Classification of Nonomuraea sp. ATCC 39727, an actinomycete that produces the glycopeptide antibiotic A40926, as Nonomuraea gerenzanensis sp. nov

Pradimicin U, a promising antimicrobial agent isolated from a newly found Nonomuraea composti sp. nov

Pradimicin U is a new dihydrobenzo[a]naphthacenequinone compound found to be active on a screen designed to investigate compounds with antimicrobial activity, produced by the actinomycete designated strain FMUSA5-5T. The strain was isolated from a bio-fertilizer of Musa spp. collected from Suphanburi province, Thailand. The chemotaxonomic characteristics and 16S rRNA gene analysis revealed that strain FMUSA5-5T is a member of the genus Nonomuraea. Low genome-based taxonomic criteria, average nucleotide identity (ANI) (82.8-88.3%), average amino-acid identity (AAI) (79.4-87.3%), and digital DNA-DNA hybridization (dDDH) (29.5-38.5%) values and several phenotypic differences between strain FMUSA5-5T and its closest type strains of the genus Nonomuraea indicated that strain FMUSA5-5T represents a novel species of the genus Nonomuraea and the name Nonomuraea composti sp. nov. is proposed for the strain. The crude extract from the culture broth of strain FMUSA5-5T displayed promising antimicrobial activity against several pathogens and led to the isolation of a novel secondary metabolite, pradimicin U. Interestingly, this compound displayed a broad spectrum of biological activities such as antimalarial activity against Plasmodium falciparum K1 (IC50 value = 3.65 µg/mL), anti-Mycobacterium tuberculosis H37Ra (MIC value = 25.0 µg/mL), anti-Alternaria brassicicola BCC 42724 (MIC value = 25.0 µg/mL), anti-Bacillus cereus ATCC 11778 and anti-Staphylococcus aureus ATCC 29213 (MIC values = 6.25 and 1.56 µg/mL, respectively). Moreover, the compound possessed strong anti-human small cell lung cancer (NCI-H187) activity with IC50 value of 5.69 µg/mL, while cytotoxicity against human breast cancer (MCF-7) and Vero cells was very weak (IC50 values of 52.49 and 21.84 µg/mL, respectively).

Improvement of the conjugation transfer of N. gerenzanensis based on the synergistic effect of quorum sensing and antibiotic interference

Nonomuraea gerenzanensis (N. gerenzanensis) is known for its ability to biosynthesize A40926, the precursor of the glycopeptide antibiotic (GPA) Dalbavancin. However, challenges and uncertainties related to the genetic manipulation of the rare actinomycetes remain. In order to improve the conjugation transfer of N. gerenzanensis, the crucial factors affecting conjugal transfer were evaluated, including agar medium, mycelial state, donor-recipient ratio, magnesium ion concentration, and antibiotic coverage time firstly. Additionally, γ-butyrolactone (GBL) for quorum sensing (QS) and antibiotics targeting bacterial walls were applied to evaluate their effects on conjugation transfer. As a result, the optimal conditions of 5%TSB of liquid medium, 24 h of the period time, V0.1 of agar medium, 30 mM of magnesium ion, the ratio 10:1 of donor-to-recipient, and 27 h of the overlaying time of antibiotic were determined. Furthermore, the results showed that autoinducer GBL and GPA teicoplanin had a synergetic effect on the conjugation transfer of N. gerenzanensis at a working concentration of 60 µM and 0.5 µg mL-1, respectively. The highest conjugation efficiency could reach about 1.3 depending on the optimal process conditions and the interference of QS and antibiotics.

Establishment of a visual gene knockout system based on CRISPR/Cas9 for the rare actinomycete Nonomuraea gerenzanensis

OBJECTIVES

To develop a modified CRISPR/Cas9 system with the β-glucuronidase (GusA) reporter and a dual sgRNA cassette for Nonomuraea gerenzanensis (N. gerenzanensis).

RESULTS

With the aid of a visual GusA reporter, the complicated and tedious process of cloning and gene identification could be abandoned entirely in the genetic editing of N. gerenzanensis. Moreover, introducing a dual sgRNA cassette into the CRISPR/Cas9 system significantly improved gene deletion efficiency compared to the single sgRNA element. Furthermore, the length of the homologous flanking sequences set to the lowest value of 500 bp in this system could still reach the relatively higher conjugation transfer frequency.

CONCLUSIONS

The enhanced CRISPR/Cas9 system could efficiently perform genetic manipulation on the rare actinomycete N. gerenzanensis.

