Transcriptome Analysis of Novosphingobium pentaromativorans US6-1 Reveals the Rsh Regulon and Potential Molecular Mechanisms of N-acyl-l-homoserine Lactone Accumulation

An improved genome editing system for Sphingomonadaceae

The sphingomonads encompass a diverse group of bacteria within the family Sphingomonadaceae, with the presence of sphingolipids on their cell surface instead of lipopolysaccharide as their main common feature. They are particularly interesting for bioremediation purposes due to their ability to degrade or metabolise a variety of recalcitrant organic pollutants. However, research and development on their full bioremediation potential has been hampered because of the limited number of tools available to investigate and modify their genome. Here, we present a markerless genome editing method for Sphingopyxis granuli TFA, which can be further optimised for other sphingomonads. This procedure is based on a double recombination triggered by a DNA double-strand break in the chromosome. The strength of this protocol lies in forcing the second recombination rather than favouring it by pressing a counterselection marker, thus avoiding laborious restreaking or passaging screenings. Additionally, we introduce a modification with respect to the original protocol to increase the efficiency of the screening after the first recombination event. We show this procedure step by step and compare our modified method with respect to the original one by deleting ecfG2, the master regulator of the general stress response in S. granuli TFA. This adds to the genetic tool repertoire that can be applied to sphingomonads and stands as an efficient option for fast genome editing of this bacterial group.

Regulation of quorum sensing activities by the stringent response gene rsh in sphingomonads is species-specific and culture condition dependent

Stringent response and quorum sensing (QS) are two essential mechanisms that control bacterial global metabolism for better survival. Sphingomonads are a clade of bacteria that survive successfully in diverse ecosystems. In silico survey indicated that 36 out of 79 investigated sphingomonads strains contained more than one luxI homolog, the gene responsible for the biosynthesis of QS signal acyl homoserine lactones (AHLs). Investigation of the regulatory effects of the stringent response gene rsh on QS related bioactivities were carried out using rsh mutants of Sphingobium japonicum UT26 and Sphingobium sp. SYK-6, both had three luxI homologs. Results indicated that deletion of rsh upregulated the overall production of AHLs and extracellular polymeric substances (EPS) in both UT26 and SYK-6 in rich medium, but affected expressions of these luxI/luxR homologs in different ways. In the poor medium (1% LB), rsh mutant of SYK-6 significantly lost AHLs production in broth cultivation but not in biofilm cultivation. The regulatory effects of rsh on QS activities were growth phase dependent in UT26 and culture condition dependent in SYK-6. Our results demonstrated the negative regulatory effect of rsh on QS activities in sphingomonads, which were very different from the positive effect found in sphingomonads containing only one luxI/R circuit. This study extends the current knowledge on the intricate networks between stringent response and QS system in sphingomonads, which would help to understand their survival advantage.

The stringent response gene rsh plays multiple roles in Novosphingobium pentaromativorans US6-1's accommodation to different environmental pollutants: Phenanthrene, copper and nZVI

The rsh based stringent response system is widely employed by bacteria to cope with environmental stresses. However, how does the stringent response involve in bacterial accommodation to environmental pollutant is largely unexplored. In this study, to comprehensively understand the roles of rsh in Novosphingobium pentaromativorans US6-1's metabolism and accommodation to different pollutants, three distinct pollutants, phenanthrene, copper and nanoparticulated zero valent iron (nZVI) were selected as exposure substances. Results indicated that rsh played important roles in US6-1's multiplication and metabolism, including survival rate at stationary phase, amino acid and nucleotide metabolism, extracellular polymeric substance (EPS) production, redox homeostasis, etc. The deletion of rsh affected phenanthrene removal rates through regulating the multiplication of US6-1 and increasing the expression of degradation related genes. The rsh mutant showed higher resistance to copper than the wild type, largely due to higher EPS production and enhanced expression of copper resistance related genes. Finally, the rsh based stringent response helped maintain the redox homeostasis when US6-1 confronted nZVI particles that exerted oxidative stress, thereby improving the survival rate. Overall, this study provides firsthand data that rsh plays multiple roles in US6-1's accommodation to environmental pollutants. The stringent response system could be a powerful tool for environmental scientists and engineers to harness bacterial activities for bioremediation purposes.

