tell us about life as a natural phenomenon? These questions are discussed from the perspective of biothermodynamics. In order to do this, elemental composition, biosynthesis reactions and standard thermodynamic properties of viroids have been determined and analyzed.
REVIEW | doi:10.20944/preprints201905.0063.v1
Subject: Biology, Ecology Keywords: biotechnologies; marine bacteria; secondary metabolites; nonribosomal biosynthesis; antibacterial strategies
Online: 6 May 2019 (12:15:50 CEST)
The highly dangerous trend of escalating bacterial resistance to modern antibiotics has evolved in recent decades, with increasingly more drug-resistant strains of pathogens emerging and spreading each year. This poses a threat to not only public health, but also to entire mankind. Marine bioresources, considered as a promising alternative to traditional antibiotics and a valuable source of biologically active compounds with high pharmacological potential, now attract increasing attention of researchers. Modern biotechnology combines the genetic engineering methods and the unusual biosynthetic pathways utilized by marine microorganisms to produce natural antibiotics. The goal of this review is to summarize the latest trends in searching for new natural antimicrobial agents based on secondary metabolites of marine bacteria. The targeted control of biosynthesis mechanisms using the metabolic engineering methods in order to create hybrid peptide synthetases or to obtain hybrid peptides by disrupting the target gene of nonribosomal synthesis becomes a noteworthy trend in modern biotechnology. This pathway is not only one of the most promising approaches to the development of new antibiotics, but also a potential target for controlling the exocrine activity of pathogenic bacteria and, consequently, their viability.
ARTICLE | doi:10.20944/preprints202105.0600.v1
Subject: Life Sciences, Biochemistry Keywords: heparan sulfate; glycosaminoglycan; carbohydrate biosynthesis; azido sugar; small molecule inhibitor
Online: 25 May 2021 (10:17:59 CEST)
The glycosaminoglycan, heparan sulphate (HS), orchestrates many developmental processes. Yet its biological role has not yet fully been elucidated. Small molecule chemical inhibitors can be used to perturb HS function and these compounds pro-vide cheap alternatives to genetic manipulation methods. However, existing chemical inhibition methods for HS also interfere with chondroitin sulphate (CS), complicating data interpretation of HS function. Herein, a simple method for the selective inhibition of HS biosynthesis is described. Using endogenous metabolic sugar pathways, Ac4GalNAz produces UDP-GlcNAz, which can target HS synthesis. Cell treatment with Ac4GalNAz resulted in defective chain elongation of the polymer and decreased HS expression. Conversely, no adverse effect on CS production was observed. The inhibition was transient and dose-dependent, affording rescue of HS expression after removal of the unnatural azido sugar. The utility of inhibition is demonstrated in cell culture and in whole or-ganisms, demonstrating that this small molecule can be used as a tool for HS inhibition in biological systems.
Subject: Biology, Plant Sciences Keywords: soybean; strigolactones; biosynthesis and signaling genes; expression patterns; salt stress
Online: 3 October 2019 (14:01:36 CEST)
Strigolactones (SLs) are a novel emerging plant hormones, which play important roles in regulating plant organ development and environmental stress tolerance. Even though the SL related genes have been identified and well characterized in some plants. The information of SL related genes in soybean is not fully established yet, especially in response to salt stress. In this study, we identified nine SL biosynthesis genes: two D27, two CCD7, two CCD8, and three MAX1, and seven SL signaling genes: two D14, two MAX2 and three D53 in soybean genome. We found that SL biosynthesis and signaling genes are conserved during evolution in different species. Syntenic analysis of these genes revealed their location on nine chromosomes as well as existence of ten pairs of duplication genes. Moreover, plant hormone and stress-responsive elements were identified in the promoter regions of SL biosynthesis and signaling genes. By using quantitative real-time PCR (qRT-PCR), we confirmed that SL genes have different tissue expression in roots, stems and leaves. Further, we also explored the expression profiles of SL biosynthesis and signaling genes under salt stress. These results suggested that SL signaling genes may play important regulatory roles in response to salt stress. In conclusion, we identified and provided valuable information on the soybean SL biosynthesis and signaling genes, and established a foundation for further functional analysis of soybean SL related genes in response to salt stress.