Nonomuraea sediminis sp. nov., a novel actinobacterium with antimicrobial activity, isolated from sediment of Dianchi Lake

A novel actinobacterium with antimicrobial activity, designated strain H16431^T, was isolated from a sediment sample collected from Dianchi Lake, Yunnan Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain H16431^T was most closely related to Nonomuraea rhizosphaerae CGMCC 4.7431^T and Nonomuraea guangzhouensis CGMCC 4.7101^T (98.1% similarity), but formed a monophyletic clade with Nonomuraea ceibae KCTC 39826^T (98.0% similarity). Phylogenomic analysis based on whole-genome sequence showed that strain H16431^T formed a separate clade within the genus Nonomuraea. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain H16431^T and its closely related Nonomuraea species were 80.0-81.5%, 71.2-74.6%, and 23.2-25.0%, respectively, which were significantly lower than the widely accepted species-defined threshold. The DNA G + C content was 70.2% based on the whole-genome sequence. The menaquinones were identified as MK-9(H₄), MK-9(H₆), and MK-9(H₂). The major fatty acids were iso-C_16:0, 10 methyl-C_17:0, and iso-C_16:0 2OH. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, and phosphatidylinositol. These chemotaxonomic characteristics were corresponded to those of the genus Nonomuraea. On the basis of the taxonomic evidence, strain H16431^T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea sediminis sp. nov. is proposed. The type strain is H16431^T (=JCM 34852^T=CICC 25119^T).

Acute Bacterial Skin and Skin-Structure Infections, efficacy of Dalbavancin: a systematic review and meta-analysis

OBJECTIVES

To know the efficacy of different doses of dalbavancin in acute bacterial skin and skin-structure infections (ABSSSIs) and versus other antibiotics.

METHODS

We performed a systematic review of dalbavancin efficacy for ABSSSIs. We selected 10 clinical trials from MEDLINE and Cochrane databases for qualitative review. Of these, five trials compared one or two doses of dalbavancin versus other antibiotics such as vancomycin or linezolid.

RESULTS

Treatment outcomes with other antibiotics were not significantly different versus two doses of dalbavancin (OR 1.13; 95% CI 0.75-1.71; p = 0.55) or single dose dalbavancin (OR 0.98; 95% CI 0.19-5.17; p = 0.98). One dose versus two doses of dalbavancin did not show significant differences in any of the treatment groups. In contrast, the global microbiological assessment results indicated a favorable outcome for two doses of dalbavancin compared to the single dose of dalbavancin (OR 2.96; 95% CI 1.19-7.39; p = 0.02) in both methicillin-resistant and methicillin-susceptible Staphylococcus aureus.

CONCLUSION

Either single dose or two dose dalbavancin treatment is as clinically effective as other antibiotics such as vancomycin and linezolid for the treatment of ABSSSIs.Abbreviations ABSSI: acute bacterial skin and skin-structure infection; AUC: area under the concentration-time curve; CE: clinical evaluable; CI: confidence interval; EOT: end of treatment; ITT: intention-to-treat; LOS: length of stay; MIC: minimum inhibitory concentration; MIC₉₀: minimum concentration to inhibit growth of 90% of isolates; MR: methicillin resistant; MRSA: methicillin-resistant Staphylococcus aureus; MS: methicillin susceptible; MSSA: methicillin-susceptible Staphylococcus aureus; OPAT: Outpatient Parenteral Antimicrobial Therapy; OR: odds ratio; PI: penicillin intermediate; PR: penicillin resistant; PS penicillin susceptible; SIRS: systemic inflammatory response syndrome; SSTI: skin and soft tissue infection; TOC: test of cure; VR: vancomycin resistant; VS: vancomycin susceptible.

Serendipity reveals the function and physiological role of a large family of proteins

Microbial metabolism involves a complex set of interactions between metabolic pathways that include proteins of both known and uncharacterized function. While investigating the physiological strategy used by actinomycetes with two RpoB paralogs, Damiano et al uncovered the endonuclease activity of a member of the Rid family. While this finding was peripheral to the original question posed by the authors, it has considerable significance. The study by Damiano et al highlights how unexpected, but fundamental, information can be gained by following phenotypic leads.

