Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome

Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes

Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here, we investigated the roles of pseudouridine in aminoglycoside-mediated translation inhibition by comparing the structural and functional properties of the yeast wild-type and the pseudouridine-free ribosomes. We showed that the pseudouridine-free ribosomes have decreased thermostability and high sensitivity to aminoglycosides. When presented with a model internal ribosomal entry site RNA, elongation factor eEF2, GTP (guanosine triphosphate), and sordarin, hygromycin B preferentially binds to the pseudouridine-free ribosomes during initiation by blocking eEF2 binding, stalling ribosomes in a nonrotated conformation. The structures captured hygromycin B bound at the intersubunit bridge B2a enriched with pseudouridine and a deformed codon-anticodon duplex, revealing a functional link between pseudouridine and aminoglycoside inhibition. Our results suggest that pseudouridine enhances both thermostability and conformational fitness of the ribosomes, thereby influencing their susceptibility to aminoglycosides.

Streptomyces sp. VITGV156 secondary metabolite binds pathogenic protein PBP2a and Beta-lactamase

Introduction

The genus Streptomyces is renowned for its prolific production of bioactive compounds, including antibiotics and secondary metabolites with pharmaceutical applications. This study focuses on Streptomyces sp. VITGV156, an isolate with promising antimicrobial properties, aiming to characterize its genomic potential and bioactive compounds through computational and experimental analyses.

Methods

Genomic sequencing of Streptomyces sp. VITGV156 was performed to identify biosynthetic gene clusters (BGCs) associated with secondary metabolite production. Antimicrobial assays were conducted using crude extracts against Gram-positive and Gram-negative pathogens. Gas Chromatography-Mass Spectrometry (GC-MS) was employed to identify secondary metabolites. Additionally, ADME (Absorption, Distribution, Metabolism, and Excretion) analysis and molecular docking studies were conducted to assess drug-like properties and binding affinities of selected compounds against bacterial target proteins (PDB IDs: 5M18 and 6NVU).

Results

The genome of Streptomyces sp. VITGV156 was determined to be 8.18 Mb with a G+C content of 72.61%, containing 29 BGCs responsible for the biosynthesis of antimicrobial agents such as nystatin and fluostatins. In vitro antimicrobial assays confirmed strong efficacy of crude extracts against various pathogens, with Escherichia coli exhibiting the highest susceptibility. Molecular docking studies of 45 identified secondary metabolites revealed binding affinities ranging from -4.0 to -7.5 kcal/mol (5M18) and -3.9 to -7.2 kcal/mol (6NVU). Among the identified compounds, squalene (ligand 43) displayed potent antibacterial and antifungal activity, whereas 2,5-piperazinedione, 3-(hydroxymethyl)-6-(phenylmethyl)- (ligand 40) exhibited strong antifungal potential. Conversely, fumaric acid, monoamide, N-benzyl-N-phenylethyl-, ethyl ester (ligand 38) demonstrated weak antifungal activity.

Discussion

The genomic and bioactive analysis of Streptomyces sp. VITGV156 highlights its potential as a valuable source of novel antimicrobial agents. The identification of unique biosynthetic genes and bioactive secondary metabolites suggests its possible application in combating multidrug-resistant pathogens. Further studies, including purification and in vivo testing, are necessary to validate these findings and explore their therapeutic potential.

Investigating Aerobic Hive Microflora: Role of Surface Microbiome of Apis Mellifera

This study investigated the surface microbiome of the honeybee (Apis mellifera), focusing on the diversity and functional roles of its associated microbial communities. While the significance of the microbiome to insect health and behavior is increasingly recognized, research on invertebrate surface microbiota lags behind that of vertebrates. A combined metagenomic and cultivation-based approach was employed to characterize the bacterial communities inhabiting the honeybee exoskeleton. Our findings reveal a complex and diverse microbiota exhibiting significant spatial and environmental heterogeneity. The identification of antimicrobial compound producers, validated through both culture and metagenomic analyses, including potentially novel Actinobacteria species, underscores the potential impact of these microbial communities on honeybee health, behavior, and hive dynamics. This research contributes to a more profound ecological understanding of the honeybee microbiome, particularly in its winter configuration.

Upgrading of the genetic engineering toolkit accelerated the discovery process of the virulence effect of PsGH7d on Phytophthora sojae invasion

The genus of Phytophthora includes numerous phytopathogens that have devastating impacts on agricultural production. However, the limited availability of selection markers for numerous pathogenicity pathogens of the genus Phytophthora genetic transformation hinders further research on their pathogenic functional genes. Here we report a gene of NAT I, which serves as a novel selection marker for the Phytophthora sojae transformation. Additionally, we developed a new genetic manipulation toolkit based on vectors containing NAT I, which facilitates gene editing in P. sojae. With the toolkit, the gene PsGH7d of P. sojae, which encodes a glycosyl hydrolase, was edited consecutively via the CRISPR/Cas9 system to obtain gene knockout and enzymatic active site mutation strains. The pathogenicity analysis of these transformants revealed that PsGH7d is a virulence factor dependent on its bifunctional glucanase-xylanase activities. This study develops an updated toolkit for the genus Phytophthora genetic transformation and provides initial insights into the virulence of the bifunctional enzyme PsGH7d.

