Unusual Two‐Component Signal Transduction Pathways in the Actinobacteria

The imidacloprid remediation, soil fertility enhancement and microbial community change in soil by Rhodopseudomonas capsulata using effluent as carbon source

The effects of Rhodopseudomonas capsulata (R. capsulata) in the treated effluent of soybean processing wastewater (SPW) on the remediation of imidacloprid in soil, soil fertility, and the microbial community structure in soil were studied. Compared with the control group, with the addition of effluent containing R. capsulata, imidacloprid was effectively removed, soil fertility was enhanced, and the microbial community structure was improved. Molecular analysis indicated that imidacloprid could exert induction effects on expression of cpm gene and regulation effects on the synthesis of cytochrome P450 monooxygenases (P450) by activating HKs gene in two-component system (TCS). For R. capsulata, this induction process required 1 day. The synthesis of P450 occurred 1 day after inoculation, because R. capsulata are a type of archaea and imidacloprid is an environmental stress. Before expression of the cpm gene and synthesis of P450, R. capsulata need a period of time to adapt to external imidacloprid stimulation. However, the lack of organic matter in the soil cannot sustain R. capsulata growth for more than 1 day. In four groups with added effluent, the remaining organic matter in the effluent provided a sufficient carbon source and energy for R. capsulata. Five days later, the microbial community structure was improved by R. capsulata in the soil. The new technique could be used to remediate imidacloprid, enhance soil fertility, treat SPW and realize the recycling and reuse of wastewater and R. capsulata cells.

Rhodopseudomonas sphaeroides treating mesosulfuron-methyl waste-water

The soybean processing wastewater (SPW) supplementation to facilitate the simultaneously treatment (SPW and mesosulfuron-methyl) of wastewater and production of biological substances by Rhodopseudomonas sphaeroides (R. sphaeroides) was discussed. Compared with the control group, with the addition of SPW, mesosulfuron-methyl was removed, and the yields of single-cell proteins, carotenoids, and bacteriochlorophyll were increased. In the 3 mg/L dose group, the mesosulfuron-methyl removal rate reached 97% after 5 days. Molecular analysis revealed that mesosulfuron-methyl exhibited induction effects on expression of the cpm gene and regulation effects on the synthesis of cytochrome P450 monooxygenases (P450) by activating HKs gene in TCS signal transduction pathway. For R. sphaeroides, this induction process required 1 day. The synthesis of P450 occurred 1 day after inoculation. Prior to expressing cpm gene and synthesizing P450, R. sphaeroides need a period of time to adapt to external mesosulfuron-methyl stimulation. However, the R. sphaeroides growth could not be maintained for more than 1 day due to the lack of organic matter in the raw wastewater. The SPW supplementation provided a sufficient carbon source in four groups with added SPW. After 5 days, R. sphaeroides became the dominant microflora in the wastewater. This new method could complete the treatment of mixed wastewater, the increased of biological substances output and the reuse of wastewater and R. sphaeroides cells as resources at the same time.

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era

Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.

Two amino acids missing of MtrA resulted in increased erythromycin level and altered phenotypes in Saccharopolyspora erythraea

The MtrA-MtrB two-component regulatory system is highly conserved in Actinobacteria and plays crucial roles in cell cycle progression, cell morphology, antibiotic resistance, and osmoprotection. Previously, we revealed that the MtrA protein of Saccharopolyspora erythraea E3 strain (a high erythromycin-producing strain) had a two amino acid (H197 and V198) deletion in the DNA recognition helices of the C-terminal domain compared to the wild type S. erythraea strain NRRL2338. Here, we identified mepA (encoding a membrane protein related to metalloendopeptidases) as an MtrA target gene, and found that deleting the two amino acids in MtrA (MtrA^del) resulted in the loss of its DNA-binding activity for the mepA gene. The mutant MtrA^del lost its regulatory activity and affected various physiological functions consistent with mtrA deletion, including increased erythromycin biosynthesis, enhanced antibiotic resistance, deregulated osmoprotection, and improved transport of substances. The introduction of the wild type mtrA gene into the S. erythraea E3 strain with the mtrA^del gene decreased the erythromycin yield by approximately 50%, confirming that MtrA repressed erythromycin production. These findings demonstrate that MtrA is an important pleiotropic regulator of erythromycin biosynthesis, antibiotic resistance, osmoprotection, and substance transport in S. erythraea and provide new insights for improving erythromycin production. Future studies linking the molecular effects of MtrA to these phenotypes will improve our understanding of the MtrA-MtrB two-component regulatory system in Actinobacteria.

