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1
Nishida, Hiromi, and Makoto Nishiyama. "Evolution of Lysine Biosynthesis in the Phylum Deinococcus-Thermus." International Journal of Evolutionary Biology 2012 (May 8, 2012): 1–6. http://dx.doi.org/10.1155/2012/745931.
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Thermus thermophilus biosynthesizes lysine through the α-aminoadipate (AAA) pathway: this observation was the first discovery of lysine biosynthesis through the AAA pathway in archaea and bacteria. Genes homologous to the T. thermophilus lysine biosynthetic genes are widely distributed in bacteria of the Deinococcus-Thermus phylum. Our phylogenetic analyses strongly suggest that a common ancestor of the Deinococcus-Thermus phylum had the ancestral genes for bacterial lysine biosynthesis through the AAA pathway. In addition, our findings suggest that the ancestor lacked genes for lysine biosynthesis through the diaminopimelate (DAP) pathway. Interestingly, Deinococcus proteolyticus does not have the genes for lysine biosynthesis through the AAA pathway but does have the genes for lysine biosynthesis through the DAP pathway. Phylogenetic analyses of D. proteolyticus lysine biosynthetic genes showed that the key gene cluster for the DAP pathway was transferred horizontally from a phylogenetically distant organism.
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Moore, Bradley. "Asymmetric Alkene and Arene Halofunctionalization Reactions in Meroterpenoid Biosynthesis." Synlett 29, no. 04 (September 27, 2017): 401–9. http://dx.doi.org/10.1055/s-0036-1590919.
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Meroterpenoid natural products are important bioactive molecules with broad distribution throughout nature. In Streptomyces bacteria, naphthoquinone-based meroterpenoids comprise a simple yet structurally fascinating group of natural product antibiotics that are enzymatically constructed through a series of asymmetric alkene and arene halofunctionalization reactions. This account article highlights our discovery and characterization of a group of vanadium-dependent chloroperoxidase enzymes that catalyze halogen-assisted cyclization and rearrangement reactions and have inspired biomimetic syntheses of numerous meroterpenoid natural products.1 Introduction2 Early Biosynthetic Insights and the Characterization of Alkene Halofunctionalization in Napyradiomycin Biosynthesis3 Discovery of the Merochlorin Natural Products and Enzymatic Aryl Halofunctionalization4 Discovery and Development of Unifying THN-Based Meroterpenoid Biosynthesis and Synthesis Approaches5 Insights into Naphterpin and Marinone Biosynthesis Involving Cryptic Aryl Halofunctionalization Reactions6 Closing Thoughts
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Helfrich, Eric J. N., Geng-Min Lin, Christopher A. Voigt, and Jon Clardy. "Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering." Beilstein Journal of Organic Chemistry 15 (November 29, 2019): 2889–906. http://dx.doi.org/10.3762/bjoc.15.283.
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Terpenoids are the largest and structurally most diverse class of natural products. They possess potent and specific biological activity in multiple assays and against diseases, including cancer and malaria as notable examples. Although the number of characterized terpenoid molecules is huge, our knowledge of how they are biosynthesized is limited, particularly when compared to the well-studied thiotemplate assembly lines. Bacteria have only recently been recognized as having the genetic potential to biosynthesize a large number of complex terpenoids, but our current ability to associate genetic potential with molecular structure is severely restricted. The canonical terpene biosynthetic pathway uses a single enzyme to form a cyclized hydrocarbon backbone followed by modifications with a suite of tailoring enzymes that can generate dozens of different products from a single backbone. This functional promiscuity of terpene biosynthetic pathways renders terpene biosynthesis susceptible to rational pathway engineering using the latest developments in the field of synthetic biology. These engineered pathways will not only facilitate the rational creation of both known and novel terpenoids, their development will deepen our understanding of a significant branch of biosynthesis. The biosynthetic insights gained will likely empower a greater degree of engineering proficiency for non-natural terpene biosynthetic pathways and pave the way towards the biotechnological production of high value terpenoids.
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Araki, Yasuko, Takayoshi Awakawa, Motomichi Matsuzaki, Rihe Cho, Yudai Matsuda, Shotaro Hoshino, Yasutomo Shinohara, et al. "Complete biosynthetic pathways of ascofuranone and ascochlorin inAcremonium egyptiacum." Proceedings of the National Academy of Sciences 116, no. 17 (April 5, 2019): 8269–74. http://dx.doi.org/10.1073/pnas.1819254116.
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Ascofuranone (AF) and ascochlorin (AC) are meroterpenoids produced by various filamentous fungi, includingAcremonium egyptiacum(synonym:Acremonium sclerotigenum), and exhibit diverse physiological activities. In particular, AF is a promising drug candidate against African trypanosomiasis and a potential anticancer lead compound. These compounds are supposedly biosynthesized through farnesylation of orsellinic acid, but the details have not been established. In this study, we present all of the reactions and responsible genes for AF and AC biosyntheses inA. egyptiacum, identified by heterologous expression, in vitro reconstruction, and gene deletion experiments with the aid of a genome-wide differential expression analysis. Both pathways share the common precursor, ilicicolin A epoxide, which is processed by the membrane-bound terpene cyclase (TPC) AscF in AC biosynthesis. AF biosynthesis branches from the precursor by hydroxylation at C-16 by the P450 monooxygenase AscH, followed by cyclization by a membrane-bound TPC AscI. All genes required for AC biosynthesis (ascABCDEFG) and a transcriptional factor (ascR) form a functional gene cluster, whereas those involved in the late steps of AF biosynthesis (ascHIJ) are present in another distantly located cluster. AF is therefore a rare example of fungal secondary metabolites requiring multilocus biosynthetic clusters, which are likely to be controlled by the single regulator, AscR. Finally, we achieved the selective production of AF inA. egyptiacumby genetically blocking the AC biosynthetic pathway; further manipulation of the strain will lead to the cost-effective mass production required for the clinical use of AF.
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Pulsawat, Nattika, Shigeru Kitani, Eriko Fukushima, and Takuya Nihira. "Hierarchical control of virginiamycin production in Streptomyces virginiae by three pathway-specific regulators: VmsS, VmsT and VmsR." Microbiology 155, no. 4 (April 1, 2009): 1250–59. http://dx.doi.org/10.1099/mic.0.022467-0.
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Two regulatory genes encoding a Streptomyces antibiotic regulatory protein (vmsS) and a response regulator (vmsT) of a bacterial two-component signal transduction system are present in the left-hand region of the biosynthetic gene cluster of the antibiotic virginiamycin, which is composed of virginiamycin M (VM) and virginiamycin S (VS), in Streptomyces virginiae. Disruption of vmsS abolished both VM and VS biosynthesis, with drastic alteration of the transcriptional profile for virginiamycin biosynthetic genes, whereas disruption of vmsT resulted in only a loss of VM biosynthesis, suggesting that vmsS is a pathway-specific regulator for both VM and VS biosynthesis, and that vmsT is a pathway-specific regulator for VM biosynthesis alone. Gene expression profiles determined by semiquantitative RT-PCR on the virginiamycin biosynthetic gene cluster demonstrated that vmsS controls the biosynthetic genes for VM and VS, and vmsT controls unidentified gene(s) of VM biosynthesis located outside the biosynthetic gene cluster. In addition, transcriptional analysis of a deletion mutant of vmsR located in the clustered regulatory region in the virginiamycin cluster (and which also acts as a SARP-family activator for both VM and VS biosynthesis) indicated that the expression of vmsS and vmsT is under the control of vmsR, and vmsR also contributes to the expression of VM and VS biosynthetic genes, independent of vmsS and vmsT. Therefore, coordinated virginiamycin biosynthesis is controlled by three pathway-specific regulators which hierarchically control the expression of the biosynthetic gene cluster.
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Liu, Yong-Cheng, Xiao-Xi Peng, Yan-Bing Lu, Xue-Xian Wu, Lin-Wu Chen, and Hong Feng. "Genome-wide association study reveals the genes associated with the leaf inclusion contents in Chinese medical tree Eucommia ulmoides." Bioscience, Biotechnology, and Biochemistry 85, no. 2 (January 20, 2021): 233–41. http://dx.doi.org/10.1093/bbb/zbaa005.
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ABSTRACT Eucommia ulmoides is an economic tree that can biosynthesize secondary metabolites with pharmacological functions. Genetic basis of biosynthesis of these compounds is almost unknown. Therefore, genomic-wide association study was performed to exploit the genetic loci maybe involved in biosynthetic pathways of 5 leaf inclusions (aucubin, chlorogenic acid, gutta-percha, polyphenols, total flavonoids). It was shown that contents of the 5 leaf metabolites have a wide variation following normal distribution. A total of 2 013 102 single nucleotide polymorphism (SNP) markers were identified in a population containing 62 individual clones. Through genome-wide association study analysis, many SNP loci were identified perhaps associated with phenotypes of the leaf inclusions. Higher transcriptional levels of the candidate genes denoted by significant SNPs in leaves suggested they may be involved in biosynthesis of the leaf inclusions. These genetic loci provide with invaluable information for further studies on the gene functions in biosynthesis of the leaf inclusions and selective breeding of the plus trees.
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Sato, Hajime, Masanobu Uchiyama, Kazuki Saito, and Mami Yamazaki. "The Energetic Viability of Δ1-Piperideine Dimerization in Lysine-derived Alkaloid Biosynthesis." Metabolites 8, no. 3 (August 31, 2018): 48. http://dx.doi.org/10.3390/metabo8030048.
