In Silico/In Vitro Strategies Leading to the Discovery of New Nonribosomal Peptide and Polyketide Antibiotics Active against Human Pathogens

Genome mining of Bacillus licheniformis MCC2514 for the identification of lasso peptide biosynthetic gene cluster and its characterization

The probiotic strain Bacillus licheniformis MCC2514 has been shown to produce a strong antibacterial peptide and the whole genome sequence of this strain is also reported in our previous study. The present study is focused on the genome level investigation of this peptide antibiotic and its characterization. Genome mining of the culture revealed the presence of three putative bacteriocin clusters, viz. lichenicidin, sonorensin and lasso peptide. Hence, the mode of action of the peptide was investigated by reporter assay, scanning electron microscopy, and Fourier Transform Infrared spectroscopy. Additionally, the peptide treated groups of Kocuria rhizophila showed a reduction in the fold expression for transcription-related genes. The gene expression studies, quantitative β-galactosidase induction assay using the RNA stress reporter strain, yvgS along with the homology studies concluded that lasso peptide is responsible for the antibacterial activity of the peptide which acts as an inhibitor of RNA biosynthesis. Gene expression analysis showed a considerable increase in fold expression of lasso peptide genes at various fermentation hours. Also, the peptide was isolated, and its time-kill kinetics and minimum inhibitory concentration against the indicator pathogen K. rhizophila were examined. The peptide was also purified and the molecular weight was determined to be ~ 2 kDa. Our study suggests that this bacteriocin can function as an effective antibacterial agent in food products as well as in therapeutics as it contains lasso peptide, which inhibits the RNA biosynthesis.

Innovative Biomedical and Technological Strategies for the Control of Bacterial Growth and Infections

Antibiotics comprise one of the most successful groups of pharmaceutical products. Still, they have been associated with developing bacterial resistance, which has become one of the most severe problems threatening human health today. This context has prompted the development of new antibiotics or co-treatments using innovative tools to reverse the resistance context, combat infections, and offer promising antibacterial therapy. For the development of new alternatives, strategies, and/or antibiotics for controlling bacterial growth, it is necessary to know the target bacteria, their classification, morphological characteristics, the antibiotics currently used for therapies, and their respective mechanisms of action. In this regard, genomics, through the sequencing of bacterial genomes, has generated information on diverse genetic resources, aiding in the discovery of new molecules or antibiotic compounds. Nanotechnology has been applied to propose new antimicrobials, revitalize existing drug options, and use strategic encapsulating agents with their biochemical characteristics, making them more effective against various bacteria. Advanced knowledge in bacterial sequencing contributes to the construction of databases, resulting in advances in bioinformatics and the development of new antimicrobials. Moreover, it enables in silico antimicrobial susceptibility testing without the need to cultivate the pathogen, reducing costs and time. This review presents new antibiotics and biomedical and technological innovations studied in recent years to develop or improve natural or synthetic antimicrobial agents to reduce bacterial growth, promote well-being, and benefit users.

A peptide encoded by a highly conserved gene belonging to the genus Streptomyces shows antimicrobial activity against plant pathogens

The genus Streptomyces has been unceasingly highlighted for the versatility and diversity of the antimicrobial agents they produce. Moreover, it is a heavily sequenced taxon in the phylum Actinobacteria. In this study, 47 sequence profiles were identified as proteins highly conserved within the genus Streptomyces. Significant hits to the 38 profiles were found in more than 2000 Streptomyces genomes, 11 of which were further conserved in more than 90% of Actinobacterial genomes analyzed. Only a few genes corresponding to these sequence profiles were functionally characterized, which play regulatory roles in the morphology and biosynthesis of antibiotics. Here a highly conserved sequence, namely, SHC-AMP (Streptomyces highly conserved antimicrobial peptide), which exhibited antimicrobial activity against bacterial and fungal plant pathogens, was reported. In particular, Arabidopsis thaliana was effectively protected against infection with Pseudomonas syringae pv. tomato DC3000 by treatment with this peptide. Results indicated the potential application of this peptide as an antimicrobial agent for control of plant diseases. Our results suggest putative target genes for controlling Streptomyces spp., including the one exhibiting antimicrobial activity against a wide range of phytopathogens.

Genome sequencing of Colletotrichum gloeosporioides ESO026 reveals plausible pathway of HupA

BACKGROUND

Colletotrichum gloeosporioides ES026, isolated as an endophytic fungal strain, was found to produce the important medicinal compound HuperzineA (HupA). In a genetic context, ES026 showed potential in elucidating the biosynthetic pathway of HupA.

METHODS AND RESULTS

The ES026 strain was sequenced using de-novo Illumina sequencing methods in this study. Assembling the cleaned data resulted in 58,594,804bp, consisting of 404 scaffolds. The G + C mol % content of this genome was 52.53%. The genome progressive-alignment with other 4 Colletotrichum strains revealed that ES026 showed closer relation with 030206, SMCG1#C and Nara gc5. More than 60 putative biosynthetic clusters were predicted with the fungal version antiSMASH4.0 program. More than 33 types I polyketide-related biosynthetic gene clusters were distributed, containing PKS and PKS-NRPS (polyketide-nonribosomal peptides) hybrid gene clusters. Another 8 NRPS biosynthetic gene clusters were distributed among the genome of ES026. The prenyltransferases, probably involved in aromatic prenyl-compounds and terpenoid biosynthesis, were analyzed using bioinformatics tools like MEGA.