Unveil the Molecular Interplay between Aminoglycosides and Pseudouridine in IRES Translation

Eukaryotic ribosomes are enriched with pseudouridine, particularly at the functional centers targeted by antibiotics. Here we investigated the roles of pseudouridine in aminoglycoside-mediated translation inhibition by comparing the structural and functional properties of the wild-type ribosomes and those lacking pseudouridine ( cbf5 -D95A). We showed that the cbf5 -D95A ribosomes have decreased thermostability and high sensitivity to aminoglycosides. When presented with an internal ribosome entry site (IRES) RNA, elongation factor eEF2, GTP, sordarin, hygromycin B preferentially binds to the cbf5 -D95A ribosomes during initiation by blocking eEF2 binding and stalls the ribosomes in a non-rotated conformation, further hindering translocation. Hygromycin B binds to the inter-subunit bridge B2a that is known to be sensitive to pseudouridine, revealing a functional link between pseudouridine and aminoglycoside inhibition. Our results suggest that pseudouridine enhances both thermostability and conformational fitness of the ribosomes, thereby influencing their susceptibility to aminoglycosides.

Highlights

Loss of pseudouridine increases cell sensitivity to aminoglycosidesPseudouridine enhances ribosome thermostabilityHygromycin B competes with eEF2 for the non-rotated ribosomeHygromycin B deforms the codon-anticodon duplex.

Premature aging in aneuploid yeast is caused in part by aneuploidy-induced defects in Ribosome Quality Control

Premature aging is a hallmark of Down syndrome, caused by trisomy of human chromosome 21, but the reason is unclear and difficult to study in humans. We used an aneuploid model in wild yeast to show that chromosome amplification disrupts nutrient-induced cell-cycle arrest, quiescence entry, and healthy aging, across genetic backgrounds and amplified chromosomes. We discovered that these defects are due in part to aneuploidy-induced dysfunction in Ribosome Quality Control (RQC). Compared to euploids, aneuploids entering quiescence display aberrant ribosome profiles, accumulate RQC intermediates, and harbor an increased load of protein aggregates. Although they have normal proteasome capacity, aneuploids show signs of ubiquitin dysregulation, which impacts cyclin abundance to disrupt arrest. Remarkably, inducing ribosome stalling in euploids produces similar aberrations, while up-regulating limiting RQC subunits or proteins in ubiquitin metabolism alleviates many of the aneuploid defects. Our results provide implications for other aneuploidy disorders including Down syndrome.

Genomic insights into an endophytic Streptomyces sp. VITGV156 for antimicrobial compounds

Endophytic Streptomyces sp. are recognized as a potential resource for valuable natural products but are less explored. This study focused on exploring endophytic Streptomyces species residing within tomato plants (Solanum lycopersicum) harboring genes for the production of a novel class of antibiotics. Our research involved the isolation and characterization of Streptomyces sp. VITGV156, a newly identified endophytic Streptomyces species that produces antimicrobial products. VITGV156 harbors a genome of 8.18 mb and codes 6,512 proteins, of which 4,993 are of known function (76.67%) and 1,519 are of unknown function (23.32%). By employing genomic analysis, we elucidate the genome landscape of this microbial strain and shed light on various BGCs responsible for producing polyketide antimicrobial compounds, with particular emphasis on the antibiotic kendomycin. We extended our study by evaluating the antibacterial properties of kendomycin. Overall, this study provides valuable insights into the genome of endophytic Streptomyces species, particularly Streptomyces sp. VITGV156, which are prolific producers of antimicrobial agents. These findings hold promise for further research and exploitation of pharmaceutical compounds, offering opportunities for the development of novel antimicrobial drugs.

History of the streptothricin antibiotics and evidence for the neglect of the streptothricin resistome

The streptothricin antibiotics were among the first antibiotics to be discovered from the environment and remain some of the most recovered antimicrobials in natural product screens. Increasing rates of antibiotic resistance and recognition that streptothricin antibiotics may play a role in countering so-called super-bugs has led to the re-evaluation of their clinical potential. Here we will review the current state of knowledge of streptothricins and their resistance in bacteria, with a focus on the potential for new resistance mechanisms and determinants to emerge in the context of potential widespread clinical adoption of this antibiotic class.