REVIEW | doi:10.20944/preprints201902.0235.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: nanotechnology; nanoparticles; biosynthesis; agriculture; food sciences; health sciences; environmental sciences
Online: 26 February 2019 (10:56:29 CET)
Agriculture sector is the backbone of developing countries for their economy. Growing world’s population is putting more pressure on agriculture sector and there is a need to develop new technology to address the crises of food safety and food shortage. Today’s agriculture has been entered in a new era where nanotechnology works as a technological advancement regarding entire agriculture crops, and food sector revolution, even though, it has prodigious applications in food production, food processing, food packaging, food storage and economic growth of industries. Moreover, nanotechnology is the best solution to solve problems related to better food and agriculture. Likewise, biotechnology, nanotechnology also raised high concerns upon safety on biodiversity, health and environment. Nanotechnology is providing efficient alternatives to increase the crop production by managing the insect/pests in agriculture in an eco-friendly manner. It also promotes plant efficiency to absorb nutrients. However, the concerns are very high regarding regulation, safety and approval of nanotechnology products by risk assessment authorities. The suggested review includes stupendous applications of nanotechnology in food and agriculture sector along with its prospective merits and associated risks.
REVIEW | doi:10.20944/preprints201909.0244.v1
Subject: Chemistry, Applied Chemistry Keywords: cofactor F420; deazaflavin; oxidoreductase; hydride transfer; hydrogenation; asymmetric synthesis; cofactor biosynthesis
Online: 21 September 2019 (01:28:13 CEST)
Asymmetric reduction of enoates, imines and ketones are among the most important reactions in biocatalysis. These reactions are routinely conducted using enzymes that use nicotinamide cofactors as reductants. The deazaflavin cofactor F420 also has electrochemical properties that make it suitable as an alternative to nicotinamide cofactors for use in asymmetric reduction reactions. However, cofactor F420-dependent enzymes remain under-explored as a resource for biocatalysis. In this review, we consider the cofactor F420-dependent enzyme families with greatest potential for the discovery of new biocatalysts: the flavin/deazaflavin-dependent oxidoreductases (FDORs) and the luciferase-like hydride transferases (LLHTs). We discuss characterized F420-dependent reductions that have potential for adaptation for biocatalysis, and we consider the enzymes best suited for use in the reduction of oxidized cofactor F420 to allow cofactor recycling in situ. We also discuss recent advances in the production of cofactor F420 and its functional analog FO-5’- phosphate, which remains an impediment to the adoption of this family of enzymes for industrial biocatalytic processes. Finally, we discuss the prospects for the use of this cofactor and dependent enzymes as a resource for industrial biocatalysis.
COMMUNICATION | doi:10.20944/preprints202209.0147.v1
Subject: Life Sciences, Microbiology Keywords: Myxochelin; Myxobacteria; Biosynthesis; Natural Products; Secondary Metabolites; Succinylation; Siderophore; Succinyl-coenzyme A
Online: 12 September 2022 (12:22:43 CEST)
Myxobacteria feature unique biological characteristics including their capability to glide on surface, undergo different multicellular developmental stages and produce structurally unique natural products such as the catecholate-type siderophores myxochelin A and B. Herein, we report the isolation, structure elucidation and biosynthesis of the new congener myxochelin B-succinate from the terrestrial myxobacterial strain MSr12020, featuring a succinyl decoration at its primary amine group. Myxochelin-B-succinate exhibited antifungal growth inhibition and moderate cytotoxic activity against selected human cancer cell lines. This unique chemical modification of myxochelin B might provide interesting insights for future microbiological studies to understand the biological function and biosynthesis of secondary metabolite succinylation.