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Lys-derived alkaloids widely distributed in plant kingdom have received considerable attention and have been intensively studied; however, little is known about their biosynthetic mechanisms. In terms of the skeleton formation, for example, of quinolizidine alkaloid biosynthesis, only the very first two steps have been identified and the later steps remain unknown. In addition, there is no available information on the number of enzymes and reactions required for their skeletal construction. The involvement of the Δ 1 -piperideine dimerization has been proposed for some of the Lys-derived alkaloid biosyntheses, but no enzymes for this dimerization reaction have been reported to date; moreover, it is not clear whether this dimerization reaction proceeds spontaneously or enzymatically. In this study, the energetic viability of the Δ 1 -piperideine dimerizations under neutral and acidic conditions was assessed using the density functional theory computations. In addition, a similar type of reaction in the dipiperidine indole alkaloid, nitramidine, biosynthesis was also investigated. Our findings will be useful to narrow down the candidate genes involved in the Lys-derived alkaloid biosynthesis.
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Wu, Tong, Yumei Liu, Jinsheng Liu, Zhenya Chen, and Yi-Xin Huo. "Metabolic Engineering and Regulation of Diol Biosynthesis from Renewable Biomass in Escherichia coli." Biomolecules 12, no. 5 (May 18, 2022): 715. http://dx.doi.org/10.3390/biom12050715.
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As bulk chemicals, diols have wide applications in many fields, such as clothing, biofuels, food, surfactant and cosmetics. The traditional chemical synthesis of diols consumes numerous non-renewable energy resources and leads to environmental pollution. Green biosynthesis has emerged as an alternative method to produce diols. Escherichia coli as an ideal microbial factory has been engineered to biosynthesize diols from carbon sources. Here, we comprehensively summarized the biosynthetic pathways of diols from renewable biomass in E. coli and discussed the metabolic-engineering strategies that could enhance the production of diols, including the optimization of biosynthetic pathways, improvement of cofactor supplementation, and reprogramming of the metabolic network. We then investigated the dynamic regulation by multiple control modules to balance the growth and production, so as to direct carbon sources for diol production. Finally, we proposed the challenges in the diol-biosynthesis process and suggested some potential methods to improve the diol-producing ability of the host.
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Pan, Guohui, Zhengren Xu, Zhikai Guo, Hindra, Ming Ma, Dong Yang, Hao Zhou, et al. "Discovery of the leinamycin family of natural products by mining actinobacterial genomes." Proceedings of the National Academy of Sciences 114, no. 52 (December 11, 2017): E11131—E11140. http://dx.doi.org/10.1073/pnas.1716245115.
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Nature’s ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF–SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF–SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm-type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature’s rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature’s biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity.
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Fujiwara, Kei, Taishi Tsubouchi, Tomohisa Kuzuyama, and Makoto Nishiyama. "Involvement of the arginine repressor in lysine biosynthesis of Thermus thermophilus." Microbiology 152, no. 12 (December 1, 2006): 3585–94. http://dx.doi.org/10.1099/mic.0.29222-0.
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Lysine biosynthesis of Thermus thermophilus proceeds in a similar way to arginine biosynthesis, and some lysine biosynthetic enzymes from T. thermophilus so far investigated have the potential to function in arginine biosynthesis. These observations suggest that arginine might regulate the expression of genes for lysine biosynthesis. To test this hypothesis, the argR gene encoding the regulator of arginine biosynthesis was cloned from T. thermophilus and its function in lysine biosynthesis was analysed. The addition of arginine to the culture medium inhibited the growth of an arginase gene knockout mutant of T. thermophilus, which presumably accumulates arginine inside the cells. Arginine-dependent growth inhibition was not alleviated by the addition of ornithine, which is a biosynthetic intermediate of arginine and serves as a peptidoglycan component of the cell wall in T. thermophilus. However, the growth inhibition was cancelled either by the simultaneous addition of lysine and ornithine or by a knockout of the argR gene, suggesting the involvement of argR in regulation of lysine biosynthesis in T. thermophilus. Electrophoretic mobility shift assay and DNase I footprinting revealed that the ArgR protein specifically binds to the promoter region of the major lysine biosynthetic gene cluster. Furthermore, an α-galactosidase reporter assay for this promoter indicated that arginine repressed the promoter in an argR-dependent manner. These results indicate that lysine biosynthesis is regulated by arginine in T. thermophilus.
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Fewer, David P., Julia Österholm, Leo Rouhiainen, Jouni Jokela, Matti Wahlsten, and Kaarina Sivonen. "Nostophycin Biosynthesis Is Directed by a Hybrid Polyketide Synthase-Nonribosomal Peptide Synthetase in the Toxic Cyanobacterium Nostoc sp. Strain 152." Applied and Environmental Microbiology 77, no. 22 (September 23, 2011): 8034–40. http://dx.doi.org/10.1128/aem.05993-11.
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ABSTRACTCyanobacteria are a rich source of natural products with interesting pharmaceutical properties. Here, we report the identification, sequencing, annotation, and biochemical analysis of the nostophycin (npn) biosynthetic gene cluster. Thenpngene cluster spans 45.1 kb and consists of three open reading frames encoding a polyketide synthase, a mixed polyketide nonribosomal peptide synthetase, and a nonribosomal peptide synthetase. The genetic architecture and catalytic domain organization of the proteins are colinear in arrangement, with the putative order of the biosynthetic assembly of the cyclic heptapeptide. NpnB contains an embedded monooxygenase domain linking nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) catalytic domains and predicted here to hydroxylate the nostophycin during assembly. Expression of the adenylation domains and subsequent substrate specificity assays support the involvement of this cluster in nostophycin biosynthesis. Biochemical analyses suggest that the loading substrate of NpnA is likely to be a phenylpropanoic acid necessitating deletion of a carbon atom to explain the biosynthesis of nostophycin. Biosyntheses of nostophycin and microcystin resemble each other, but the phylogenetic analyses suggest that they are distantly related to one another.
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Mohammed, Yousef, Ding Ye, Mudan He, Houpeng Wang, Zuoyan Zhu, and Yonghua Sun. "Production of Astaxanthin by Animal Cells via Introduction of an Entire Astaxanthin Biosynthetic Pathway." Bioengineering 10, no. 9 (September 11, 2023): 1073. http://dx.doi.org/10.3390/bioengineering10091073.
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Astaxanthin is a fascinating molecule with powerful antioxidant activity, synthesized exclusively by specific microorganisms and higher plants. To expand astaxanthin production, numerous studies have employed metabolic engineering to introduce and optimize astaxanthin biosynthetic pathways in microorganisms and plant hosts. Here, we report the metabolic engineering of animal cells in vitro to biosynthesize astaxanthin. This was accomplished through a two-step study to introduce the entire astaxanthin pathway into human embryonic kidney cells (HEK293T). First, we introduced the astaxanthin biosynthesis sub-pathway (Ast subp) using several genes encoding β-carotene ketolase and β-carotene hydroxylase enzymes to synthesize astaxanthin directly from β-carotene. Next, we introduced a β-carotene biosynthesis sub-pathway (β-Car subp) with selected genes involved in Ast subp to synthesize astaxanthin from geranylgeranyl diphosphate (GGPP). As a result, we unprecedentedly enabled HEK293T cells to biosynthesize free astaxanthin from GGPP with a concentration of 41.86 µg/g dry weight (DW), which represented 66.19% of the total ketocarotenoids (63.24 µg/g DW). Through optimization steps using critical factors in the astaxanthin biosynthetic process, a remarkable 4.14-fold increase in total ketocarotenoids (262.10 µg/g DW) was achieved, with astaxanthin constituting over 88.82%. This pioneering study holds significant implications for transgenic animals, potentially revolutionizing the global demand for astaxanthin, particularly within the aquaculture sector.
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Chen, Fu, Le Yuan, Shaozhen Ding, Yu Tian, and Qian-Nan Hu. "Data-driven rational biosynthesis design: from molecules to cell factories." Briefings in Bioinformatics 21, no. 4 (June 26, 2019): 1238–48. http://dx.doi.org/10.1093/bib/bbz065.
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Abstract A proliferation of chemical, reaction and enzyme databases, new computational methods and software tools for data-driven rational biosynthesis design have emerged in recent years. With the coming of the era of big data, particularly in the bio-medical field, data-driven rational biosynthesis design could potentially be useful to construct target-oriented chassis organisms. Engineering the complicated metabolic systems of chassis organisms to biosynthesize target molecules from inexpensive biomass is the main goal of cell factory design. The process of data-driven cell factory design could be divided into several parts: (1) target molecule selection; (2) metabolic reaction and pathway design; (3) prediction of novel enzymes based on protein domain and structure transformation of biosynthetic reactions; (4) construction of large-scale DNA for metabolic pathways; and (5) DNA assembly methods and visualization tools. The construction of a one-stop cell factory system could achieve automated design from the molecule level to the chassis level. In this article, we outline data-driven rational biosynthesis design steps and provide an overview of related tools in individual steps.
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Blatzer, Michael, Markus Schrettl, Bettina Sarg, Herbert H. Lindner, Kristian Pfaller, and Hubertus Haas. "SidL, an Aspergillus fumigatus Transacetylase Involved in Biosynthesis of the Siderophores Ferricrocin and Hydroxyferricrocin." Applied and Environmental Microbiology 77, no. 14 (May 27, 2011): 4959–66. http://dx.doi.org/10.1128/aem.00182-11.