Rid7C, a member of the YjgF/YER057c/UK114 (Rid) protein family, is a novel endoribonuclease that regulates the expression of a specialist RNA polymerase involved in differentiation in Nonomuraea gerenzanensis

The YjgF/YER057c/UK114 (Rid) is a protein family breadth conserved in all domains of life and includes the widely distributed archetypal RidA (YjgF) subfamily and seven other subfamilies (Rid1 to Rid7). Among these subfamilies, RidA is the only family to have been biochemically well characterized and is involved in the deamination of the reactive enamine/imine intermediates. In this study, we have characterized a protein of the Rid7 subfamily, named Rid7C, in Nonomuraea gerenzanensis, an actinomycete that is characterized by the presence of two types of RNA polymerases. This is due to the co-existence in its genome of two RNAP β chain-encoding genes: rpoB(S) (the wild-type rpoB gene) and rpoB(R) (a specialist, mutant-type rpoB gene) that controls A40926 antibiotic production and a wide range of metabolic adaptive behaviors. Here, we found that expression of rpoB(R) is regulated post-transcriptionally by RNA processing in the 5'-UTR of rpoB(R) mRNA, and that the endoribonuclease activity of Rid7C is responsible for mRNA processing thereby overseeing several tracts of morphological and biochemical differentiation. We also provide evidence that Rid7C may be associated with ribonuclease P M1 RNA, although M1 RNA is not required for rpoB(R) mRNA processing in vitro, and that Rid7C endoribonuclease activity is inhibited by A40926 suggesting the existence of a negative feedback loop on A40926 production, and a role of the endogenous synthesis of A40926 in the modulation of biochemical differentiation in this microorganism. Importance The YjgF/YER057c/UK114 family includes many proteins with diverse functions involved in detoxification, RNA maturation, and control of mRNA translation. We found that Rid7C is an endoribonuclease that is involved in processing of rpoB(R) mRNA, coding for a specialized RNA polymerase beta subunit that oversees morphological differentiation and A40926 antibiotic production in Nonomuraea gerenzanensis. Rid7C-mediated processing promotes rpoB(R) mRNA translation and antibiotic production, while Rid7C endoribonuclease activity is inhibited by A40926 suggesting a role of the endogenous synthesis of A40926 in modulation of biochemical differentiation in this microorganism. Finally, we show that recombinant Rid7C co-purified with M1 RNA (the RNA subunit of ribonuclease P) from Escherichia coli extract, suggesting a functional interaction between Rid7C and M1 RNA activities.

Enhancing Ristomycin A Production by Overexpression of ParB-Like StrR Family Regulators Controlling the Biosynthesis Genes

Amycolatopsis sp. strain TNS106 harbors a ristomycin-biosynthetic gene cluster (asr) in its genome and produces ristomycin A. Deletion of the sole cluster-situated StrR family regulatory gene, asrR, abolished ristomycin A production and the transcription of the asr genes orf5 to orf39. The ristomycin A fermentation titer in Amycolatopsis sp. strain TNS106 was dramatically improved by overexpression of asrR and a heterologous StrR family regulatory gene, bbr, from the balhimycin-biosynthetic gene cluster (BGC) utilizing strong promoters and multiple gene copies. Ristomycin A production was improved by approximately 60-fold, resulting in a fermentation titer of 4.01 g/liter in flask culture, in one of the engineered strains. Overexpression of AsrR and Bbr upregulated transcription of tested asr biosynthetic genes, indicating that these asr genes were positively regulated by AsrR and Bbr. However, only the promoter region of the asrR operon and the intergenic region upstream of orf12 were bound by AsrR and Bbr in gel retardation assays, suggesting that AsrR and Bbr directly regulated the asrR operon and probably orf12 to orf14 but no other asr biosynthetic genes. Further assays with synthetic short probes showed that AsrR and Bbr specifically bound not only probes containing the canonical inverted repeats but also a probe with only one 7-bp element of the inverted repeats in its native context. AsrR and Bbr have an N-terminal ParB-like domain and a central winged helix-turn-helix DNA-binding domain. Site-directed mutations indicated that the N-terminal ParB-like domain was involved in activation of ristomycin A biosynthesis and did not affect the DNA-binding activity of AsrR and Bbr. IMPORTANCE This study showed that overexpression of either a native StrR family regulator (AsrR) or a heterologous StrR family regulator (Bbr) dramatically improved ristomycin A production by increasing the transcription of biosynthetic genes directly or indirectly. The conserved ParB-like domain of AsrR and Bbr was demonstrated to be involved in the regulation of asr BGC expression. These findings provide new insights into the mechanism of StrR family regulators in the regulation of glycopeptide antibiotic biosynthesis. Furthermore, the regulator overexpression plasmids constructed in this study could serve as valuable tools for strain improvement and genome mining for new glycopeptide antibiotics. In addition, ristomycin A is a type III glycopeptide antibiotic clinically used as a diagnostic reagent due to its side effects. The overproduction strains engineered in this study are ideal materials for industrial production of ristomycin A.