REVIEW | doi:10.20944/preprints202201.0342.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Anthocyanin biosynthesis; biosafety regulations; colored vegetables; crossbreeding; gene editing; human health; transgenes
Online: 24 January 2022 (10:38:22 CET)
Malnutrition, unhealthy diets, and lifestyle changes have become major risk factors for non-communicable diseases while ad-versely impacting economic growth and sustainable development. Anthocyanins, a group of flavonoids that are rich in fruits and vegetables, contribute positively to human health. This review focuses on genetic variation harnessed through crossbreeding and biotechnology-led approaches for developing anthocyanins-rich fruit and vegetable crops. Significant progress has been made in identifying genes involved in anthocyanin biosynthesis in various crops. Thus, the use of genetics has led to the development and release of anthocyanin-rich crop cultivars in Europe and USA. Such a trend is emerging in the developing world. The purple pota-to “Kufri Neelkanth” has been released for cultivation in northern India, and a few colored grain wheat lines, developed through crossbreeding, are being tested for their productivity and adaptation. Although tomato is deficient in anthocyanins, some of its wild relatives are known to accumulate anthocyanins in their sub-epidermal fruit tissue. In Europe, anthocyanin-rich tomato cul-tivar ‘Sun Black’ developed via the introgression of Aft and atv genes has been released. The development of anthocyanin-rich food crops without any significant yield penalty has been due to the use of genetic engineering involving specific transcription factors or gene editing. The anthocyanin-rich food ingredients have the potential of being more nutritious than those devoid of anthocyanins. The inclusion of anthocyanins as a target characteristic in breeding programs can ensure the development of culti-vars to meet the nutritional needs for human consumption, particularly in the developing world.
ARTICLE | doi:10.20944/preprints201608.0120.v1
Subject: Chemistry, Other Keywords: green nanotechnology; gold nanoparticles; biosynthesis; high resolution transmission electron microscopy; Cape flora
Online: 11 August 2016 (09:53:19 CEST)
The preparation of gold nanoparticles (AuNPs) involves a variety of chemical and physical methods. These methods use toxic and environmentally harmful chemicals. Consequently, the synthesis of AuNPs using green chemistry has been under investigation to develop eco-friendly nanoparticles. One method to achieve this is the use of plant-derived phytochemicals capable of reducing gold ions to produce AuNPs. The aim of this study was to implement a facile microtitre-plate method to screen a large number of aqueous plant extracts to determine the optimum concentration (OC) to bio-synthesize the AuNPs. Several AuNPs of different sizes and shapes were successfully synthesized and characterized from seventeen South African plants. The characterization was done using Ultra Violet-Visible Spectroscopy, Dynamic Light Scattering, High Resolution Transmission Electron Microscopy and Energy-Dispersive X-ray Spectroscopy. We also studied the effects of temperature on the synthesis of the nanoparticles and measured its effect on the particle size of the synthesized AuNPs and the data showed that changes in temperatures affect the size and dispersity of the generated AuNPs. Further, some of the synthesized AuNPs were stable upon incubation with different biological solutions in vitro.
ARTICLE | doi:10.20944/preprints202212.0454.v1
Subject: Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Vaccine; Attenuation; Biothermodynamics; Gibbs energy; Permissiveness; Biosynthesis; Multiplication
Online: 23 December 2022 (08:15:06 CET)
Live attenuated vaccines have through history proved themselves as safe and efficient. Pasteur has developed a vaccine against rabies, through a long process of passage of the virus wild type through rabbits. The result was one of the most efficient attenuated live-virus vaccines. This paper suggests a method based on calculations of biothermodynamic properties of potential tissues for vaccine application, predilected host tissue and virus wild type. Gibbs energy of biosynthesis represents the thermodynamic driving force for virus multiplication. The attenuated strain of the virus should possess Gibbs energy of biosynthesis, which is less negative than the predilected target tissue, but more negative than the vaccine portal tissue. In that way, the attenuated virus strain should be able to multiply in the vaccine portal of entry tissue and cause an immune response, making it efficient. On the other hand, the attenuated strain cannot multiply in the predilected host tissue, making it safe. The attenuation is achieved by adding a gene to the virus, which encodes a ballast protein. Production of the ballast protein would make virus multiplication less favorable, since it would require energy, but be useless to the virus.