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ABSTRACTThe opportunistic fungal pathogenAspergillus fumigatusproduces four types of siderophores, low-molecular-mass iron chelators: it excretes fusarinine C (FsC) and triacetylfusarinine C (TAFC) for iron uptake and accumulates ferricrocin (FC) for hyphal and hydroxyferricrocin (HFC) for conidial iron distribution and storage. Siderophore biosynthesis has recently been shown to be crucial for fungal virulence. Here we identified a new component of the fungal siderophore biosynthetic machinery: AFUA_1G04450, termed SidL. SidL is conserved only in siderophore-producing ascomycetes and shows similarity to transacylases involved in bacterial siderophore biosynthesis and theN5-hydroxyornithine:anhydromevalonyl coenzyme A-N5-transacylase SidF, which is essential for TAFC biosynthesis. Inactivation of SidL inA. fumigatusdecreased FC biosynthesis during iron starvation and completely blocked FC biosynthesis during iron-replete growth. In agreement with these findings, SidL deficiency blocked conidial accumulation of FC-derived HFC under iron-replete conditions, which delayed germination and decreased the size of conidia and their resistance to oxidative stress. Remarkably, thesidLgene is not clustered with other siderophore-biosynthetic genes, and its expression is not affected by iron availability. Tagging of SidL with enhanced green fluorescent protein suggested a cytosolic localization of the FC-biosynthetic machinery. Taken together, these data suggest that SidL is a constitutively activeN5-hydroxyornithine-acetylase required for FC biosynthesis, in particular under iron-replete conditions. Moreover, this study revealed the unexpected complexity of siderophore biosynthesis, indicating the existence of an additional, iron-repressedN5-hydroxyornithine-acetylase.
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Meechuen, Methat, Lalita Pimsawang, Tanapon Chaisan, Sompid Samipak, Wanchai Pluempanupat, and Piyada Juntawong. "Comparative Transcriptome Analysis Reveals Genes Associated with Alkaloid Diversity in Javanese Long Pepper (Piper retrofractum) Fruits." International Journal of Plant Biology 14, no. 4 (October 6, 2023): 896–909. http://dx.doi.org/10.3390/ijpb14040066.
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Alkaloids are a class of secondary metabolites that play multifaceted roles in plant physiology, including defense mechanisms and interactions with other organisms. The alkaloids from Piper retrofractum (Javanese long pepper) fruits offer potential alternatives to synthetic pesticides due to their natural origin and insecticide properties. However, information on particular alkaloid biosynthesis pathways is required to enhance individual alkaloid production via metabolic engineering. Here, we perform HPLC profiling to demonstrate that fruit ripening influences the alkaloid diversity in P. retrofractum. De novo transcriptomic profiling of young, green mature, and red ripened fruits revealed that the piperine biosynthesis pathway genes were highly upregulated in the mature fruits. However, an enhanced accumulation of methyl piperate and guineensine in the ripened fruit was observed, entailing ripening-related differential gene expression to synchronize the alkaloid biosyntheses. Gene expression clustering and functional enrichment analysis identified a large group of genes involved in diverse biosynthetic processes explicitly enriched in the ripened fruits. A cohort of genes encoding for “Alkaloid Biosynthesis”, remarkably upregulated in the ripening fruits, indicates they may function directly in alkaloid diversity during a later stage of fruit development. This study provides the basis for metabolic engineering to enhance alkaloid diversity and production.
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Li, Li, Jun Wu, Zixin Deng, T. Mark Zabriskie, and Xinyi He. "Streptomyces lividans Blasticidin S Deaminase and Its Application in Engineering a Blasticidin S-Producing Strain for Ease of Genetic Manipulation." Applied and Environmental Microbiology 79, no. 7 (February 1, 2013): 2349–57. http://dx.doi.org/10.1128/aem.03254-12.
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ABSTRACTBlasticidin S is a peptidyl nucleoside antibiotic produced byStreptomyces griseochromogenesthat exhibits strong fungicidal activity. To circumvent an effective DNA uptake barrier system in the native producer and investigate its biosynthesisin vivo, the blasticidin S biosynthetic gene cluster (bls) was engrafted to the chromosome ofStreptomyces lividans. However, the resulting mutant, LL2, produced the inactive deaminohydroxyblasticidin S instead of blasticidin S. Subsequently, a blasticidin S deaminase (SLBSD, forS. lividansblasticidin S deaminase) was identified inS. lividansand shown to govern thisin vivoconversion. Purified SLBSD was found to be capable of transforming blasticidin S to deaminohydroxyblasticidin Sin vitro. It also catalyzed deamination of the cytosine moiety of cytosylglucuronic acid, an intermediate in blasticidin S biosynthesis. Disruption of the SLBSD gene inS. lividansLL2 led to successful production of active blasticidin S in the resultant mutant,S. lividansWJ2. To demonstrate the easy manipulation of the blasticidin S biosynthetic gene cluster,blsE,blsF, andblsL, encoding a predicted radicalS-adenosylmethionine (SAM) protein, an unknown protein, and a guanidino methyltransferase, were individually inactivated to access their role in blasticidin S biosynthesis.
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Shams, Somayeh, Ahmad Ismaili, Farhad Nazarian Firouzabadi, Hasan Mumivand, and Karim Sorkheh. "Comparative transcriptome analysis to identify putative genes involved in carvacrol biosynthesis pathway in two species of Satureja, endemic medicinal herbs of Iran." PLOS ONE 18, no. 7 (July 7, 2023): e0281351. http://dx.doi.org/10.1371/journal.pone.0281351.
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Satureja is rich in phenolic monoterpenoids, mainly carvacrol, that is of interest due to diverse biological activities including antifungal and antibacterial. However, limited information is available regarding the molecular mechanisms underlying carvacrol biosynthesis and its regulation for this wonderful medicinal herb. To identify the putative genes involved in carvacrol and other monoterpene biosynthesis pathway, we generated a reference transcriptome in two endemic Satureja species of Iran, containing different yields (Satureja khuzistanica and Satureja rechingeri). Cross-species differential expression analysis was conducted between two species of Satureja. 210 and 186 transcripts related to terpenoid backbone biosynthesis were identified for S. khuzistanica and S. rechingeri, respectively. 29 differentially expressed genes (DEGs) involved in terpenoid biosynthesis were identified, and these DEGs were significantly enriched in monoterpenoid biosynthesis, diterpenoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, carotenoid biosynthesis and ubiquinone and other terpenoid-quinone biosynthesis pathways. Expression patterns of S. khuzistanica and S. rechingeri transcripts involved in the terpenoid biosynthetic pathway were evaluated. In addition, we identified 19 differentially expressed transcription factors (such as MYC4, bHLH, and ARF18) that may control terpenoid biosynthesis. We confirmed the altered expression levels of DEGs that encode carvacrol biosynthetic enzymes using quantitative real-time PCR (qRT-PCR). This study is the first report on de novo assembly and transcriptome data analysis in Satureja which could be useful for an understanding of the main constituents of Satureja essential oil and future research in this genus.
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O'Hanlon, Karen A., Lorna Gallagher, Markus Schrettl, Christoph Jöchl, Kevin Kavanagh, Thomas O. Larsen, and Sean Doyle. "Nonribosomal Peptide Synthetase GenespesLandpes1Are Essential for Fumigaclavine C Production in Aspergillus fumigatus." Applied and Environmental Microbiology 78, no. 9 (February 17, 2012): 3166–76. http://dx.doi.org/10.1128/aem.07249-11.
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ABSTRACTThe identity of metabolites encoded by the majority of nonribosomal peptide synthetases in the opportunistic pathogen,Aspergillus fumigatus, remains outstanding. We found that the nonribosomal peptide (NRP) synthetases PesL and Pes1 were essential for fumigaclavine C biosynthesis, the end product of the complex ergot alkaloid (EA) pathway inA. fumigatus. Deletion of eitherpesL(ΔpesL) orpes1(Δpes1) resulted in complete loss of fumigaclavine C biosynthesis, relatively increased production of fumitremorgins such as TR-2, fumitremorgin C and verruculogen, increased sensitivity to H2O2, and increased sensitivity to the antifungals, voriconazole, and amphotericin B. Deletion ofpesLresulted in severely reduced virulence in an invertebrate infection model (P< 0.001). These findings indicate that NRP synthesis plays an essential role in mediating the final prenylation step of the EA pathway, despite the apparent absence of NRP synthetases in the proposed EA biosynthetic cluster forA. fumigatus. Liquid chromatography/diode array detection/mass spectrometry analysis also revealed the presence of fumiquinazolines A to F in bothA. fumigatuswild-type and ΔpesLstrains. This observation suggests that alternative NRP synthetases can also function in fumiquinazoline biosynthesis, since PesL has been shown to mediate fumiquinazoline biosynthesisin vitro. Furthermore, we provide here the first direct link between EA biosynthesis and virulence, in agreement with the observed toxicity associated with EA exposure. Finally, we demonstrate a possible cluster cross-talk phenomenon, a theme which is beginning to emerge in the literature.
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Awad, Agape M., Michelle C. Bradley, Lucía Fernández-del-Río, Anish Nag, Hui S. Tsui, and Catherine F. Clarke. "Coenzyme Q10 deficiencies: pathways in yeast and humans." Essays in Biochemistry 62, no. 3 (July 6, 2018): 361–76. http://dx.doi.org/10.1042/ebc20170106.