Heterogeneous A40926 Self-Resistance Profile in Nonomuraea gerenzanensis Population Informs Strain Improvement

Nonomuraea gerenzanensis ATCC 39727 produces the glycopeptide antibiotic A40926, which is the natural precursor of the semi-synthetic, last-resort drug dalbavancin. To reduce the cost of dalbavancin production, it is mandatory to improve the productivity of the producing strain. Here, we report that the exposure of N. gerenzanensis wild-type population to sub-inhibitory concentrations of A40926 led to the isolation of differently resistant phenotypes to which a diverse A40926 productivity was associated. The most resistant population (G, grand colonies) represented at least the 20% of the colonies growing on 2 µg/mL of A40926. It showed a stable phenotype after sub-culturing and a homogeneous profile of self-resistance to A40926 in population analysis profile (PAP) experiments. The less resistant population (P, petit) was represented by slow-growing colonies to which a lower A40926 productivity was associated. At bioreactor scale, the G variant produced twice more than the wild-type (ca. 400 mg/L A40926 versus less than 200 mg/L, respectively), paving the way for a rational strain improvement based on the selection of increasingly self-resistant colonies.

Systematic review and meta-analysis on the safety of dalbavancin

BACKGROUND

Dalbavancin is a semisynthetic lipoglycopeptide antimicrobial agent with activity against Gram-positive bacteria including anaerobes.

RESEARCH DESIGN AND METHODS

Meta-analysis of randomized control trials and large case series (more than 20 patients), were identified by searching Pubmed and Cochrane databases through 14 December 2020.

RESULTS

3,073 patients from 6 RCTs met the inclusion criteria. Treatment emergent adverse effects were described in 30.6% dalbavancin patients, and 38.1% patients with other treatments. Our meta-analysis supports favorable results for dalbavancin treatment (OR 0.79; 95%CI 0.66-0.94; p = 0.01). 2.74% dalbavancin patients had to discontinue treatment versus 2.49% patients on other antibiotics. 4.80% dalbavancin patients versus 5.30% patients with other treatments had severe adverse events. 0.31% in the dalbavancin group and 0.95% receiving other antibiotics died. There was no statistically significant difference in severe adverse effects with OR 0.77; 95% CI 0.52-1.14; p = 0.19. Dalbavancin therapy was shown to have statistically significant lower mortality rate (OR 0.26; 95% CI 0.07-0.90; p = 0.03). Observational studies reported few side effects but included a heterogeneous population of patients concerning their diagnosis and the duration of antibiotic treatment.

CONCLUSIONS

Dalbavancin has comparable safety profile relative to other antibiotics and is well-tolerated.

Streptomycetes: Attractive Hosts for Recombinant Protein Production

Enzymes are increasingly applied as biocatalysts for fulfilling industrial needs in a variety of applications and there is a bursting of interest for novel therapeutic proteins. Consequently, developing appropriate expression platforms for efficiently producing such recombinant proteins represents a crucial challenge. It is nowadays widely accepted that an ideal ‘universal microbial host’ for heterologous protein expression does not exist. Indeed, the first-choice microbes, as Escherichia coli or yeasts, possess known intrinsic limitations that inevitably restrict their applications. In this scenario, bacteria belonging to the Streptomyces genus need to be considered with more attention as promising, alternative, and versatile platforms for recombinant protein production. This is due to their peculiar features, first-of-all their natural attitude to secrete proteins in the extracellular milieu. Additionally, streptomycetes are considered robust and scalable industrial strains and a wide range of tools for their genetic manipulation is nowadays available. This mini-review includes an overview of recombinant protein production in streptomycetes, covering nearly 100 cases of heterologous proteins expressed in these Gram-positives from the 1980s to December 2019. We investigated homologous sources, heterologous hosts, and molecular tools (promoters/vectors/signal peptides) used for the expression of these recombinant proteins. We reported on their final cellular localization and yield. Thus, this analysis might represent a useful source of information, showing pros and cons of using streptomycetes as platform for recombinant protein production and paving the way for their more extensive use in future as alternative heterologous hosts.