Identification of the key exosomal lncRNAs/mRNAs in the serum during distraction osteogenesis

Background

Distraction osteogenesis (DO), a kind of bone regenerative process, is not only extremely effective, but the osteogenesis rate is far beyond ordinary bone fracture (BF) healing. Exosomes (Exo) are thought to play a part in bone regeneration and healing as key players in cell-to-cell contact. The object of this work was to determine whether exosomes derived from DO and BF serum could stimulate the Osteogenic Differentiation in these two processes, and if so, which genes could be involved.

Methods

The osteogenesis in DO-gap or BF-gap was evaluated using radiographic analysis and histological analysis. On the 14th postoperative day, DO-Exos and BF-Exos were isolated and cocultured with the jaw of bone marrow mesenchymal stem cells (JBMMSCs). Proliferation, migration and osteogenic differentiation of JBMMSCs were ascertained, after which exosomes RNA-seq was performed to identify the relevant gene.

Results

Radiographic and histological analyses manifested that osteogenesis was remarkably accelerated in DO-gap in comparison with BF-gap. Both of the two types of Exos were taken up by JBMMSCs, and their migration and osteogenic differentiation were also seen to improve. However, the proliferation showed no significant difference. Finally, exosome RNA-seq revealed that the lncRNA MSTRG.532277.1 and the mRNA F-box and leucine-rich repeat protein 14(FBXL14) may play a key role in DO.

Conclusions

Our findings suggest that exosomes from serum exert a critical effect on the rapid osteogenesis in DO. This promoting effect might have relevance with the co-expression of MSTRG.532277.1 and FBXL14. On the whole, these findings provide new insights into bone regeneration, thereby outlining possible therapeutic targets for clinical intervention.

Benzo[a]pyrene might be transported by a TonB-dependent transporter in Novosphingobium pentaromativorans US6-1

Sphingomonads are well known for their ability to efficiently degrade polycyclic aromatic hydrocarbons (PAHs), but little is known about the mechanism of PAH uptake and transport across the cell membrane. RNA sequencing analysis of a sphingomonad, Novosphingobium pentaromativorans US6-1 showed that 38 TonB-dependent transporter (TBDT) genes were significantly upregulated under 5-ring PAH-benzo[a]pyrene (BaP) stress. In order to reveal whether TBDTs are involved in uptake and transport BaP in US6-1, the key TBDT genes were deleted to generate mutants. The results showed that the growth status of these mutants was not different from that of the wild-type strains, but the PAH degradation ability decreased, especially for the mutant strain Δtbdt-11, which did not encode the tbdt-11 gene. Meanwhile, the cell surface hydrophobicity (CSH) of Δtbdt-11 was found to be significantly lower than that of the wild-type strain under BaP stress. Furthermore, the transcriptional activity of genes encoding PAH degradative enzymes was found to be greatly reduced in Δtbdt-11. Confocal microscopy observations showed that US6-1 could transport BaP across the outer membrane, but this transport capacity was significantly reduced in Δtbdt-11 and wild-type US6-1 treated with PMF uncoupler, further confirming that the tbdt-11 gene was associated with PAH active transport.

Oxygen availability affects the synthesis of quorum sensing signal in the facultative anaerobe Novosphingobium pentaromativorans US6-1

Bacterial populations rely on quorum sensing (QS) to coordinate their behaviors and are often challenged by the fluctuation in oxygen concentrations in their habitats. Oxygen is a crucial factor that affects bacterial metabolism in multiple ways. However, little is known about whether and how oxygen availability affects QS activities. To fill this gap, we used the facultative anaerobe Novosphingobium pentaromativorans US6-1 as a model system, and observed that the QS signal acyl homoserine-lactones (AHLs) were produced only in anoxic environments, such as biofilm, or liquid medium that initially contained less than 2 mg/L dissolved oxygen, but not in highly oxic environments. Comparative transcriptome analysis revealed that oxygen availability significantly affected the physiological activities in US6-1, including fatty acid metabolism, oxidative phosphorylation, citrate cycle, QS activities, and flagellar assembly. The absence of AHLs in the oxic culture was not due to degradation, but to the very low expression of the AHL synthase gene novI. High concentration of NADH during the middle log phase under static cultivation may be a trigger for AHL synthesis. This is the first report that production of AHLs is coupled with anoxic metabolism in a facultative anaerobe, which extends our knowledge on factors affecting bacterial QS occurrence. KEY POINTS: • AHL production is anoxic cultivation related. • Oxygen availability affects AHL synthesis by influencing novI expression. • Oxygen availability changes many metabolism activities including NADH production.