Streptothricin-F Inhibition of FtsZ Function: A Promising Approach for Controlling Pseudomonas syringae pv. actinidiae

Pseudomonas syringae pv. actinidiae (Psa) is a significant pathogenic bacterium affecting the kiwifruit industry. This study investigated the target sites of streptothricin-F (ST-F), produced by Streptomyces lavendulae gCLA4. The inhibition of ST-F on Psa was examined by the microscopic structural differences of Psa before and after treatment with ST-F, as well as the interaction between ST-F and cell division-related proteins. The results revealed filamentation of Psa after ST-F treatment, and fluorescence microscopy showed that ST-F inhibited the formation of the Z-ring composed of FtsZ protein. In vitro experiments and molecular docking demonstrated that ST-F can bind to FtsZ with a binding energy of 0.4 μM and inhibit FtsZ's GTP-dependent polymerization reaction. In addition, ST-F does not exert inhibitory effects on cell division in Psa strains overexpressing ftsZ. In conclusion, FtsZ is one of the target sites for ST-F inhibition of Psa, highlighting its potential as a therapeutic target for controlling Psa-induced kiwifruit bacterial canker.

Discovery of Streptomyces species CS-62, a novel producer of the Acinetobacter baumannii selective antibiotic factumycin

Narrow-spectrum antibiotics are of great interest given their ability to spare the microbiome and decrease widespread antibiotic resistance compared to broad-spectrum antibiotics. Herein, we screened an in-house library of Actinobacteria strains for selective activity against Acinetobacter baumannii and successfully identified Streptomyces sp. CS-62 as a producer of a natural product with this valuable activity. Analysis of the cultures via high-resolution mass spectrometry and tandem mass spectrometry, followed by comparison with molecules in the Natural Product Atlas and the Global Natural Products Social Molecular Networking platform, suggested a novel natural product. Genome mining analysis initially supported the production of a novel kirromycin derivative. Isolation and structure elucidation via mass spectrometry and Nuclear Magnetic Resonance (NMR) analyses revealed that the active natural product was the known natural product factumycin, exposing omissions and errors in the consulted databases. While public databases are generally very useful for avoiding rediscovery of known molecules, rediscovery remains a problem due to public databases either being incomplete or having errors that result in failed dereplication. Overall, the work describes the ongoing problem of dereplication and the continued need for public database curation.

Genome-based analysis of biosynthetic potential from antimycotic Streptomyces rochei strain A144

Streptomyces rochei is a species of Streptomyces with a diverse range of biological activities. Streptomyces rochei strain A144 was isolated from desert soils and exhibits antagonistic activity against several plant pathogenic fungi. The genome of S. rochei A144 was sequenced and revealed the presence of one linear chromosome and one plasmid. The chromosome length was found to be 8 085 429 bp, with a GC content of 72.62%, while the Plas1 length was 177 399 bp, with a GC content (proportion of guanine and cytosine in DNA sequences) of 69.08%. Comparative genomics was employed to analyse the S. rochei group. There is a high degree of collinearity between the genomes of S. rochei strains. Based on pan-genome analysis, S. rochei has 10 315 gene families, including 4051 core and 2322 unique genes. AntiSMASH was used to identify the gene clusters for secondary metabolites, identifying 33 secondary metabolite genes on the A144 genome. Among them, 18 clusters were found to be >70% identical to known biosynthetic gene clusters (BGCs), indicating that A144 has the potential to synthesize secondary metabolites. The majority of the BGCs were found to be conserved within the S. rochei group, including those encoding polyketide synthases, terpenes, non-ribosomal peptide synthetases, other ribosomally synthesized and post-translationally modified peptides, nicotianamine-iron transporters, lanthipeptides, and a few other types. The S. rochei group can be a potential genetic source of useful secondary metabolites with applications in medicine and biotechnology.

Antimicrobial Resistance in Bacteria from Meat and Meat Products: A One Health Perspective

According to the 2030 Agenda of the United Nations, one of the sustainable development goals is to ensure sustainable consumption and production patterns. The need to ensure food safety includes, other than microbiological hazards, concerns with antimicrobial-resistant (AMR) bacteria. The emergence of resistant bacteria in the food industry is essentially due to the abusive, and sometimes incorrect, administration of antimicrobials. Although not allowed in Europe, antimicrobials are often administered to promote animal growth. Each time antimicrobials are used, a selective pressure is applied to AMR bacteria. Moreover, AMR genes can be transmitted to humans through the consumption of meat-harbouring-resistant bacteria, which highlights the One Health dimension of antimicrobial resistance. Furthermore, the appropriate use of antimicrobials to ensure efficacy and the best possible outcome for the treatment of infections is regulated through the recommendations of antimicrobial stewardship. The present manuscript aims to give the current state of the art about the transmission of AMR bacteria, particularly methicillin-resistant S. aureus, ESBL-producing Enterobacteriaceae, and vancomycin-resistant Enterococcus spp., along with other ESKAPE bacteria, from animals to humans through the consumption of meat and meat products, with emphasis on pork meat and pork meat products, which are considered the most consumed worldwide.