Description of the bacterial RNA polymerase inhibitor GE23077-producer Actinomadura sp. NRRL B-65521T as Actinomadura lepetitiana sp. nov

The filamentous actinomycete that produces the antibiotic GE23077 was isolated by the Lepetit Research Group from a soil sample collected in Thailand, and it was classified as a member of the genus Actinomadura on the basis of its morphology and cell-wall composition. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain formed a distinct monophyletic line within the genus Actinomadura, and it was most closely related to Actinomadura bangladeshensis DSM 45347^T (99.31 % similarity) and Actinomadura mexicana DSM 44485^T (98.94 %). The GE23077-producing strain formed an extensively branched, non-fragmented vegetative mycelium; no pseudosporangia were formed and the arthrospores were organized in slightly twisted chains. The cell wall contained meso-2,6-diaminopimelic acid and the diagnostic sugar was madurose. The predominant menaquinone was MK-9(H₆), with minor amounts of MK-9(H₈) and MK-9(H₄). The diagnostic phospholipids were phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were C_16 : 0 and tuberculostearic acid (10-methyloctadecanoic acid), followed by minor amounts of C_18:1ω9c, C_16:1ω7c and 10-methylheptadecanoic acid. The genomic DNA G+C content was 71.77 mol%. Significant differences in the morphological, chemotaxonomic and biochemical data, and the low DNA-DNA relatedness between the GE23077-producing strain and closely related type strains clearly demonstrate that it represents a novel species of the genus Actinomadura, for which the name Actinomadura lepetitiana sp. nov. is proposed. The type strain is NRRL B-65521^T(=LMG 31258^T=DSM 109019^T).

Nonomuraea typhae sp. nov., an endophytic actinomycete isolated from the root of cattail pollen (Typha angustifolia L.)

A novel endophytic actinomycete, designated strain p1410^T, was isolated from the root of cattail pollen (Typha angustifolia L.) and characterized using a polyphasic approach. The strain had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Nonomuraea. It produced spiral chains of spores on aerial mycelium as well as forming a pseudosporangium. Whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, ribose and madurose. The menaquinones detected were MK-9(H₂), MK-9(H₄) and MK-9(H₀). The major fatty acids were 10-methyl C_17 : 0, iso-C_16 : 0 and C_17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol mannoside and an unknown glycolipid. The DNA G+C content of the draft genome sequence, consisting of 11.4 Mbp, was 70.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain p1410^T belongs to the genus Nonomuraea with the highest sequence similarity to Nonomuraea candida HMC10^T (98.6 %), but phylogenetically clustered with Nonomuraea endophytica YIM 65601^T (98.4 %) and Nonomuraea longicatena NRRL 15532^T (98.3 %). Based on its phenotypic characteristics, DNA-DNA relatedness and average nucleotide identity, the strain is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea typhae sp. nov. is proposed. The type strain is p1410^T (=CCTCC AA 2019044^T=JCM 33461^T).

A Silkworm Infection Model for In Vivo Study of Glycopeptide Antibiotics

Glycopeptide antibiotics (GPAs) are drugs of last resort for treating infections by Gram-positive bacteria. They inhibit bacterial cell wall assembly by binding to the d-Ala-d-Ala terminus of peptidoglycan precursors, leading to cell lysis. Vancomycin and teicoplanin are first generation GPAs, while dalbavancin is one of the few, recently approved, second generation GPAs. In this paper, we developed an in vivo insect model to compare, for the first time, the efficacy of these three GPAs in curing Staphylococcus aureus infection. Differently from previous reports, Bombyx mori larvae were reared at 37 °C, and the course of infection was monitored, following not only larval survival, but also bacterial load in the insect body, hemocyte activity, phenoloxidase activity, and antimicrobial peptide expression. We demonstrated that the injection of S. aureus into the hemolymph of B. mori larvae led to a marked reduction of their survival rate within 24-48 hours. GPAs were not toxic to the larvae and cured S. aureus infection. Dalbavancin was more effective than first generation GPAs. Due to its great advantages (i.e., easy and safe handling, low rearing costs, low antibiotic amount needed for the tests, no restrictions imposed by ethical and regulatory issues), this silkworm infection model could be introduced in preclinical phases-prior to the use of mice-accelerating the discovery/development rate of novel GPAs.