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Coenzyme Q (ubiquinone or CoQ) is an essential lipid that plays a role in mitochondrial respiratory electron transport and serves as an important antioxidant. In human and yeast cells, CoQ synthesis derives from aromatic ring precursors and the isoprene biosynthetic pathway. Saccharomyces cerevisiae coq mutants provide a powerful model for our understanding of CoQ biosynthesis. This review focusses on the biosynthesis of CoQ in yeast and the relevance of this model to CoQ biosynthesis in human cells. The COQ1–COQ11 yeast genes are required for efficient biosynthesis of yeast CoQ. Expression of human homologs of yeast COQ1–COQ10 genes restore CoQ biosynthesis in the corresponding yeast coq mutants, indicating profound functional conservation. Thus, yeast provides a simple yet effective model to investigate and define the function and possible pathology of human COQ (yeast or human gene involved in CoQ biosynthesis) gene polymorphisms and mutations. Biosynthesis of CoQ in yeast and human cells depends on high molecular mass multisubunit complexes consisting of several of the COQ gene products, as well as CoQ itself and CoQ intermediates. The CoQ synthome in yeast or Complex Q in human cells, is essential for de novo biosynthesis of CoQ. Although some human CoQ deficiencies respond to dietary supplementation with CoQ, in general the uptake and assimilation of this very hydrophobic lipid is inefficient. Simple natural products may serve as alternate ring precursors in CoQ biosynthesis in both yeast and human cells, and these compounds may act to enhance biosynthesis of CoQ or may bypass certain deficient steps in the CoQ biosynthetic pathway.
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Müller, Michael, and Syed Husain. "Fungal Dihydroxynaphthalene-Melanin: Diversity-Oriented Biosynthesis through Enzymatic and Non-enzymatic Transformations." Synlett 28, no. 18 (August 31, 2017): 2360–72. http://dx.doi.org/10.1055/s-0036-1588526.
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Tetrahydroxynaphthalene reductase (T4HNR) from Magnaporthe grisea catalyzes the reduction of polyhydroxynaphthalenes, hydroxynaphthoquinones, and 1,4-diketones, with extensive ramifications for the biosynthesis of (shunt) metabolites related to 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis. Hence, an extended model for DHN-melanin biosynthesis has been developed which is based on a screening hypothesis involving non-enzymatic transformations such as oxidations and tautomerism. This has led to the broadening of the functions of several short-chain dehydrogenases/reductases (SDRs) capable of reducing polyhydroxyanthracenes, polyhydroxynaphthalenes, and polyhydroxybenzenes. Our work, broadening the scope of enzymatic dearomatization reactions, provides access to the biocatalytic synthesis of a variety of natural and natural-like products. Furthermore, the results described in this account provide the basis for the identification of other SDRs amenable to reducing aromatic compounds, and thus enable the identification of biosynthetic gene clusters most likely involved in the biosynthesis of aromatic polyketides.1 Introduction2 Biosynthesis of 1,8-Dihydroxynaphthalene (DHN)3 Biosynthesis of Shunt Metabolites and the Origin of Molecular Diversity3.1 Role of Spontaneous Non-enzymatic Oxidations3.2 Role of T4HNR and T3HNR3.3 Role of Tautomerism in the Biosynthesis of (Shunt) Metabolites4 Extended Melanin Biosynthesis: A Screening Hypothesis5 Useful Outcomes of the Newly Identified Melanin Biosynthetic Pathway5.1 NADP+ Regeneration Using Lawsone as Mediator5.2 Anthrahydroquinone as an Intermediate in the Biosynthesis of Chrysophanol and Other Anthraquinone-Derived Products5.3 Combination of T3HNR and GDH To Access trans-Ketodiols5.4 Phloroglucinol Reductases (PGRs) To Dearomatize Monomeric Phenols6 Conclusion
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Chin Zi Hang, Neeraj Kumar Fuloria, Oh Jian Hong, Chuah Bee Kim, Bernice Yii Shu Ting, Chiam Sin Ru, Mok Yong Ko, and Shivkanya Fuloria. "Biosynthesis of DLLAE blended silver nanoparticles and their response against periodontitis triggering bacteria." International Journal of Research in Pharmaceutical Sciences 11, no. 2 (April 15, 2020): 1849–56. http://dx.doi.org/10.26452/ijrps.v11i2.2092.
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Facts over microorganisms to predominate periodontitis, shifting of human microbiota by Dimocarpus longan (D. longan) plant, and potentiation of antimicrobial activity by biosynthetic silver nanoparticles (SNPs) intended present study to biosynthesize, optimize, characterize and evaluate the antimicrobial potential of silver nanoparticles (SNPs) obtained using D. longan leaves aqueous extract (DLLAE). Study involved preparation of DLLAE using decoction method. The DLLAE was subjected to biosynthesis of SNPs followed by optimization (using UV-Visible spectrometry), characterization (by FTIR, FESEM, XRD, and EDX), stability, and antimicrobial activity of SNPs against periodontitis triggering human microflora. Biosynthesized SNPs exhibited signal between 416-453 nm. Optimization study established AgNO3 concentration (5 mM), pH 4, DLLAE and AgNO3 ratio (1:9) and temperature (60°C) as parametric requirement for SNPs biosynthesis using DLLAE. Stability study exhibited signal between 489-553 nm supporting SNPs stability. Characterization data of FESEM showed that SNPs were poly dispersed, and spherical shaped. Biosynthesized SNPs size ranged from 74.82 nm to 131.5 nm. The XRD data revealed presence of signals at 38.08°, 44.33°, 64.47°, and 78.83° 2θ values indexed to silver cubic structure planes. In EDX study, silver exhibited strong signal (55.54%). Antimicrobial investigation explored the high inhibitory potential of SNPs against B. subtilis and P. aeruginosa; and low inhibitory potential against S. aureus and E. coli. Present study conclude that biosynthesis of SNPs using DLLAE is an efficient method and biosynthetic SNPs possess high antimicrobial potential against P. aeruginosa and B. subtilis the periodontitis triggering pathogens.
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Wilton, D. C. "The effect of excess mevalonic acid on ubiquinone and tetrahymanol biosynthesis in Tetrahymena pyriformis." Biochemical Journal 229, no. 2 (July 15, 1985): 551–53. http://dx.doi.org/10.1042/bj2290551.
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When T. pyriformis is grown in the presence of 10(-2)M-mevalonic acid, the uptake exceeds the cell's requirement for this biosynthetic intermediate. The majority of the excess mevalonic acid is diverted into ubiquinone-8 biosynthesis whereas the biosynthesis of tetrahymanol, the major product of the mevalonic acid pathway, is unchanged. In the presence of excess external mevalonic acid, the biosynthesis of mevalonic acid by the cell is inhibited. It is proposed that ubiquinone biosynthesis is normally regulated by mevalonic acid availability, whereas tetrahymanol biosynthesis is regulated primarily at a later point in the pathway.
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Tan, Gao-Yi, Zixin Deng, and Tiangang Liu. "Recent advances in the elucidation of enzymatic function in natural product biosynthesis." F1000Research 4 (December 4, 2015): 1399. http://dx.doi.org/10.12688/f1000research.7187.1.
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With the successful production of artemisinic acid in yeast, the promising potential of synthetic biology for natural product biosynthesis is now being realized. The recent total biosynthesis of opioids in microbes is considered to be another landmark in this field. The importance and significance of enzymes in natural product biosynthetic pathways have been re-emphasized by these advancements. Therefore, the characterization and elucidation of enzymatic function in natural product biosynthesis are undoubtedly fundamental for the development of new drugs and the heterologous biosynthesis of active natural products. Here, discoveries regarding enzymatic function in natural product biosynthesis over the past year are briefly reviewed.
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Tan, Gao-Yi, Zixin Deng, and Tiangang Liu. "Recent advances in the elucidation of enzymatic function in natural product biosynthesis." F1000Research 4 (February 25, 2016): 1399. http://dx.doi.org/10.12688/f1000research.7187.2.
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With the successful production of artemisinic acid in yeast, the promising potential of synthetic biology for natural product biosynthesis is now being realized. The recent total biosynthesis of opioids in microbes is considered to be another landmark in this field. The importance and significance of enzymes in natural product biosynthetic pathways have been re-emphasized by these advancements. Therefore, the characterization and elucidation of enzymatic function in natural product biosynthesis are undoubtedly fundamental for the development of new drugs and the heterologous biosynthesis of active natural products. Here, discoveries regarding enzymatic function in natural product biosynthesis over the past year are briefly reviewed.
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Kawada, Kojiro, Yuya Uchida, Ikuo Takahashi, Takahito Nomura, Yasuyuki Sasaki, Tadao Asami, Shunsuke Yajima, and Shinsaku Ito. "Triflumizole as a Novel Lead Compound for Strigolactone Biosynthesis Inhibitor." Molecules 25, no. 23 (November 25, 2020): 5525. http://dx.doi.org/10.3390/molecules25235525.