REVIEW | doi:10.20944/preprints202203.0124.v2
Subject: Biology, Plant Sciences Keywords: anthocyanins; proanthocyanidins; flavonols; flavones; flavonoid transport; flavonoid biosynthesis; flavonoid accumulation; ligandin; MATE; ABCC
Online: 28 March 2022 (17:03:39 CEST)
Flavonoids are a biochemically diverse group of specialized metabolites in plants that are derived from phenylalanine. While the biosynthesis of the flavonoid aglycone is highly conserved across species and well characterized, numerous species-specific decoration steps and their relevance remained largely unexplored. The flavonoid biosynthesis takes place at the cytosolic site of the endoplasmatic reticulum (ER), but accumulation of various flavonoids was observed in the central vacuole. A universal explanation for the subcellular transport of flavonoids has eluded researchers for decades. Current knowledge suggests that a glutathione S-transferase-like protein (ligandin) protects anthocyanins and potentially proanthocyanidin precursors during the transport to the central vacuole. ABCC transporters and to a lower extend MATE transporters sequester anthocyanins into the vacuole. Glycosides of specific proanthocyanidin precursors are sequestered through MATE transporters. A P-ATPase in the tonoplast and potentially other proteins generate the proton gradient that is required for the MATE-mediated antiport. Vesicle-mediated transport of flavonoids from the ER to the vacuole is considered as an alternative or additional route.
REVIEW | doi:10.20944/preprints202105.0430.v1
Subject: Life Sciences, Biochemistry Keywords: ethylene biosynthesis; ethylene inhibitors; in vitro culture; plant hormones; S-adenosylmethionine; stress responses
Online: 19 May 2021 (07:50:29 CEST)
Ethylene is a plant hormone controlling physiological and developmental processes such fruit maturation, hairy root formation and leaf abscission. Its effect on regeneration systems, such as organogenesis and somatic embryogenesis (SE), has been studied and progresses in molecular biology techniques have contributed to unveil mechanisms behind its effects. This compound affects regeneration differently, depending on the species, genotype and explant. In some species, ethylene seems to revert recalcitrance in genotypes with low regeneration capacity. However, its effect is not addictive, since in genotypes with high regeneration capacity this ability decreases in the presence of ethylene precursors, suggesting that regeneration is modulated by ethylene. Several lines of evidence have shown that the role of ethylene on regeneration is markedly connected to biotic and abiotic stresses as well as to hormonal-crosstalk, in particular with key regeneration hormones and growth regulators of the auxin and cytokinin families. Transcriptional factors of the ethylene response factor (ERF) family are regulated by ethylene and strongly connected to SE induction. Thus, an evident connection between ethylene, stress responses and regeneration capacity is markedly established. In this review the effect of ethylene and the way it interacts with other players during organogenesis and somatic embryogenesis is discussed.
ARTICLE | doi:10.20944/preprints202107.0315.v1
Subject: Chemistry, Analytical Chemistry Keywords: Myxobacteria; myxochelin; nicotinic acid; secondary metabolites; natural product discovery; precursor-directed biosynthesis; total synthesis
Online: 14 July 2021 (10:03:32 CEST)
Myxobacteria represent a viable source of chemically diverse and biologically active secondary metabolites. The myxochelins are a well-studied family of catecholate-type siderophores produced by various myxobacterial strains. Here, we report the discovery, isolation and structure elucidation of three new myxochelins N1–N3 from the terrestrial myxobacterium Corallococcus sp. MCy9049, featuring an unusual nicotinic acid moiety. Precursor-directed biosynthesis (PDB) experiments and total synthesis were performed in order to confirm structures, improve access to pure compounds for bioactivity testing and to devise a biosynthesis proposal. The combined evaluation of metabolome and genome data covering myxobacteria supports the notion that the new myxochelin congeners reported here are in fact frequent side products of the known myxochelin A biosynthetic pathway in myxobacteria.