Polyphasic classification of Nonomuraea strains isolated from the Karakum Desert and description of Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov

Five actinobacteria isolates, KC201^T, KC401, KC310^T, KC712^T and 6K102^T, were recovered from the Karakum Desert during an investigation of novel actinobacteria with biotechnological potential. A polyphasic approach confirmed the affiliation of the strains to the genus Nonomuraea. The strains showed chemotaxonomic and morphological properties consistent with their classification in the genus Nonomuraea. Furthermore, these strains clearly distinguished and formed well supperted clades in phylogenetic and phylogenomic trees. Low ANI and dDDH values and distinguishing phenotypic properties between isolates KC201^T, KC310^T, KC712^T and 6K102^T showed that these strains belonged to novel Nonomuraea species, the names proposed for these taxa are Nonomuraea deserti sp. nov., Nonomuraea diastatica sp. nov., Nonomuraea longispora sp. nov. and Nonomuraea mesophila sp. nov., with the type strains KC310^T (=CGMCC 4.7331^T =DSM 102919^T =KCTC 39774^T), KC712^T (=CGMCC 4.7334^T =DSM 102925^T =KCTC 39776), KC201^T (=CGMCC 4.7339^T =DSM 102917^T =KCTC 39781^T) and 6K102^T (=CGMCC 4.7541^T =JCM 32916), respectively.

Preparation of pH-Responsive Alginate-Chitosan Microspheres for L-Valine Loading and Their Effects on the A40926 Production

The glycopeptide A40926 biosynthesized by Nonomuraea gerenzanensis is a precursor of the second generation glycopeptide antibiotic dalbavancin. The skeleton of this glycopeptide consists of seven amino acids and is biosynthesized by the NRPS gene module. L-valine, a branched amino acid, is also a significant precursor for A40926 production. This study details the use of pH-responsive alginate-chitosan microspheres loaded with L-valine prepared by internal emulsification gelation. The effects of process and formulation variables on microsphere size, loading capacity, and encapsulation efficiency were investigated. Then, effects on A40926 production by the pH-responsive microspheres were evaluated in a 10-L fermenter. Results demonstrated that use of the pH-responsive microspheres could improve A40926 yield from 465 to 602 mg L^-1 in a 10-L scale fermenter.

New Molecular Tools for Regulation and Improvement of A40926 Glycopeptide Antibiotic Production in Nonomuraea gerenzanensis ATCC 39727

Genome sequencing has revealed that Nonomuraea spp. represent a still largely unexplored source of specialized metabolites. Nonomuraea gerenzanensis ATCC 39727 is the most studied representative species since it produces the glycopeptide antibiotic (GPA) A40926 – the precursor of the clinically relevant antibiotic dalbavancin, approved by the FDA in 2014 for the treatment of acute skin infections caused by multi-drug resistant Gram-positive pathogens. The clinical relevance of dalbavancin has prompted increased attention on A40926 biosynthesis and its regulation. In this paper, we investigated how to enhance the genetic toolkit for members of the Nonomuraea genus, which have proved quite recalcitrant to genetic manipulation. By constructing promoter-probe vectors, we tested the activity of 11 promoters (heterologous and native) using the GusA reporter system in N. gerenzanensis and in Nonomuraea coxensis; this latter species is phylogenetically distant from N. gerenzanesis and also possesses the genetic potential to produce A40926 or a very similar GPA. Finally, the strongest constitutive promoter analyzed in this study, aac(3)IVp, was used to overexpress the cluster-situated regulatory genes controlling A40926 biosynthesis (dbv3 and dbv4 from N. gerenzanensis and nocRI from N. coxensis) in N. gerenzanensis, and the growth and productivity of the best performing strains were assessed at bioreactor scale using an industrial production medium. Overexpression of positive pathway-specific regulatory genes resulted in a significant increase in the level of A40926 production in N. gerenzanensis, providing a new knowledge-based approach to strain improvement for this valuable glycopeptide antibiotic.