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Strigolactones (SLs) are carotenoid-derived plant hormones involved in the development of various plants. SLs also stimulate seed germination of the root parasitic plants, Striga spp. and Orobanche spp., which reduce crop yield. Therefore, regulating SL biosynthesis may lessen the damage of root parasitic plants. Biosynthetic inhibitors effectively control biological processes by targeted regulation of biologically active compounds. In addition, biosynthetic inhibitors regulate endogenous levels in developmental stage- and tissue-specific manners. To date, although some chemicals have been found as SL biosynthesis inhibitor, these are derived from only three lead chemicals. In this study, to find a novel lead chemical for SL biosynthesis inhibitor, 27 nitrogen-containing heterocyclic derivatives were screened for inhibition of SL biosynthesis. Triflumizole most effectively reduced the levels of rice SL, 4-deoxyorobanchol (4DO), in root exudates. In addition, triflumizole inhibited endogenous 4DO biosynthesis in rice roots by inhibiting the enzymatic activity of Os900, a rice enzyme that converts the SL intermediate carlactone to 4DO. A Striga germination assay revealed that triflumizole-treated rice displayed a reduced level of germination stimulation for Striga. These results identify triflumizole as a novel lead compound for inhibition of SL biosynthesis.
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Kellmann, Ralf, Troco Kaan Mihali, Young Jae Jeon, Russell Pickford, Francesco Pomati, and Brett A. Neilan. "Biosynthetic Intermediate Analysis and Functional Homology Reveal a Saxitoxin Gene Cluster in Cyanobacteria." Applied and Environmental Microbiology 74, no. 13 (May 16, 2008): 4044–53. http://dx.doi.org/10.1128/aem.00353-08.
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ABSTRACT Saxitoxin (STX) and its analogues cause the paralytic shellfish poisoning (PSP) syndrome, which afflicts human health and impacts coastal shellfish economies worldwide. PSP toxins are unique alkaloids, being produced by both prokaryotes and eukaryotes. Here we describe a candidate PSP toxin biosynthesis gene cluster (sxt) from Cylindrospermopsis raciborskii T3. The saxitoxin biosynthetic pathway is encoded by more than 35 kb, and comparative sequence analysis assigns 30 catalytic functions to 26 proteins. STX biosynthesis is initiated with arginine, S-adenosylmethionine, and acetate by a new type of polyketide synthase, which can putatively perform a methylation of acetate, and a Claisen condensation reaction between propionate and arginine. Further steps involve enzymes catalyzing three heterocyclizations and various tailoring reactions that result in the numerous isoforms of saxitoxin. In the absence of a gene transfer system in these microorganisms, we have revised the description of the known STX biosynthetic pathway, with in silico functional inferences based on sxt open reading frames combined with liquid chromatography-tandem mass spectrometry analysis of the biosynthetic intermediates. Our results indicate the evolutionary origin for the production of PSP toxins in an ancestral cyanobacterium with genetic contributions from diverse phylogenetic lineages of bacteria and provide a quantum addition to the catalytic collective available for future combinatorial biosyntheses. The distribution of these genes also supports the idea of the involvement of this gene cluster in STX production in various cyanobacteria.
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Glawischnig, E. "The role of cytochrome P450 enzymes in the biosynthesis of camalexin." Biochemical Society Transactions 34, no. 6 (October 25, 2006): 1206–8. http://dx.doi.org/10.1042/bst0341206.
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The biosynthesis of camalexin, the main phytoalexin of the model plant Arabidopsis thaliana, involves at least two CYP (cytochrome P450) steps. It is synthesized from tryptophan via indole-3-acetaldoxime in a reaction catalysed by CYP79B2 and CYP79B3. Based on the pad3 mutant phenotype, CYP71B15 (PAD3) had also been suggested as a camalexin biosynthetic gene. CYP71B15 catalyses the final step in camalexin biosynthesis, as recombinant CYP71B15 and microsomes from Arabidopsis leaves expressing functional PAD3 converted dihydrocamalexic acid into camalexin. The biosynthetic pathway is co-ordinately induced, strictly localized to the site of pathogen infection. This provides a model system to study the regulation of CYP enzymes involved in phytoalexin biosynthesis.
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ZHANG, Xiaodong, Caixia LI, Chonlong CHIO, Ayyappa K. S. KAMESHWAR, Tianxiao MA, and Wensheng QIN. "Transcriptome analysis to identify genes involved in lignan, sesquiterpenoid and triterpenoid biosynthesis in medicinal plant Kadsura heteroclita." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 48, no. 4 (December 22, 2020): 1802–31. http://dx.doi.org/10.15835/nbha48412044.
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Stems and roots of Kadsura plant species were the significant ingredients of traditional Chinese medicine. Kadsura heteroclita is one of the popular medicinal plants used in Tujia and Yao nationalities of China. Antioxidant compounds like lignan, sesquiterpenoid and triterpenoid are the major active components of K. hetroclita. Mass cultivation and bio-manufacturing strategies were being proposed to meet the increasing demand of Kadsura species plant parts. Therefore, it is important to reveal the molecular networks involved in biosynthesis of these highly efficient medicinal compounds. Here, transcriptomes of roots, stems and leaves in K. heteroclite seedling were sequenced by Hiseq2000 and unigenes involved in biosynthesis of lignan, sesquiterpenoid and triterpenoid biosynthesis were mined. As a result, 472 million clean reads were obtained which after aligning resulted in 160,248 transcripts and 98,005 genes. 191 and 279 unigenes were expected to be involved in biosynthesis of lignan, sesquiterpenoid and triterpenoid biosynthetic pathways respectively. Lignan, sesquiterpenoid and triterpenoid biosynthesis pathway genes were highly significant and differentially upregulated in roots and stems and downregulated in leaves. Also, genes encoding for MYB and bHLH transcription factors possibly involved in regulation of lignan, sesquiterpenoid and triterpenoid biosynthesis were discovered. These results provide the fundamental genomic resources for dissecting of biosynthetic pathways of the active components in K. hetroclita.
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Roberts Buceta, Paloma M., Laura Romanelli-Cedrez, Shannon J. Babcock, Helen Xun, Miranda L. VonPaige, Thomas W. Higley, Tyler D. Schlatter, et al. "The kynurenine pathway is essential for rhodoquinone biosynthesis in Caenorhabditis elegans." Journal of Biological Chemistry 294, no. 28 (June 7, 2019): 11047–53. http://dx.doi.org/10.1074/jbc.ac119.009475.
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A key metabolic adaptation of some species that face hypoxia as part of their life cycle involves an alternative electron transport chain in which rhodoquinone (RQ) is required for fumarate reduction and ATP production. RQ biosynthesis in bacteria and protists requires ubiquinone (Q) as a precursor. In contrast, Q is not a precursor for RQ biosynthesis in animals such as parasitic helminths, and most details of this pathway have remained elusive. Here, we used Caenorhabditis elegans as a model animal to elucidate key steps in RQ biosynthesis. Using RNAi and a series of C. elegans mutants, we found that arylamine metabolites from the kynurenine pathway are essential precursors for RQ biosynthesis de novo. Deletion of kynu-1, encoding a kynureninase that converts l-kynurenine (KYN) to anthranilic acid (AA) and 3-hydroxykynurenine (3HKYN) to 3-hydroxyanthranilic acid (3HAA), completely abolished RQ biosynthesis but did not affect Q levels. Deletion of kmo-1, which encodes a kynurenine 3-monooxygenase that converts KYN to 3HKYN, drastically reduced RQ but not Q levels. Knockdown of the Q biosynthetic genes coq-5 and coq-6 affected both Q and RQ levels, indicating that both biosynthetic pathways share common enzymes. Our study reveals that two pathways for RQ biosynthesis have independently evolved. Unlike in bacteria, where amination is the last step in RQ biosynthesis, in worms the pathway begins with the arylamine precursor AA or 3HAA. Because RQ is absent in mammalian hosts of helminths, inhibition of RQ biosynthesis may have potential utility for targeting parasitic infections that cause important neglected tropical diseases.
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Horbal, Liliya, Marc Stierhof, Anja Palusczak, Nikolas Eckert, Josef Zapp, and Andriy Luzhetskyy. "Cyclofaulknamycin with the Rare Amino Acid D-capreomycidine Isolated from a Well-Characterized Streptomyces albus Strain." Microorganisms 9, no. 8 (July 28, 2021): 1609. http://dx.doi.org/10.3390/microorganisms9081609.
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Targeted genome mining is an efficient method of biosynthetic gene cluster prioritization within constantly growing genome databases. Using two capreomycidine biosynthesis genes, alpha-ketoglutarate-dependent arginine beta-hydroxylase and pyridoxal-phosphate-dependent aminotransferase, we identified two types of clusters: one type containing both genes involved in the biosynthesis of the abovementioned moiety, and other clusters including only arginine hydroxylase. Detailed analysis of one of the clusters, the flk cluster from Streptomyces albus, led to the identification of a cyclic peptide that contains a rare D-capreomycidine moiety for the first time. The absence of the pyridoxal-phosphate-dependent aminotransferase gene in the flk cluster is compensated by the XNR_1347 gene in the S. albus genome, whose product is responsible for biosynthesis of the abovementioned nonproteinogenic amino acid. Herein, we report the structure of cyclofaulknamycin and the characteristics of its biosynthetic gene cluster, biosynthesis and bioactivity profile.
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ZHOU, CHAOBIN, JUNJIE DING, XIAOJING HU, and WEI GONG. "COMPARATIVE PROTEOMIC ANALYSIS OF THE THICK-WALLED RAY FORMATION PROCESS OF HALOXYLON AMMODENDRON IN THE GURBANTUNGGUT DESERT, CHINA." WOOD RESEARCH 66(5) 2021 66, no. 5 (November 2, 2021): 833–43. http://dx.doi.org/10.37763/wr.1336-4561/66.5.833843.
