Grisein, an Antibiotic Produced by Certain Strains of Streptomyces griseus

The chemistry and biology of natural ribomimetics and related compounds

Natural ribomimetics represent an important group of specialized metabolites with significant biological activities. Many of the activities, e.g., inhibition of seryl-tRNA synthetases, glycosidases, or ribosomes, are manifestations of their structural resemblance to ribose or related sugars, which play roles in the structural, physiological, and/or reproductive functions of living organisms. Recent studies on the biosynthesis and biological activities of some natural ribomimetics have expanded our understanding on how they are made in nature and why they have great potential as pharmaceutically relevant products. This review article highlights the discovery, biological activities, biosynthesis, and development of this intriguing class of natural products.

Biosynthesis and Chemical Synthesis of Albomycin Nucleoside Antibiotics

The widespread emergence of antibiotic-resistant bacteria highlights the urgent need for new antimicrobial agents. Albomycins are a group of naturally occurring sideromycins with a thionucleoside antibiotic conjugated to a ferrichrome-type siderophore. The siderophore moiety serves as a vehicle to deliver albomycins into bacterial cells via a “Trojan horse” strategy. Albomycins function as specific inhibitors of seryl-tRNA synthetases and exhibit potent antimicrobial activities against both Gram-negative and Gram-positive bacteria, including many clinical pathogens. These distinctive features make albomycins promising drug candidates for the treatment of various bacterial infections, especially those caused by multidrug-resistant pathogens. We herein summarize findings on the discovery and structure elucidation, mechanism of action, biosynthesis and immunity, and chemical synthesis of albomcyins, with special focus on recent advances in the biosynthesis and chemical synthesis over the past decade (2012–2022). A thorough understanding of the biosynthetic pathway provides the basis for pathway engineering and combinatorial biosynthesis to create new albomycin analogues. Chemical synthesis of natural congeners and their synthetic analogues will be useful for systematic structure–activity relationship (SAR) studies, and thereby assist the design of novel albomycin-derived antimicrobial agents.

Analysis of microbiota in the stomach and midgut of two penaeid shrimps during probiotic feeding

In mammals, the intestine harbors numerous bacteria that play an important role in health. Intestinal microbiota have also been thought to be an important factor in the health of shrimp. However, the barrier systems of the digestive tracts of shrimp seem to be different from those of mammals. In this study, we analyzed the bacterial composition in the stomach and midgut of two species of shrimp during administration of a probiotic, Bacillus amyloliquefaciens strain TOA5001 by analysis of 16S rRNA genes with Illumina sequencing technology. Whiteleg shrimp Litopenaeus vannamei were observed under laboratory conditions and kuruma shrimp Marsupenaeus japonicus were observed in an aquaculture farm. The diversities of bacteria in the stomachs of both shrimps were significantly higher than those in the midgut. Also, the microbiota changed during probiotic feeding. Feeding whiteleg shrimp the probiotic after being challenged with an acute hepatopancreatic necrosis disease (AHPND)-causing strain of Vibrio parahaemolyticus increased their survival compared to the control group, which suggested that the probiotic prevented AHPND. These results appear to show that a probiotic can affect the microbiota throughout digestive tract of penaeid shrimps and that probiotic can have a role in preventing disease.

Natural Trojan horse inhibitors of aminoacyl-tRNA synthetases

For most antimicrobial compounds with intracellular targets, getting inside the cell is the major obstacle limiting their activity. To pass this barrier some antibiotics mimic the compounds of specific interest for the microbe (siderophores, peptides, carbohydrates, etc.) and hijack the transport systems involved in their active uptake followed by the release of a toxic warhead inside the cell. In this review, we summarize the information about the structures, biosynthesis, and transport of natural inhibitors of aminoacyl-tRNA synthetases (albomycin, microcin C-related compounds, and agrocin 84) that rely on such "Trojan horse" strategy to enter the cell. In addition, we provide new data on the composition and distribution of biosynthetic gene clusters reminiscent of those coding for known Trojan horse aminoacyl-tRNA synthetases inhibitors. The products of these clusters are likely new antimicrobials that warrant further investigation.