Metagenome-Sourced Microbial Chitinases as Potential Insecticide Proteins

Microbial chitinases are gaining interest as promising candidates for controlling plant pests. These enzymes can be used directly as biocontrol agents as well as in combination with chemical pesticides or other biopesticides, reducing their environmental impact and/or enhancing their efficacy. Chitinolytic enzymes can target two different structures in insects: the cuticle and the peritrophic matrix (PM). PM, formed by chitin fibrils connected to glycoproteins and proteoglycans, represents a physical barrier that plays an essential role in midgut physiology and insect digestion, and protects the absorptive midgut epithelium from food abrasion or pathogen infections. In this paper, we investigate how two recently discovered metagenome-sourced chitinases (Chi18H8 and 53D1) affect, in vitro and in vivo, the PM integrity of Bombyx mori, a model system among Lepidoptera. The two chitinases were produced in Escherichia coli or, alternatively, in the unconventional – but more environmentally acceptable – Streptomyces coelicolor. Although both the proteins dramatically altered the structure of B. mori PM in vitro, when administered orally only 53D1 caused adverse and marked effects on larval growth and development, inducing mortality and reducing pupal weight. These in vivo results demonstrate that 53D1 is a promising candidate as insecticide protein.

Toward Single-Peak Dalbavancin Analogs through Biology and Chemistry

Glycopeptide antibiotics are used to treat severe multidrug resistant infections caused by Gram-positive bacteria. Dalbavancin is a second generation glycopeptide approved for human use, which is obtained from A40926, a lipoglycopeptide produced by Nonomuraea sp. ATCC39727 as a mixture of biologically active congeners mainly differing in the fatty acid chains present on the glucuronic moiety. In this study, we constructed a double mutant of the A40926 producer strain lacking dbv23, and thus defective in mannose acetylation, a feature that increases A40926 production, and lacking the acyltransferases Dbv8, and thus incapable of installing the fatty acid chains. The double mutant afforded the desired deacyl, deacetyl A40926 intermediates, which could be converted by chemical reacylation yielding A40926 analogs with a greatly reduced number of congeners. The newly acylated analogs could then be transformed into dalbavancin analogs possessing the same in vitro properties as the approved drug.

Specificity of Induction of Glycopeptide Antibiotic Resistance in the Producing Actinomycetes

Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by Gram-positive pathogens. It is widely believed that glycopeptide-resistance determinants (van genes) are ultimately derived from the producing actinomycetes. We hereby investigated the relationship between the antimicrobial activity of vancomycin and teicoplanins and their differential ability to induce van gene expression in Actinoplanes teichomyceticus—the producer of teicoplanin—and Nonomuraea gerenzanensis—the producer of the teicoplanin-like A40926. As a control, we used the well-characterized resistance model Streptomyces coelicolor. The enzyme activities of a cytoplasmic-soluble d,d-dipeptidase and of a membrane-associated d,d-carboxypeptidase (corresponding to VanX and VanY respectively) involved in resistant cell wall remodeling were measured in the actinomycetes grown in the presence or absence of subinhibitory concentrations of vancomycin, teicoplanin, and A40926. Results indicated that actinomycetes possess diverse self-resistance mechanisms, and that each of them responds differently to glycopeptide induction. Gene swapping among teicoplanins-producing actinomycetes indicated that cross-talking is possible and provides useful information for predicting the evolution of future resistance gene combinations emerging in pathogens.

Complex Regulatory Networks Governing Production of the Glycopeptide A40926

Glycopeptides (GPAs) are an important class of antibiotics, with vancomycin and teicoplanin being used in the last 40 years as drugs of last resort to treat infections caused by Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus. A few new GPAs have since reached the market. One of them is dalbavancin, a derivative of A40926 produced by the actinomycete Nonomuraea sp. ATCC 39727, recently classified as N. gerenzanensis. This review summarizes what we currently know on the multilevel regulatory processes governing production of the glycopeptide A40926 and the different approaches used to increase antibiotic yields. Some nutrients, e.g., valine, l-glutamine and maltodextrin, and some endogenous proteins, e.g., Dbv3, Dbv4 and RpoB^R, have a positive role on A40926 biosynthesis, while other factors, e.g., phosphate, ammonium and Dbv23, have a negative effect. Overall, the results available so far point to a complex regulatory network controlling A40926 in the native producing strain.

Old and new glycopeptide antibiotics: From product to gene and back in the post-genomic era

Glycopeptide antibiotics are drugs of last resort for treating severe infections caused by multi-drug resistant Gram-positive pathogens. First-generation glycopeptides (vancomycin and teicoplanin) are produced by soil-dwelling actinomycetes. Second-generation glycopeptides (dalbavancin, oritavancin, and telavancin) are semi-synthetic derivatives of the progenitor natural products. Herein, we cover past and present biotechnological approaches for searching for and producing old and new glycopeptide antibiotics. We review the strategies adopted to increase microbial production (from classical strain improvement to rational genetic engineering), and the recent progress in genome mining, chemoenzymatic derivatization, and combinatorial biosynthesis for expanding glycopeptide chemical diversity and tackling the never-ceasing evolution of antibiotic resistance.