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Thick-walled ray cells of Haloxylon ammodendronwere first reported by Zhou and Gong in 2017, but their formation mechanism remains unknown. In this study, we performeda proteomic analysis of ray cell wall formation in the xylem. H. ammodendronin Shihezi exhibits a thicker ray cell wall than that in Jinghe. During the process of cell wall biosynthesisin the xylem of H. ammodendron, the nonspecific lipid-transfer protein and beta expansin EXPB2.1 (Mirabilis jalapa) first loosen the cell wall, and this step is followed by extension and expansion. Subsequently, xyloglucan endotransglycosylase/hydrolase 1 cleaves and linksthe xyloglucan chains. Photosystem I P700 apoprotein A1, reversibly glycosylated polypeptide 1 and GDP-mannose-3′,5′-epimerase are involved in the cellulose, hemicellulose and pectin biosynthesis processes in the cell wall by providing components or energy. Finally, the proteins involved in phenylpropanoid biosynthesis promote lignification of the ray cell wall and complete the biosynthetic process of the cell wall.
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Jensen, Susan E., Kenneth J. Elder, Kwamena A. Aidoo, and Ashish S. Paradkar. "Enzymes Catalyzing the Early Steps of Clavulanic Acid Biosynthesis Are Encoded by Two Sets of Paralogous Genes inStreptomyces clavuligerus." Antimicrobial Agents and Chemotherapy 44, no. 3 (March 1, 2000): 720–26. http://dx.doi.org/10.1128/aac.44.3.720-726.2000.
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ABSTRACT Genes encoding the proteins required for clavulanic acid biosynthesis and for cephamycin biosynthesis are grouped into a “supercluster” in Streptomyces clavuligerus. Nine open reading frames (ORFs) associated with clavulanic acid biosynthesis were located in a 15-kb segment of the supercluster, including six ORFs encoding known biosynthetic enzymes or regulatory proteins, two ORFs that have been reported previously but whose involvement in clavulanic acid biosynthesis is unclear, and one ORF not previously reported. Evidence for the involvement of these ORFs in clavulanic acid production was obtained by generating mutants and showing that all were defective for clavulanic acid production when grown on starch asparagine medium. However, when five of the nine mutants, including mutants defective in known clavulanic acid biosynthetic enzymes, were grown in a soy-based medium, clavulanic acid-producing ability was restored. This ability to produce clavulanic acid when seemingly essential biosynthetic enzymes have been mutated suggests that paralogous genes encoding functionally equivalent proteins exist for each of the five genes but that these paralogues are expressed only in the soy-based medium. The five genes that have paralogues encode proteins involved in the early steps of the pathway common to the biosynthesis of both clavulanic acid and the other clavam metabolites produced by this organism. No evidence was seen for paralogues of the four remaining genes involved in late, clavulanic acid-specific steps in the pathway.
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Fang, Jie, Yiping Zhang, Lijuan Huang, Xinying Jia, Qi Zhang, Xu Zhang, Gongli Tang, and Wen Liu. "Cloning and Characterization of the Tetrocarcin A Gene Cluster from Micromonospora chalcea NRRL 11289 Reveals a Highly Conserved Strategy for Tetronate Biosynthesis in Spirotetronate Antibiotics." Journal of Bacteriology 190, no. 17 (June 27, 2008): 6014–25. http://dx.doi.org/10.1128/jb.00533-08.
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ABSTRACT Tetrocarcin A (TCA), produced by Micromonospora chalcea NRRL 11289, is a spirotetronate antibiotic with potent antitumor activity and versatile modes of action. In this study, the biosynthetic gene cluster of TCA was cloned and localized to a 108-kb contiguous DNA region. In silico sequence analysis revealed 36 putative genes that constitute this cluster (including 11 for unusual sugar biosynthesis, 13 for aglycone formation, and 4 for glycosylations) and allowed us to propose the biosynthetic pathway of TCA. The formation of d-tetronitrose, l-amicetose, and l-digitoxose may begin with d-glucose-1-phosphate, share early enzymatic steps, and branch into different pathways by competitive actions of specific enzymes. Tetronolide biosynthesis involves the incorporation of a 3-C unit with a polyketide intermediate to form the characteristic spirotetronate moiety and trans-decalin system. Further substitution of tetronolide with five deoxysugars (one being a deoxynitrosugar) was likely due to the activities of four glycosyltransferases. In vitro characterization of the first enzymatic step by utilization of 1,3-biphosphoglycerate as the substrate and in vivo cross-complementation of the bifunctional fused gene tcaD3 (with the functions of chlD3 and chlD4) to ΔchlD3 and ΔchlD4 in chlorothricin biosynthesis supported the highly conserved tetronate biosynthetic strategy in the spirotetronate family. Deletion of a large DNA fragment encoding polyketide synthases resulted in a non-TCA-producing strain, providing a clear background for the identification of novel analogs. These findings provide insights into spirotetronate biosynthesis and demonstrate that combinatorial-biosynthesis methods can be applied to the TCA biosynthetic machinery to generate structural diversity.
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Gull�n, Sonia, Carlos Olano, Mohamed S. Abdelfattah, Alfredo F. Bra�a, J�rgen Rohr, Carmen M�ndez, and Jos� A. Salas. "Isolation, Characterization, and Heterologous Expression of the Biosynthesis Gene Cluster for the Antitumor Anthracycline Steffimycin." Applied and Environmental Microbiology 72, no. 6 (June 2006): 4172–83. http://dx.doi.org/10.1128/aem.00734-06.
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ABSTRACT The biosynthetic gene cluster for the aromatic polyketide steffimycin of the anthracycline family has been cloned and characterized from “Streptomyces steffisburgensis” NRRL 3193. Sequence analysis of a 42.8-kbp DNA region revealed the presence of 36 open reading frames (ORFs) (one of them incomplete), 24 of which, spanning 26.5 kb, are probably involved in steffimycin biosynthesis. They code for all the activities required for polyketide biosynthesis, tailoring, regulation, and resistance but show no evidence of genes involved in l-rhamnose biosynthesis. The involvement of the cluster in steffimycin biosynthesis was confirmed by expression of a region of about 15 kb containing 15 ORFS, 11 of them forming part of the cluster, in the heterologous host Streptomyces albus, allowing the isolation of a biosynthetic intermediate. In addition, the expression in S. albus of the entire cluster, contained in a region of 34.8 kb, combined with the expression of plasmid pRHAM, directing the biosynthesis of l-rhamnose, led to the production of steffimycin. Inactivation of the stfX gene, coding for a putative cyclase, revealed that this enzymatic activity participates in the cyclization of the fourth ring, making the final steps in the biosynthesis of the steffimycin aglycon similar to those in the biosynthesis of jadomycin or rabelomycin. Inactivation of the stfG gene, coding for a putative glycosyltransferase involved in the attachment of l-rhamnose, allowed the production of a new compound corresponding to the steffimycin aglycon compound also observed in S. albus upon expression of the entire cluster.
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White, R. "Methanopterin biosynthesis: methylation of the biosynthetic intermediates." Biochimica et Biophysica Acta (BBA) - General Subjects 1380, no. 2 (April 10, 1998): 257–67. http://dx.doi.org/10.1016/s0304-4165(97)00148-7.
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Kon, Takahide, Naoki Nemoto, Tairo Oshima, and Akihiko Yamagishi. "Effects of a Squalene Epoxidase Inhibitor, Terbinafine, on Ether Lipid Biosyntheses in a Thermoacidophilic Archaeon, Thermoplasma acidophilum." Journal of Bacteriology 184, no. 5 (March 1, 2002): 1395–401. http://dx.doi.org/10.1128/jb.184.5.1395-1401.2002.
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ABSTRACT The archaeal plasma membrane consists mainly of diether lipids and tetraether lipids instead of the usual ester lipids found in other organisms. Although a molecule of tetraether lipid is thought to be synthesized from two molecules of diether lipids, there is no direct information about the biosynthetic pathway(s) or intermediates of tetraether lipid biosynthesis. In this study, we examined the effects of the fungal squalene epoxidase inhibitor terbinafine on the growth and ether lipid biosyntheses in the thermoacidophilic archaeon Thermoplasma acidophilum. Terbinafine was found to inhibit the growth of T. acidophilum in a concentration-dependent manner. When growing T. acidophilum cells were pulse-labeled with [2-14C]mevalonic acid in the presence of terbinafine, incorporation of radioactivity into the tetraether lipid fraction was strongly suppressed, while accumulation of radioactivity was noted at the position corresponding to diether lipids, depending on the concentration of terbinafine. After the cells were washed with fresh medium and incubated further without the radiolabeled substrate and the inhibitor, the accumulated radioactivity in the diether lipid fraction decreased quickly while that in the tetraether lipids increased simultaneously, without significant changes in the total radioactivity of ether lipids. These results strongly suggest that terbinafine inhibits the biosynthesis of tetraether lipids from a diether-type precursor lipid(s). The terbinafine treatment will be a tool for dissecting tetraether lipid biosynthesis in T. acidophilum.
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Storbeck, Sonja, Sarah Rolfes, Evelyne Raux-Deery, Martin J. Warren, Dieter Jahn, and Gunhild Layer. "A Novel Pathway for the Biosynthesis of Heme inArchaea: Genome-Based Bioinformatic Predictions and Experimental Evidence." Archaea 2010 (2010): 1–15. http://dx.doi.org/10.1155/2010/175050.