The Conserved Actinobacterial Two-Component System MtrAB Coordinates Chloramphenicol Production with Sporulation in Streptomyces venezuelae NRRL B-65442

Streptomyces bacteria make numerous secondary metabolites, including half of all known antibiotics. Production of antibiotics is usually coordinated with the onset of sporulation but the cross regulation of these processes is not fully understood. This is important because most Streptomyces antibiotics are produced at low levels or not at all under laboratory conditions and this makes large scale production of these compounds very challenging. Here, we characterize the highly conserved actinobacterial two-component system MtrAB in the model organism Streptomyces venezuelae and provide evidence that it coordinates production of the antibiotic chloramphenicol with sporulation. MtrAB are known to coordinate DNA replication and cell division in Mycobacterium tuberculosis where TB-MtrA is essential for viability but MtrB is dispensable. We deleted mtrB in S. venezuelae and this resulted in a global shift in the metabolome, including constitutive, higher-level production of chloramphenicol. We found that chloramphenicol is detectable in the wild-type strain, but only at very low levels and only after it has sporulated. ChIP-seq showed that MtrA binds upstream of DNA replication and cell division genes and genes required for chloramphenicol production. dnaA, dnaN, oriC, and wblE (whiB1) are DNA binding targets for MtrA in both M. tuberculosis and S. venezuelae. Intriguingly, over-expression of TB-MtrA and gain of function TB- and Sv-MtrA proteins in S. venezuelae also switched on higher-level production of chloramphenicol. Given the conservation of MtrAB, these constructs might be useful tools for manipulating antibiotic production in other filamentous actinomycetes.

Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences

To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes.

Selective overproduction of the proteasome inhibitor salinosporamide A via precursor pathway regulation

The chlorinated natural product salinosporamide A is a potent 20S proteasome inhibitor currently in clinical trials as an anticancer agent. To deepen our understanding of salinosporamide biosynthesis, we investigated the function of a LuxR-type pathway-specific regulatory gene, salR2, and observed a selective effect on the production of salinosporamide A over its less active aliphatic analogs. SalR2 specifically activates genes involved in the biosynthesis of the halogenated precursor chloroethylmalonyl-CoA, which is a dedicated precursor of salinosporamide A. Specifically, SalR2 activates transcription of two divergent operons-one of which contains the unique S-adenosyl-L-methionine-dependent chlorinase encoding gene salL. By applying this knowledge to rational engineering, we were able to selectively double salinosporamide A production. This study exemplifies the specialized regulation of a polyketide precursor pathway and its application to the selective overproduction of a specific natural product congener.