Nonomuraea lycopersici sp. nov., isolated from the root of tomato plants (Solanum lycopersicum L.)

Two novel bacterial strains were isolated from the roots of tomato plants (Solanum lycopersicum L.) from Dengfeng, Henan Province, China. Phylogenetic analysis of 16S rRNA gene sequences showed that the isolates NEAU-DE8(1)^T and NEAU-HE1(2) are closely related to one another (99.6% similarity) and are closely relate to Nonomuraea zeae NEAU-ND5^T (98.3, 98.3%) and Nonomuraea gerenzanensis DSM 100948^T (98.3, 98.0%). Phylogenetic trees constructed based on 16S rRNA gene sequences revealed that both strains grouped with N. zeae NEAU-ND5^T within the clade comprising the members of the genus Nonomuraea. Moreover, key chemotaxonomic properties including major menaquinones, fatty acid composition and phospholipid profiles also confirmed the affiliation of the two strains to the genus Nonomuraea. However, DNA-DNA hybridization data, together with physiological and morphological properties, showed that two isolates could be readily distinguished from their close phylogenetic relatives. Thus, on the basis of these phenotypic and genotypic data, strains NEAU-DE8(1)^T and NEAU-HE1(2) are concluded to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea lycopersici sp. nov. is proposed. The type strain is NEAU-DE8(1)^T (= CGMCC 4.7412^T = DSM 104642^T).

A valuable peroxidase activity from the novel species Nonomuraea gerenzanensis growing on alkali lignin

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Actinomycetes represent an attractive source of ligninolytic enzymes.

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43 actinomycetes were screened for laccase and peroxidase activities.

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The novel species N. gerenzanensis produces a valuable bacterial peroxidase activity.

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The dye-decolorizing activity paves the way for an industrial use of this peroxidase.

Degradation of lignin constitutes a key step in processing biomass to become useful monomers but it remains challenging. Compared to fungi, bacteria are much less characterized with respect to their lignin metabolism, although it is reported that many soil bacteria, especially actinomycetes, attack and solubilize lignin. In this work, we screened 43 filamentous actinomycetes by assaying their activity on chemically different substrates including a soluble and semi-degraded lignin derivative (known as alkali lignin or Kraft lignin), and we discovered a novel and valuable peroxidase activity produced by the recently classified actinomycete Nonomuraea gerenzanensis. Compared to known fungal manganese and versatile peroxidases, the stability of N. gerenzanensis peroxidase activity at alkaline pHs and its thermostability are significantly higher. From a kinetic point of view, N. gerenzanensis peroxidase activity shows a K_m for H₂O₂ similar to that of Phanerochaete chrysosporium and Bjerkandera enzymes and a lower affinity for Mn²⁺, whereas it differs from the six Pleurotus ostreatus manganese peroxidase isoenzymes described in the literature. Additionally, N. gerenzanensis peroxidase shows a remarkable dye-decolorizing activity that expands its substrate range and paves the way for an industrial use of this enzyme. These results confirm that by exploring new bacterial diversity, we may be able to discover and exploit alternative biological tools putatively involved in lignin modification and degradation.

The complete 12 Mb genome and transcriptome of Nonomuraea gerenzanensis with new insights into its duplicated "magic" RNA polymerase

In contrast to the widely accepted consensus of the existence of a single RNA polymerase in bacteria, several actinomycetes have been recently shown to possess two forms of RNA polymerases due the to co-existence of two rpoB paralogs in their genome. However, the biological significance of the rpoB duplication is obscure. In this study we have determined the genome sequence of the lipoglycopeptide antibiotic A40926 producer Nonomuraea gerenzanensis ATCC 39727, an actinomycete with a large genome and two rpoB genes, i.e. rpoB(S) (the wild-type gene) and rpoB(R) (the mutant-type gene). We next analyzed the transcriptional and metabolite profiles in the wild-type gene and in two derivative strains over-expressing either rpoB(R) or a mutated form of this gene to explore the physiological role and biotechnological potential of the "mutant-type" RNA polymerase. We show that rpoB(R) controls antibiotic production and a wide range of metabolic adaptive behaviors in response to environmental pH. This may give interesting perspectives also with regard to biotechnological applications.