A two-component system gene SACE_0101 regulates copper homeostasis in Saccharopolyspora erythraea

Divergent prokaryotic microbial assembly, co-existence patterns and functions in surrounding river sediments of a Cu-polymetallic deposit in Tibet

The exploitation of polymetallic deposits produces large amounts of mine drainage, which poses great challenges to the surrounding aquatic ecosystem. However, the prokaryotic microbial community assembly and co-existence patterns in the polluted area are poorly understood, especially in high-altitude localities. Herein, we investigated the prokaryotic microbial assembly, co-existence patterns and their potential functional responses in surrounding river sediments of a Cu-polymetallic deposit in Tibet. The sediments from mine drainage and surrounding tributaries exhibited distinct geochemical gradients, especially the changes in Cu content. The microbial community structure changed significantly, accompanied by decreased richness and diversity with increased Cu content. Interestingly, the relative abundances of some potential functional bacteria (e.g., Planctomycetota) actually increased as the Cu levels raised. In low contaminated area, ecological drift was the most important assembly process, whereas deterministic processes gained importance with pollution levels. Meanwhile, negative interactions in co-occurrence networks were more frequent with higher modularity and reduced keystone taxa in high contaminated area. Notably, the functions related to ABC transporters and quorum sensing (QS) were more abundant with high Cu content, which helped bacteria work together to cope with the stressful environment. Taken together, the physicochemical gradients dominated by Cu content drove the distribution, assembly and co-existence patterns of microbial communities in surrounding river sediments of a Cu-polymetallic deposit. These findings provide new insights into the maintenance mechanisms of prokaryotic microbial communities in response to heavy metal stress at high altitudes.

Two strategies to improve the supply of PKS extender units for ansamitocin P-3 biosynthesis by CRISPR-Cas9

Ansamitocin P-3 (AP-3) produced by Actinosynnema pretiosum is a potent antitumor agent. However, lack of efficient genome editing tools greatly hinders the AP-3 overproduction in A. pretiosum. To solve this problem, a tailor-made pCRISPR-Cas9apre system was developed from pCRISPR-Cas9 for increasing the accessibility of A. pretiosum to genetic engineering, by optimizing cas9 for the host codon preference and replacing pSG5 with pIJ101 replicon. Using pCRISPR-Cas9apre, five large-size gene clusters for putative competition pathway were individually deleted with homology-directed repair (HDR) and their effects on AP-3 yield were investigated. Especially, inactivation of T1PKS-15 increased AP-3 production by 27%, which was most likely due to the improved intracellular triacylglycerol (TAG) pool for essential precursor supply of AP-3 biosynthesis. To enhance a "glycolate" extender unit, two combined bidirectional promoters (BDPs) ermEp-kasOp and j23119p-kasOp were knocked into asm12-asm13 spacer in the center region of gene cluster, respectively, by pCRISPR-Cas9apre. It is shown that in the two engineered strains BDP-ek and BDP-jk, the gene transcription levels of asm13-17 were significantly upregulated to improve the methoxymalonyl-acyl carrier protein (MM-ACP) biosynthetic pathway and part of the post-PKS pathway. The AP-3 yields of BDP-ek and BDP-jk were finally increased by 30% and 50% compared to the parent strain L40. Both CRISPR-Cas9-mediated engineering strategies employed in this study contributed to the availability of AP-3 PKS extender units and paved the way for further metabolic engineering of ansamitocin overproduction.

RclS Sensor Kinase Modulates Virulence of Pseudomonas capeferrum

Signal transduction systems are the key players of bacterial adaptation and survival. The orthodox two-component signal transduction systems perceive diverse environmental stimuli and their regulatory response leads to cellular changes. Although rarely described, the unorthodox three-component systems are also implemented in the regulation of major bacterial behavior such as the virulence of clinically relevant pathogen P. aeruginosa. Previously, we described a novel three-component system in P. capeferrum WCS358 (RclSAR) where the sensor kinase RclS stimulates the intI1 transcription in stationary growth phase. In this study, using rclS knock-out mutant, we identified RclSAR regulon in P. capeferrum WCS358. The RNA sequencing revealed that activity of RclSAR signal transduction system is growth phase dependent with more pronounced regulatory potential in early stages of growth. Transcriptional analysis emphasized the role of RclSAR in global regulation and indicated the involvement of this system in regulation of diverse cellular activities such as RNA binding and metabolic and biocontrol processes. Importantly, phenotypic comparison of WCS358 wild type and ΔrclS mutant showed that RclS sensor kinase contributes to modulation of antibiotic resistance, production of AHLs and siderophore as well as host cell adherence and cytotoxicity. Finally, we proposed the improved model of interplay between RclSAR, RpoS and LasIR regulatory systems in P. capeferrum WCS358.

Comparative genomic and transcriptomic analysis guides to further enhance the biosynthesis of erythromycin by an overproducer

Omics approaches have been applied to understand the boosted productivity of natural products by industrial high-producing microorganisms. Here, with the updated genome sequence and transcriptomic profiles derived from high-throughput sequencing, we exploited comparative omics analysis to further enhance the biosynthesis of erythromycin in an industrial overproducer, Saccharopolyspora erythraea HL3168 E3. By comparing the genome of E3 with the wild type NRRL23338, we identified fragment deletions inside 56 coding sequences and 255 single nucleotide polymorphisms over the genome of E3. A substantial number of genomic variations were observed in genes responsible for pathways which were interconnected to the biosynthesis of erythromycin by supplying precursors/cofactors or by signal transduction. Furthermore, the transcriptomic data suggested that genes involved in the biosynthesis of erythromycin were significantly up-regulated constantly, whereas some genes in biosynthesis clusters of other secondary metabolites contained nonsense mutations and were expressed at extremely low levels. Through comparative transcriptomic analysis, L-glutamine/L-glutamate and 2-oxoglutarate were identified as reporter metabolites. Around the node of 2-oxoglutarate, genomic mutations were also observed. Based on the omics association analysis, readily available strategies were proposed to engineer E3 by simultaneously overexpressing sucB (coding for 2-oxoglutarate dehydrogenase E2 component) and sucA (coding for 2-oxoglutarate dehydrogenase E1 component), which increased the erythromycin titer by 71% compared to E3 in batch culture. This work provides more promising molecular targets to engineer for enhanced production of erythromycin by the overproducer. This article is protected by copyright. All rights reserved.