Cascades and networks of regulatory genes that control antibiotic biosynthesis

Onset of the biosynthesis of bioactive secondary metabolites in batch cultures of actinomycetes occurs after the rapid growth phase, following a transition phase which involves complex metabolic changes. This transition is triggered by nutrient starvation or by other environmental stress signals. Expression of genes encoding bioactive secondary metabolites is governed by cascades of pathway specific regulators and networks of cross-talking global regulators. Pathway specific regulators such as Streptomyces antibiotic regulatory proteins, LAL-type and LysR-type regulators respond to autoregulatory proteins that act in concert with their cognate ligands (e.g. γ-butyrolactone receptor proteins and their cognate γ-butyrolactone ligands). Global regulators such as PhoR-PhoP and other two component systems and orphan response regulators, such as GlnR, control set of genes affecting primary and secondary metabolism. GlnR and, therefore, nitrogen metabolism genes are under phosphate control exerted by binding of PhoP to PHO boxes located in the promoter region of GlnR. A few pleiotropic regulatory genes, such as areB (ndgR), dmdR1 or dasR connect primary metabolism (amino acid biosynthesis, N-acetylglucosamine or iron levels) with antibiotic biosynthesis. Some atypical response regulators that require specific small ligands appear to be involved in feedback control of antibiotic production. All these mechanisms together modulate, in a coordinated manner, different aspects of Streptomyces metabolism as a real "protection net" that prevents drastic changes in metabolism that may be deleterious for cell survival.

Dissecting the complete lipoprotein biogenesis pathway in Streptomyces scabies

Following translocation, bacterial lipoproteins are lipidated by lipoprotein diacylglycerol transferase (Lgt) and cleaved of their signal peptides by lipoprotein signal peptidase (Lsp). In Gram-negative bacteria and mycobacteria, lipoproteins are further lipidated by lipoprotein N-acyl transferase (Lnt), to give triacylated lipoproteins. Streptomyces are unusual amongst Gram-positive bacteria because they export large numbers of lipoproteins via the twin arginine protein transport (Tat) pathway. Furthermore, some Streptomyces species encode two Lgt homologues and all Streptomyces species encode two homologues of Lnt. Here we characterize lipoprotein biogenesis in the plant pathogen Streptomyces scabies and report that lgt and lsp mutants are defective in growth and development while only moderately affected in virulence. Lipoproteins are lost from the membrane in an S. scabies lgt mutant but restored by expression of Streptomyces coelicolor lgt1 or lgt2 confirming that both encode functional Lgt enzymes. Furthermore, lipoproteins are N-acylated in Streptomyces with efficient N-acylation dependent on Lnt1 and Lnt2. However, deletion of lnt1 and lnt2 has no effect on growth, development or virulence. We thus present a detailed study of lipoprotein biogenesis in Streptomyces, the first study of Lnt function in a monoderm bacterium and the first study of bacterial lipoproteins as virulence factors in a plant pathogen.

Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium

Micrococcus luteus (NCTC2665, "Fleming strain") has one of the smallest genomes of free-living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to encode 2,403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 insertion sequence (IS) elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the rrs gene of one of only two rrn operons found in M. luteus. The genome encodes only four sigma factors and 14 response regulators, a finding indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of M. luteus to beta-lactam antibiotics may result from the presence of a reduced set of penicillin-binding proteins and the absence of a wblC gene, which plays an important role in the antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth, M. luteus has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria, M. luteus appears to be able to metabolize glycogen only via trehalose and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to most other actinobacteria, M. luteus encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy, and its complement of other dormancy-related proteins is also much reduced. M. luteus is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three-gene cluster essential for this metabolism has been identified in the genome.

Autoregulation of antibiotic biosynthesis by binding of the end product to an atypical response regulator

In bacteria, many "atypical" response regulators (ARRs) lack the conserved residues important for phosphorylation by which typical response regulators switch their output response, suggesting the existence of alternative regulatory mechanisms. However, such mechanisms have not been established. JadR1, an OmpR-type ARR of Streptomyces venezuelae, appears to activate the transcription of jadomycin B (JdB) biosynthetic genes while repressing its own gene. JadR1 activities were inhibited in cells induced to produce JdB, which was found to bind directly to the N-terminal receiver domain of JadR1, causing JadR1 to dissociate from target promoters. The activity of a NarL-type ARR, RedZ, that regulates production of another antibiotic was likewise modulated by the end product (undecylprodigisines), implying that end-product-mediated control of antibiotic pathway-specific ARRs may be widespread. These results could prove relevant to knowledge-based improvements in yield of commercially important antibiotics.