ARTICLE | doi:10.20944/preprints202204.0137.v1
Subject: Biology, Animal Sciences & Zoology Keywords: Taihe silky fowl; metabolic components; un-targeted metabolome; breed and feed; biosynthesis of amino acids
Online: 15 April 2022 (05:47:06 CEST)
Chinese Taihe Black-bone silky fowl (TBsf) is the homology of medicine and food and has high nutritional and medical value all over the world. However, the nutritional compositions and specific metabolite advantages of Taihe silky fowl muscle are still poorly understood. In this study, we investigated the differences of nutritional components between TBsf and another similar breed (Black Feathered chicken and laid green-shelled eggs, BF-gsc). Meanwhile, we also explored the divergences in muscle characteristics of Taihe silky fowl fed with two different diets, that is normal chicken feed (TBsf-ncf) and Broussonetia papyrifera-fermented feed (TBsf-bpf). Firstly, the growth performance and biochemical index of Taihe silky fowl was significantly different compared with black-feathered chicken. Secondly, we identified the metabolic alterations in Taihe silky fowl by performing an un-targeted UHPLC-Q-TOF-MS/MS analysis. Our results suggested that the whole metabonomic characteristics had obvious separation between TBsf-ncf, TBsf-bpf and BF-gsc groups both in the positive and negative ion mode by PCA analysis. Next, OPLS-DA multivariate analysis revealed that 57 metabolites (in positive mode) and 49 metabolites (in negative mode) were identified as differential metabolites between TBsf-ncf and BF-gsc group. These differential metabolites were mainly enriched to ABC transporters, biosynthesis of amino acids and aminoacyl-tRNA biosynthesis. Besides, there were 47 metabolites (in positive) and 13 metabolites (in negative) were differentially regulated between TBsf-ncf and TBsf-bpf group, which were majorly involved in histidine metabolism and linoleic metabolism. Furthermore, the integrated network analysis suggested that DL-arginine, DL-isoleucine, linoleoylcarnitine, stearoylcarnitine (positive) and ricionleic acid, D-proline, uric acid (negative) were the significantly metabolic biomarkers in Taihe silky fowl. Moreover, the metabolites of primaquine, ticlpoidine, riboflavin, acetylcarnitine (positive) and salicylic acid, acetaminophen sulfate, glutamic acid (negative) were markedly changed in the Taihe silky fowl fed with BP-fermented feed. In summary, a global survey of the nutritional components and metabolite differences were performed in muscle tissues of Taihe silky fowl between various breeds and feeds. The comprehensive expression profiles of the metabolites in Taihe silky fowl affected by genetic and environmental factors were acquired. This study provided valuable evidence fo breed and feed-induced putative biomarkers as well as improved the economic value of Taihe silky fowl through targeted metabolite regulation.
COMMUNICATION | doi:10.20944/preprints201911.0051.v1
Subject: Chemistry, Organic Chemistry Keywords: lactones; lactames; isoindolinones; non-enzymatic biosynthesis; benzophenones; polyketides; reactive natural products; SAHA; aniline, hydroxamic acids
Online: 6 November 2019 (02:53:57 CET)
The structures of recently discovered primarolides A and B suggest their non-enzymatic formation from a common 2-formylbenzophenone precursor. This hypothesis is based on the experimentally proven facile conversion of pestalone (also a 2-formyl-benzophenone) either into the isomeric lactone pestalalactone or the structurally related isoindolinone pestalachloride A. In a related fashion, the racemic isoindolinone natural product mariline A is supposed to biosynthetically originate from the corresponding keto-aldehyde and an aniline, as experimentally supported by model studies. Due to the close structural relationship with known systems, it appears highly probable that primarolides A and B were generated under the fermentation conditions from a massarinin-related 2-formylbenzophenone (proprimarolide) by reaction either with aniline or a nucleophilic catalyst, respectively. Suberoylanilide hydroxamic acid (SAHA), used as an additive during the fermentation, is supposed to act both as a source of aniline and as a nucleophilic catalyst.