Natural Hydroxamate-Containing Siderophore Acremonpeptides A-D and an Aluminum Complex of Acremonpeptide D from the Marine-Derived Acremonium persicinum SCSIO 115

Four new hydroxamate-containing natural product cyclopeptides designated acremonpeptides A-D (1-4), together with Al(III)-acremonpeptide D (5) were obtained from the marine fungus Acremonium persicinum SCSIO 115. The planar structures of 1-5 were established on the basis of HRMS as well as 1D and 2D NMR data sets. Moreover, the amino acid absolute configurations were determined using Marfey's method. Compounds 1-5 all feature three 2-amino-5-(N-hydroxyacetamido)pentanoic acid (N⁵-hydroxy-N⁵-acetyl-l-ornithine) metal ion chelating moieties. Beyond their discovery and structure elucidation, in vitro bioassays revealed acremonpeptides A (1), B (2), and Al(III)-acremonpeptide D (5) as moderate antiviral agents for herpes simplex virus 1 with EC₅₀ values of 16, 8.7, and 14 μM, respectively.

Total synthesis and antimicrobial evaluation of natural albomycins against clinical pathogens

Development of effective antimicrobial agents continues to be a great challenge, particularly due to the increasing resistance of superbugs and frequent hospital breakouts. There is an urgent need for more potent and safer antibiotics with novel scaffolds. As historically many commercial drugs were derived from natural products, discovery of antimicrobial agents from complex natural product structures still holds a great promise. Herein, we report the total synthesis of natural albomycins δ₁ (1a), δ₂ (1b), and ε (1c), which validates the structures of these peptidylnucleoside compounds and allows for synthetic access to bioactive albomycin analogs. The efficient synthesis of albomycins enables extensive evaluations of these natural products against model bacteria and clinical pathogens. Albomycin δ₂ has the potential to be developed into an antibacterial drug to treat Streptococcus pneumoniae and Staphylococcus aureus infections.

Albomycins are promising drug candidates for the treatment of bacterial infections. Here, the authors describe the total syntheses of albomycins δ₁, δ₂, and ε, and evaluate their antimicrobial activity, identifying albomycin δ₂ as a strong agent against S. pneumoniae and S. aureus infections.

Dolyemycins A and B, two novel cyclopeptides isolated from Streptomyces griseus subsp. griseus HYS31

Two novel cyclopeptides with special skeleton, namely, dolyemycins A (1) and B (2) were isolated from Streptomyces griseus subsp. griseus HYS31 by bio-guided isolation. Their structures were elucidated by detailed analysis of spectroscopic data. These two compounds were cyclopeptides containing eleven amino acids including five unusual amino acids (hydroxyglycine, 3-hydroxyleucine, 3-phenylserine, β-hydroxy-O-methyltyrosine, 2,3-diaminobutyric acid) in both of them and an extra nonprotein amino acids (3-methylaspartic acid) in Dolyemycin B only. Dolyemycins A and B performed antiproliferative activity against human lung cancer A549 cells with IC₅₀ values of 1.0 and 1.2 µM, respectively.

Nature's combinatorial biosynthesis and recently engineered production of nucleoside antibiotics in Streptomyces

Modified nucleosides produced by Streptomyces and related actinomycetes are widely used in agriculture and medicine as antibacterial, antifungal, anticancer and antiviral agents. These specialized small-molecule metabolites are biosynthesized by complex enzymatic machineries encoded within gene clusters in the genome. The past decade has witnessed a burst of reports defining the key metabolic processes involved in the biosynthesis of several distinct families of nucleoside antibiotics. Furthermore, genome sequencing of various Streptomyces species has dramatically increased over recent years. Potential biosynthetic gene clusters for novel nucleoside antibiotics are now apparent by analysis of these genomes. Here we revisit strategies for production improvement of nucleoside antibiotics that have defined mechanisms of action, and are in clinical or agricultural use. We summarize the progress for genetically manipulating biosynthetic pathways for structural diversification of nucleoside antibiotics. Microorganism-based biosynthetic examples are provided and organized under genetic principles and metabolic engineering guidelines. We show perspectives on the future of combinatorial biosynthesis, and present a working model for discovery of novel nucleoside natural products in Streptomyces.

A Branch Point of Streptomyces Sulfur Amino Acid Metabolism Controls the Production of Albomycin

Albomycin (ABM), also known as grisein, is a sulfur-containing metabolite produced by Streptomyces griseus ATCC 700974. Genes predicted to be involved in the biosynthesis of ABM and ABM-like molecules are found in the genomes of other actinomycetes. ABM has potent antibacterial activity, and as a result, many attempts have been made to develop ABM into a drug since the last century. Although the productivity of S. griseus can be increased with random mutagenesis methods, understanding of Streptomyces sulfur amino acid (SAA) metabolism, which supplies a precursor for ABM biosynthesis, could lead to improved and stable production. We previously characterized the gene cluster (abm) in the genome-sequenced S. griseus strain and proposed that the sulfur atom of ABM is derived from either cysteine (Cys) or homocysteine (Hcy). The gene product, AbmD, appears to be an important link between primary and secondary sulfur metabolic pathways. Here, we show that propargylglycine or iron supplementation in growth media increased ABM production by significantly changing the relative concentrations of intracellular Cys and Hcy. An SAA metabolic network of S. griseus was constructed. Pathways toward increasing Hcy were shown to positively impact ABM production. The abmD gene and five genes that increased the Hcy/Cys ratio were assembled downstream of hrdBp promoter sequences and integrated into the chromosome for overexpression. The ABM titer of one engineered strain, SCAK3, in a chemically defined medium was consistently improved to levels ∼400% of the wild type. Finally, we analyzed the production and growth of SCAK3 in shake flasks for further process development.