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Heme is an essential prosthetic group for many proteins involved in fundamental biological processes in all three domains of life. InEukaryotaandBacteriaheme is formedviaa conserved and well-studied biosynthetic pathway. Surprisingly, inArchaeaheme biosynthesis proceedsviaan alternative route which is poorly understood. In order to formulate a working hypothesis for this novel pathway, we searched 59 completely sequenced archaeal genomes for the presence of gene clusters consisting of established heme biosynthetic genes and colocalized conserved candidate genes. Within the majority of archaeal genomes it was possible to identify such heme biosynthesis gene clusters. From this analysis we have been able to identify several novel heme biosynthesis genes that are restricted to archaea. Intriguingly, several of the encoded proteins display similarity to enzymes involved in hemed1biosynthesis. To initiate an experimental verification of our proposals twoMethanosarcina barkeriproteins predicted to catalyze the initial steps of archaeal heme biosynthesis were recombinantly produced, purified, and their predicted enzymatic functions verified.
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Kusajima, Miyuki, Moeka Fujita, Takumi Nishiuchi, Hideo Nakashita, and Tadao Asami. "Induction of tocopherol biosynthesis through heat shock treatment in Arabidopsis." Bioscience, Biotechnology, and Biochemistry 85, no. 3 (January 21, 2021): 502–9. http://dx.doi.org/10.1093/bbb/zbaa053.
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ABSTRACT Plants have developed various self-defense systems to survive many types of unfavorable conditions. Heat shock (HS) treatment, an abiotic stress, activates salicylic acid (SA) biosynthesis to enhance resistance to biotic stresses in some plant species. Since SA is produced from the shikimate pathway, other related metabolic pathways were expected to be upregulated by HS treatment. We speculated that tocopherol biosynthesis utilizing chorismic acid would be activated by HS treatment. In Arabidopsis, expression analysis of tocopherol biosynthetic genes, HPPD, VTE2, VTE3, VTE1, and VTE4, in combination with measurement of metabolites, indicated that HS treatment enhanced the biosynthesis and accumulation of tocopherols. Analyses using an SA biosynthesis-deficient mutant indicated that the upregulation of tocopherol biosynthesis was independent of the SA-mediated signaling pathway.
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STINSON, E. E. "Mycotoxins - Their Biosynthesis in Alternaria." Journal of Food Protection 48, no. 1 (January 1, 1985): 80–91. http://dx.doi.org/10.4315/0362-028x-48.1.80.
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Alternaria produce a wide assortment of toxic and nontoxic secondary metabolites. A brief summary of the numerous secondary metabolites of Alternaria and their toxicity is followed by a presentation of the current view of the polyketide biosynthetic mechanism and its application to the biosynthesis of these compounds. Possible mechanisms for the biosynthesis of alternariol, alternariol methyl ether, and other dibenzo-α-pyrones are presented, as well as mechanisms for the biosynthesis of tenuazonic acid and altertoxin I. Bioregulation of the production of these materials by light, heat, nutrients and NADPH production, and the role of mannitol in NADPH formation are also discussed.
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R, Tevan, Saravanan Jayakumar, Nor Haledah Ahmad Sahimi, Nur Farah Ain Iqbal, Iffah Zapri, Natanamurugaraj Govindan, Solachuddin J. A. Ichwan, and Gaanty Pragas Maniam. "BIOSYNTHESIS OF SILVER NANOPARTICLES USING MARINE MICROALGAE ISOCHRYSIS sp." Journal of Chemical Engineering and Industrial Biotechnology 2, no. 1 (April 1, 2017): 1–12. http://dx.doi.org/10.15282/jceib.v2i1.3738.
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Biosynthesis of metal nanoparticles has received a remarkable attention due to their eco-friendly and potential applications in pharmaceutical and medical fields. The searches for natural alternatives to replace biosynthetic nanoparticles have resulted in extensive studies of microalgal derived metal nanoparticles. Since there are very limited reports on Isochrysis sp. in synthesising metal nanoparticles, a novel initiative was taken to induce an environmentally friendly and low cost technique to biosynthesise the silver nanoparticles (AgNPs) using marine microalgae, Isochrysis sp. Further, the synthesised silver nanoparticles were screened against human pathogen for antimicrobial effects. The characterisation of nanoparticles were confirmed by UV visible spectroscopy, field emission scanning electron microscopy (FESEM), Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRD). The results obtained from characterisations indicate that the AgNPs have an almost spherical shape with a various size of 98.1 to 193 nm. The synthesised nanoparticles exhibited outstanding antioxidant and antimicrobial activities.
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Ferla, Matteo P., and Wayne M. Patrick. "Bacterial methionine biosynthesis." Microbiology 160, no. 8 (August 1, 2014): 1571–84. http://dx.doi.org/10.1099/mic.0.077826-0.
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Methionine is essential in all organisms, as it is both a proteinogenic amino acid and a component of the cofactor, S-adenosyl methionine. The metabolic pathway for its biosynthesis has been extensively characterized in Escherichia coli; however, it is becoming apparent that most bacterial species do not use the E. coli pathway. Instead, studies on other organisms and genome sequencing data are uncovering significant diversity in the enzymes and metabolic intermediates that are used for methionine biosynthesis. This review summarizes the different biochemical strategies that are employed in the three key steps for methionine biosynthesis from homoserine (i.e. acylation, sulfurylation and methylation). A survey is presented of the presence and absence of the various biosynthetic enzymes in 1593 representative bacterial species, shedding light on the non-canonical nature of the E. coli pathway. This review also highlights ways in which knowledge of methionine biosynthesis can be utilized for biotechnological applications. Finally, gaps in the current understanding of bacterial methionine biosynthesis are noted. For example, the paper discusses the presence of one gene (metC) in a large number of species that appear to lack the gene encoding the enzyme for the preceding step in the pathway (metB), as it is understood in E. coli. Therefore, this review aims to move the focus away from E. coli, to better reflect the true diversity of bacterial pathways for methionine biosynthesis.
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Xiong, Fei, Jingyi Wei, Youxiang Zhou, Yanchun Shao, Jiao Liu, and Fusheng Chen. "Exploring the Subcellular Localization of Monascus Pigments Biosynthases: Preliminary Unraveling of the Compartmentalization Mechanism." Journal of Fungi 10, no. 6 (May 24, 2024): 375. http://dx.doi.org/10.3390/jof10060375.
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Monascus pigments (MPs), a class of secondary metabolites produced by Monascus spp., can be classified into yellow, orange, and red MPs according to their differences in the wavelength of the maximum absorption. However, the biosynthetic sequence and cellular biosynthesis mechanism of different MPs components are still not yet completely clear in Monascus spp. In this study, the subcellular localization of five MPs synthases was investigated using fluorescent protein fusion expression. The results revealed that the proteins encoded by the MPs biosynthetic gene cluster were compartmentalized in various subcellular locations, including the mitochondrial polyketide synthase MrPigA, cytosolic enzymes consisting of the ketoreductase MrPigC, the oxidoreductase MrPigE, and the monooxygenase MrPigN, and the cell-wall-bound oxidoreductase MrPigF. Moreover, the correct localization of MrPigF to the cell wall was crucial for the synthesis of orange MPs. Lastly, we discussed the compartmentalized biosynthetic pathway of MPs. This study will not only be helpful in clarifying the biosynthetic sequence and biosynthesis mechanism of different MPs but also provides new insights into the cellular biosynthesis of secondary metabolites in filamentous fungi.
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Dobrzyn, Pawel. "CoA in Health and Disease." International Journal of Molecular Sciences 23, no. 8 (April 15, 2022): 4371. http://dx.doi.org/10.3390/ijms23084371.
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Coenzyme A (CoA) and its thioester derivatives are crucial components of numerous biosynthetic and degradative pathways of the cellular metabolism (including fatty acid synthesis and oxidation, the Krebs cycle, ketogenesis, cholesterol and acetylcholine biosynthesis, amino acid degradation, and neurotransmitter biosynthesis), post-translational modifications of proteins, and the regulation of gene expression [...]
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Dietl, Anna-Maria, Ulrike Binder, Ingo Bauer, Yana Shadkchan, Nir Osherov, and Hubertus Haas. "Arginine Auxotrophy Affects Siderophore Biosynthesis and Attenuates Virulence of Aspergillus fumigatus." Genes 11, no. 4 (April 15, 2020): 423. http://dx.doi.org/10.3390/genes11040423.
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Aspergillus fumigatus is an opportunistic human pathogen mainly infecting immunocompromised patients. The aim of this study was to characterize the role of arginine biosynthesis in virulence of A. fumigatus via genetic inactivation of two key arginine biosynthetic enzymes, the bifunctional acetylglutamate synthase/ornithine acetyltransferase (argJ/AFUA_5G08120) and the ornithine carbamoyltransferase (argB/AFUA_4G07190). Arginine biosynthesis is intimately linked to the biosynthesis of ornithine, a precursor for siderophore production that has previously been shown to be essential for virulence in A. fumigatus. ArgJ is of particular interest as it is the only arginine biosynthetic enzyme lacking mammalian homologs. Inactivation of either ArgJ or ArgB resulted in arginine auxotrophy. Lack of ArgJ, which is essential for mitochondrial ornithine biosynthesis, significantly decreased siderophore production during limited arginine supply with glutamine as nitrogen source, but not with arginine as sole nitrogen source. In contrast, siderophore production reached wild-type levels under both growth conditions in ArgB null strains. These data indicate that siderophore biosynthesis is mainly fueled by mitochondrial ornithine production during limited arginine availability, but by cytosolic ornithine production during high arginine availability via cytosolic arginine hydrolysis. Lack of ArgJ or ArgB attenuated virulence of A. fumigatus in the insect model Galleria mellonella and in murine models for invasive aspergillosis, indicating limited arginine availability in the investigated host niches.