ARTICLE | doi:10.20944/preprints201902.0082.v1
Subject: Life Sciences, Biochemistry Keywords: positional isomerism; PUFA biosynthesis; membrane remodelling; membrane lipidomics; lipidomic analysis; fluidity; functional two photon microscopy
Online: 8 February 2019 (09:43:06 CET)
Palmitic acid metabolism involves delta-9 and delta-6 desaturase enzymes forming palmitoleic acid (9cis-16:1; n-7 series) and sapienic acid (6cis-16:1; n-10 series), respectively. The corresponding biological consequences and lipidomic research on these positional MUFA isomers are under development. Furthermore, sapienic acid can bring to the de novo synthesis of the n-10 polyunsaturated fatty acid (PUFA) sebaleic acid (5cis,8cis-18:2), but such transformations in cancer cells are not known. The model of Caco-2 cell line was used to monitor sapienic acid supplementation (150 and 300 μM) and evidence the formation of n-10 fatty acids as well as their incorporation at levels of membrane phospholipids and triglycerides. Comparison with palmitoleic and palmitic acids evidenced that lipid remodeling was influenced by the type of fatty acid and positional isomer, with increase of 8cis-18:1, n-10 PUFA and decrease of saturated fats in case of sapienic acid. Cholesteryl esters were formed only in case of sapienic acid. EC50 of sapienic acid (232.3 μM at 96 hrs) was the highest found among the tested fatty acids, thus influencing cell viability that was only reduced at 25% at 300 μM, whereas palmitoleic acid induced cell death. Two-photon fluorescent microscopy with Laurdan as a fluorescent dye provided information on membrane fluidity, highlighting that sapienic acid increases the distribution of fluid regions, probably connected with the formation of 8cis-18:1 and the n-10 PUFA in cell lipidome. Our results bring evidence for MUFA positional isomers and de novo PUFA synthesis for developing lipidomic analysis and cancer research.
ARTICLE | doi:10.20944/preprints201808.0548.v1
Subject: Biology, Plant Sciences Keywords: Origanum vulgare; Spodoptera littoralis; terpenoid biosynthesis; larval survival; antioxidant enzyme activity and gene expression; toxicity
Online: 31 August 2018 (13:28:51 CEST)
Terpenoids are toxic compounds produced by plants as a defense strategy against insect herbivores. We tested the effect of Origanum vulgare terpenoids on the generalist herbivore Spodoptera littoralis and the response of the plant to herbivory. Terpenoids were analyzed by GC-FID and GC-MS and quantitative gene expression (qPCR) was evaluated on selected plant genes involved in both terpene biosynthesis. The insect detoxification response to terpenes was evaluated by monitoring antioxidant enzymes activity and expression of insect genes involved in terpene detoxification. O. vulgare terpenoid biosynthesis and gene expression was modulated by S. littoralis feeding. The herbivore-induced increased level of terpenoids (particularly carvacrol and p-cymene) interacted with the herbivore by decreasing larval survival and growth rate. The assimilation by S. littoralis of more than 50% of ingested terpenes correlated with the possible toxic effects of O. vulgare terpenoids. In choice test experiments, carvacrol and γ-terpinene mediated the larval feeding preferences, wherease the prolonged feeding on O. vulgare terpenoids (particularly on γ-terpinene) exerted relevant antinutritional effects on larvae. S. littoralis was found to react to O. vulgare terpenoids by increasing its antioxidant enzymes activities and gene expression, although this was not sufficient to sustain the toxicity of O. vulgare terpenoids.