Beyond iron: non-classical biological functions of bacterial siderophores

Bacteria secrete small molecules known as siderophores to acquire iron from their surroundings. For over 60 years, investigations into the bioinorganic chemistry of these molecules, including fundamental coordination chemistry studies, have provided insight into the crucial role that siderophores play in bacterial iron homeostasis. The importance of understanding the fundamental chemistry underlying bacterial life has been highlighted evermore in recent years because of the emergence of antibiotic-resistant bacteria and the need to prevent the global rise of these superbugs. Increasing reports of siderophores functioning in capacities other than iron transport have appeared recently, but reports of "non-classical" siderophore functions have long paralleled those of iron transport. One particular non-classical function of these iron chelators, namely antibiotic activity, was documented before the role of siderophores in iron transport was established. In this Perspective, we present an exposition of past and current work into non-classical functions of siderophores and highlight the directions in which we anticipate that this research is headed. Examples include the ability of siderophores to function as zincophores, chalkophores, and metallophores for a variety of other metals, sequester heavy metal toxins, transport boron, act as signalling molecules, regulate oxidative stress, and provide antibacterial activity.

Biodiversity in production of antibiotics and other bioactive compounds

Microbes continue to play a highly considerable role in the drug discovery and development process. Nevertheless, the number of new chemical entities (NCEs) of microbial origin that has been approved by the Food and Drug Administration (FDA) has been reduced in the past decade. This scarcity can be partly attributed to the redundancy in the discovered molecules from microbial isolates, which are isolated from common terrestrial ecological units. However, this situation can be partly overcome by exploring rarely exploited ecological niches as the source of microbes, which reduces the chances of isolating compounds similar to existing ones. The use of modern and advanced isolation techniques, modification of the existing fermentation methods, genetic modifications to induce expression of silent genes, analytical tools for the detection and identification of new chemical entities, use of polymers in fermentation to enhance yield of fermented compounds, and so on, have all aided in enhancing the frequency of acquiring novel compounds. These compounds are representative of numerous classes of diverse compounds. Thus, compounds of microbial origin and their analogues undergoing clinical trials continue to demonstrate the importance of compounds from microbial sources in modern drug discovery.

EFFECTS OF MINERALS ON NEOMYCIN PRODUCTION BY STREPTOMYCES FRADIAE

A study was made on the mineral requirements of Streptomyces fradiae strain 3535 for neomycin production. It was observed that optimal levels of the elements Ca, Fe, and Zn per milliliter of a synthetic medium for neomycin production were 10.8, 1.0, and 0.115 mug, respectively. K(2)HPO(4) was required at a concentration of 0.1% for maximal yield of neomycin, whereas NaCl and the metals Mn and Cu were without any effect. High doses of Zn (0.23 mug/ml or above) caused destruction of neomycin after the fifth day of fermentation.

Mineral nutrition of Streptomyces kanamyceticus for kanamycin formation

Kanamycin production by Streptomyces kanamyceticus ATCC 12853 requires magnesium sulfate and potassium phosphate at concentrations of 0.4 and 1.0 g per liter, respectively. The optimal concentrations of Fe and Zn for production of kanamycin are 0.25 and 0.575 mug/ml, respectively, whereas Mo at 0.04 mug/ml allows maximal cellular growth and antibiotic synthesis. Mn and Ca are without any effect. Cu, Co, Ni, and V have inhibitory effect on growth of the organism as well as kanamycin formation.

Penalty of isolationism

Research on new antibiotics is engaged in at present throughout the world with such intensity that one must be able to compare cultures of organisms producing such antibiotics, as well as the isolated substances themselves, if one is to avoid needless duplication and great confusion. As long as no international center exists where such comparisons can be made, only close collaboration among scientific laboratories can make possible these essential comparisons. The repetitions and the frequently unjustified creation of "new species" of antibiotic-producing organisms and of "new antibiotics" can be avoided only by close collaboration among the scientific workers throughout the world. The creation of an International Antibiotics Board is also highly essential at the present time.