CONCLUSION

We predicted a new possible biosynthetic pathway for the HupA from the pipecolic acid, based on the published HupA biosynthesis proposed pathway, the biosynthesis and pipecolic acid-derived compounds. We hypothesize that a hybrid PKS-NRPS mega-enzyme was probably involved in the biosynthesis of HupA with the pipecolic acid, the building block of rapamycin, as a HupA precursor. The rapamycin is produced from a polyketide biosynthesis pathway, and the domain incorporating the pipecolic acid is studied.

Overexpression of llm1 Affects the Synthesis of Secondary Metabolites of Aspergillus cristatus

Putative methyltransferases are thought to be involved in the regulation of secondary metabolites in filamentous fungi. Here, we report the effects of overexpression of a predicted LaeA-like methyltransferase gene llm1 on the synthesis of secondary metabolites in Aspergillus cristatus. Our results revealed that overexpression of the gene llm1 in A. cristatus significantly hindered the production of conidia and enhanced sexual development, and reduced oxidative tolerance to hydrogen peroxide. Compared with the wild-type, the metabolic profile of the overexpression transformant was distinct, and the contents of multiple secondary metabolites were markedly increased, mainly including terpenoids and flavonoids, such as (S)-olEuropeic acid, gibberellin A62, gibberellin A95, ovalitenone, PD 98059, and 1-isomangostin. A total of 600 significantly differentially expressed genes (DEGs) were identified utilizing transcriptome sequencing, and the DEGs were predominantly enriched in transmembrane transport and secondary metabolism-related biological processes. In summary, the strategy of overexpressing global secondary metabolite regulators successfully activated the expression of secondary metabolite gene clusters, and the numerous secondary metabolites were greatly strengthened in A. cristatus. This study provides new insights into the in-depth exploitation and utilization of novel secondary metabolites of A. cristatus.

Carbon-nitrogen bond formation to construct novel polyketide-indole hybrids from the indole-3-carbinol exposed culture of Daldinia eschscholzii

A plenty of cytochrome P450s have been annotated in the Daldinia eschosholzii genome. Inspired by the fact that some P450s have been reported to catalyze the carbon-nitrogen (C-N) bond formation, we were curious about whether hybrids through C-N bond formation could be generated in the indole-3-carbinol (I3C) exposed culture of D. eschscholzii. As expected, two skeletally undescribed polyketide-indole hybrids, designated as indolpolyketone A and B (1 and 2), were isolated and assigned to be constructed through C-N bond formation. Their structures were elucidated by 1D and 2D NMR spectra. The absolute configurations of 1 and 2 were determined by comparing the recorded and calculated electronic circular dichroism (ECD) spectra. Furthermore, the plausible biosynthetic pathways for 1 and 2 were proposed. Compounds 1 and 2 exhibited significant antiviral activity against H1N1 with IC50 values of 45.2 and 31.4 μM, respectively. In brief, compounds 1 and 2 were reported here for the first time and were the first example of polyketide-indole hybrids pieced together through C-N bond formation in the I3C-exposed culture of D. eschscholzii. Therefore, this study expands the knowledge about the chemical production of D. eschscholzii through precursor-directed biosynthesis (PDB).

Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting

Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.

Recent research progress of biologically active peptides

With the rapid development of molecular biology and biochemical technology, great progress has been made in the study of peptides. Peptides are easy to digest and absorb, with lowering of blood pressure and cholesterol, improving immunity, regulating hormones, antibacterial, and antiviral effects. Peptides also have physiological regulation and biological metabolism functions with applications in the fields of feed production and biomedical research. In the future, the research focus of bioactive peptides will focus on their efficient preparation and application. This article introduces a comprehensive review of the types, synthesis, functionalization, and bio-related applications of bioactive peptides. For this aim, we introduced in detail various biopeptides and then presented the production methods of bioactive peptides, such as enzymatic synthesis, microbial fermentation, chemical synthesis, and others. The applications of bioactive peptides for anticancers, immune therapy, antibacterial, and other applications have been introduced and discussed. And discussed the development prospects of biologically active peptides.

Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments

The environmental conditions of caves shape microbiota. Within caves' microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves' actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves' actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes' outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens.

Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants

Background: The emergence and diffusion of strains of pathogenic bacteria resistant to antibiotics constitutes a real public health challenge. Antibiotic resistance genes (ARGs) can be carried by both pathogenic and non-pathogenic bacteria, including commensal bacteria from the human microbiota, which require special monitoring in the fight against antimicrobial resistance. Methods: We analyzed the proteomes of 335 new bacterial species from human microbiota to estimate its whole range of ARGs using the BLAST program against ARGs reference databases. Results: We found 278 bacteria that harbor a total of 883 potential ARGs with the following distribution: 264 macrolides-lincosamides-streptogramin, 195 aminoglycosides, 156 tetracyclines, 58 β-lactamases, 58 fosfomycin, 51 glycopeptides, 36 nitroimidazoles, 33 phenicols and 32 rifamycin. Furthermore, evolutionary analyses revealed the potential horizontal transfer with pathogenic bacteria involving mobile genetic elements such as transposase and plasmid. We identified many ARGs that may represent new variants in fosfomycin and β-lactams resistance. Conclusion: These findings show that new bacterial species from human microbiota should be considered as an important reservoir of ARGs that can be transferred to pathogenic bacteria. In vitro analyses of their phenotypic potential are required to improve our understanding of the functional role of this bacterial community in the development of antibiotic resistance.