ARTICLE | doi:10.20944/preprints202212.0122.v1
Subject: Life Sciences, Virology Keywords: COVID-19; Elemental composition; Gibbs energy of biosynthesis; Gibbs energy of binding; Variant of concern (VOC)
Online: 7 December 2022 (09:19:10 CET)
RNA viruses exhibit a great tendency to mutate. Starting from 2019, the wild type that was labeled Hu-1 has during the last 3 years evolved to produce several dozen new variants, as a consequence of mutations. Mutations cause changes in empirical formulas of new virus strains, which lead to change in thermodynamic properties of biosynthesis and binding. These changes cause changes in the rate of reactions of binding of virus antigen to the host cell receptor and the rate of virus multiplication in the host cell. Changes in thermodynamic and kinetic parameters lead to changes in biological parameters of infectivity and pathogenicity. SARS-CoV-2 has starting from in 2019, until today, evolved towards increase in infectivity and maintaining constant pathogenicity, or for some variants a slight decrease in pathogenicity. In the case of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants pathogenicity is identical as in the Omicron BA.2.75 variant. On the other hand, infectivity of the Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants is greater than those of previous variants. This will most likely result in the phenomenon of asymmetric coinfection, that is circulation of several variants in the population, some being dominant.
REVIEW | doi:10.20944/preprints202012.0583.v1
Subject: Life Sciences, Biochemistry Keywords: sideroflexin; mitochondria; mitochondrial transporters; iron homeostasis; iron-sulfur cluster; heme biosynthesis; one-carbon metabolism; ferroptosis; ferritinophagy.
Online: 23 December 2020 (10:40:15 CET)
Sideroflexins (SLC56 family) are highly conserved multi-spanning transmembrane proteins inserted in the inner mitochondrial membrane in eukaryotes. Few data are available on their molecular function but, since their first description, they were thought to be metabolite transporters probably required for iron utilization inside the mitochondrion. Such as numerous mitochondrial transporters, sideroflexins remain poorly characterized. The prototypic member SFXN1 has been recently identified as the previously unknown mitochondrial transporter of serine. Nevertheless, pending questions on the molecular function of sideroflexins remain unsolved, especially their link with iron metabolism. Here, we review the current knowledge on sideroflexins, their presumed mitochondrial functions and the sparse - but growing - evidence linking sideroflexins to iron homeostasis and iron-sulfur cluster biogenesis. Since an imbalance in iron homeostasis can be detrimental at the cellular and organismal levels, we also investigate the relationship between sideroflexins, iron and physiological disorders. Investigating Sideroflexins’ functions constitutes an emerging research field of great interest and will certainly lead to main discoveries on mitochondrial physiopathology.
ARTICLE | doi:10.20944/preprints202210.0386.v1
Subject: Life Sciences, Biophysics Keywords: COVID-19; SARS-CoV-2; Pandemic; Empirical formula; Growth stoichiometry; Thermodynamic properties of biosynthesis; Multiplication rate; Enthalpy; Entropy; Gibbs energy
Online: 25 October 2022 (10:53:13 CEST)
SARS-CoV-2 belongs to the group of RNA viruses with a pronounced tendency to mutate. Omicron BA.2.75 is a subvariant believed to be able to suppress the currently dominant BA.5. Omicron BA.2.75 is characterized by a greater infectivity compared to earlier Omicron variants. However, Gibbs energy of biosynthesis of virus particles is slightly less negative compared to those of other variants. Thus, the multiplication rate of Omicron BA.2.75 is lower than that of other variants. This leads to slower accumulation of newly formed virions and less damage to host cells, indicating evolution of SARS-CoV-2 towards decreasing pathogenicity.