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Yin, Hua, Sihai Xiang, Jianting Zheng, Keqiang Fan, Tingting Yu, Xu Yang, Yanfeng Peng, et al. "Induction of Holomycin Production and Complex Metabolic Changes by theargRMutation in Streptomyces clavuligerus NP1." Applied and Environmental Microbiology 78, no. 9 (February 17, 2012): 3431–41. http://dx.doi.org/10.1128/aem.07699-11.
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ABSTRACTIn bacteria, arginine biosynthesis is tightly regulated by a universally conserved regulator, ArgR, which regulates the expression of arginine biosynthetic genes, as well as other important genes. Disruption ofargRinStreptomyces clavuligerusNP1 resulted in complex phenotypic changes in growth and antibiotic production levels. To understand the metabolic changes underlying the phenotypes, comparative proteomic studies were carried out between NP1 and itsargRdisruption mutant (designated CZR). In CZR, enzymes involved in holomycin biosynthesis were overexpressed; this is consistent with its holomycin overproduction phenotype. The effects on clavulanic acid (CA) biosynthesis are more complex. Several proteins from the CA cluster were moderately overexpressed, whereas several proteins from the 5S clavam biosynthetic cluster and from the paralog cluster of CA and 5S clavam biosynthesis were severely downregulated. Obvious changes were also detected in primary metabolism, which are mainly reflected in the altered expression levels of proteins involved in acetyl-coenzyme A (CoA) and cysteine biosynthesis. Since acetyl-CoA and cysteine are precursors for holomycin synthesis, overexpression of these proteins is consistent with the holomycin overproduction phenotype. The complex interplay between primary and secondary metabolism and between secondary metabolic pathways were revealed by these analyses, and the insights will guide further efforts to improve production levels of CA and holomycin inS. clavuligerus.
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Du, Guozhong, Xue Yang, Zhengxiong Wu, Minghui Pan, Zhuoxu Dong, Yanyan Zhang, Wensheng Xiang, and Shanshan Li. "Influence of Cluster-Situated Regulator PteF in Filipin Biosynthetic Cluster on Avermectin Biosynthesis in Streptomyces avermitilis." Biology 13, no. 5 (May 15, 2024): 344. http://dx.doi.org/10.3390/biology13050344.
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Crosstalk regulation is widespread in Streptomyces species. Elucidating the influence of a specific regulator on target biosynthetic gene clusters (BGCs) and cell metabolism is crucial for strain improvement through regulatory protein engineering. PteF and PteR are two regulators that control the biosynthesis of filipin, which competes for building blocks with avermectins in Streptomyces avermitilis. However, little is known about the effects of PteF and PteR on avermectin biosynthesis. In this study, we investigated their impact on avermectin biosynthesis and global cell metabolism. The deletion of pteF resulted in a 55.49% avermectin titer improvement, which was 23.08% higher than that observed from pteR deletion, suggesting that PteF plays a more significant role in regulating avermectin biosynthesis, while PteF hardly influences the transcription level of genes in avermectin and other polyketide BGCs. Transcriptome data revealed that PteF exhibited a global regulatory effect. Avermectin production enhancement could be attributed to the repression of the tricarboxylic acid cycle and fatty acid biosynthetic pathway, as well as the enhancement of pathways supplying acyl-CoA precursors. These findings provide new insights into the role of PteF on avermectin biosynthesis and cell metabolism, offering important clues for designing and building efficient metabolic pathways to develop high-yield avermectin-producing strains.
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Zhang, Zhuan, Hai-Xue Pan, and Gong-Li Tang. "New insights into bacterial type II polyketide biosynthesis." F1000Research 6 (February 21, 2017): 172. http://dx.doi.org/10.12688/f1000research.10466.1.
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Bacterial aromatic polyketides, exemplified by anthracyclines, angucyclines, tetracyclines, and pentangular polyphenols, are a large family of natural products with diverse structures and biological activities and are usually biosynthesized by type II polyketide synthases (PKSs). Since the starting point of biosynthesis and combinatorial biosynthesis in 1984–1985, there has been a continuous effort to investigate the biosynthetic logic of aromatic polyketides owing to the urgent need of developing promising therapeutic candidates from these compounds. Recently, significant advances in the structural and mechanistic identification of enzymes involved in aromatic polyketide biosynthesis have been made on the basis of novel genetic, biochemical, and chemical technologies. This review highlights the progress in bacterial type II PKSs in the past three years (2013–2016). Moreover, novel compounds discovered or created by genome mining and biosynthetic engineering are also included.
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Cao, Xue-Qiang, Xing-Yu Ouyang, Bo Chen, Kai Song, Lian Zhou, Bo-Le Jiang, Ji-Liang Tang, Guanghai Ji, Alan R. Poplawsky, and Ya-Wen He. "Genetic Interference Analysis Reveals that Both 3-Hydroxybenzoic Acid and 4-Hydroxybenzoic Acid Are Involved in Xanthomonadin Biosynthesis in the Phytopathogen Xanthomonas campestris pv. campestris." Phytopathology® 110, no. 2 (February 2020): 278–86. http://dx.doi.org/10.1094/phyto-08-19-0299-r.
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A characteristic feature of phytopathogenic Xanthomonas bacteria is the production of yellow membrane-bound pigments called xanthomonadins. Previous studies showed that 3-hydroxybenzoic acid (3-HBA) was a xanthomonadin biosynthetic intermediate and also, that it had a signaling role. The question of whether the structural isomers 4-HBA and 2-HBA (salicylic acid) have any role in xanthomonadin biosynthesis remained unclear. In this study, we have selectively eliminated 3-HBA, 4-HBA, or the production of both by expression of the mhb, pobA, and pchAB gene clusters in the Xanthomonas campestris pv. campestris strain XC1. The resulting strains were different in pigmentation, virulence factor production, and virulence. These results suggest that both 3-HBA and 4-HBA are involved in xanthomonadin biosynthesis. When both 3-HBA and 4-HBA are present, X. campestris pv. campestris prefers 3-HBA for Xanthomonadin-A biosynthesis; the 3-HBA–derived Xanthomonadin-A was predominant over the 4-HBA–derived xanthomonadin in the wild-type strain XC1. If 3-HBA is not present, then 4-HBA is used for biosynthesis of a structurally uncharacterized Xanthomonadin-B. Salicylic acid had no effect on xanthomonadin biosynthesis. Interference with 3-HBA and 4-HBA biosynthesis also affected X. campestris pv. campestris virulence factor production and reduced virulence in cabbage and Chinese radish. These findings add to our understanding of xanthomonadin biosynthetic mechanisms and further help to elucidate the biological roles of xanthomonadins in X. campestris pv. campestris adaptation and virulence in host plants.
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He, Shutao, Xiaomeng Hao, Shanshan Wang, Wenzhi Zhou, Qiuxiang Ma, Xinlu Lu, Luonan Chen, and Peng Zhang. "Starch synthase II plays a crucial role in starch biosynthesis and the formation of multienzyme complexes in cassava storage roots." Journal of Experimental Botany 73, no. 8 (February 4, 2022): 2540–57. http://dx.doi.org/10.1093/jxb/erac022.
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Abstract Starch is a glucose polymer synthesized by green plants for energy storage and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis and the formation of protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII, and MeISAII. MeSSII-RNAi cassava lines showed increased amylose content and reduced biosynthesis of the intermediate chain of amylopectin (B1 type) in their storage roots, leading to altered starch physicochemical properties. Furthermore, gel permeation chromatography analysis of starch biosynthetic enzymes between wild type and MeSSII-RNAi lines confirmed the key role of MeSSII in the organization of heteromeric starch synthetic protein complexes. The lack of MeSSII in cassava also reduced the capacity of MeSSI, MeSBEII, MeISAI, and MeISAII to bind to starch granules. These findings shed light on the key components of the starch biosynthesis machinery in root crops.
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Micklefield, Jason. "Biosynthesis and biosynthetic engineering of calcium-dependent lipopeptide antibiotics." Pure and Applied Chemistry 81, no. 6 (May 5, 2009): 1065–74. http://dx.doi.org/10.1351/pac-con-08-08-29.
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Biosynthetic engineering involves the reprogramming of genes that are involved in the biosynthesis of natural products to generate new "non-natural" products, which might otherwise not exist in nature. Potentially this approach can be used to provide large numbers of secondary metabolites variants, with altered biological activities, many of which are too complex for effective total synthesis. Recently we have been investigating the biosynthesis of the calcium-dependent antibiotics (CDAs) which are members of the therapeutically relevant class of acidic lipopeptide antibiotics. CDAs are assembled by nonribosomal peptide synthetase (NRPS) enzymes. These large modular assembly-line enzymes process intermediates that are covalently tethered to peptidyl carrier protein (PCP) domain bonds bonds, which makes them particularly amenable to reprogramming. The CDA producer, Streptomyces coelicolor, is also a genetically tractable model organism which makes CDA an ideal template for biosynthetic engineering. To this end we have elucidated many of the key steps in CDA biosynthesis and utilized this information to develop methods that have enabled the engineered biosynthesis of wide range of CDA-type lipopeptides.