Enzyme characterization and biological activities of a resuscitation promoting factor from an oil degrading bacterium Rhodococcus erythropolis KB1

Resuscitation Promotion Factor: A Pronounced Bacterial Cytokine in Propelling Bacterial Resuscitation

While confronted with unfavorable growth conditions, bacteria may transform into the dormant state, such as viable but nonculturable (VBNC) state, which is a reversible state characterized by low metabolic activity and lack of division. These dormant cells can be reactivated through the influence of the resuscitation promoting factor (Rpf) family, which are classified as autocrine growth factors and possess peptidoglycan hydrolase activities. To date, with the significant resuscitation or growth promotion ability of Rpf, it has been extensively applied to increasing bacterial diversity and isolating functional microbial species. This review provides a comprehensive analysis of the distribution, mode of action, and functional mechanisms of Rpf proteins in various bacterial species. The aim is to create opportunities for decoding microbial communities and extracting microbial resources from real samples across different research fields.

Unveiling the distribution characteristics of rpf-like genes and indigenous resuscitation promoting factor production in PCB-contaminated soils

Resuscitation promoting factors (Rpfs), known for their anti-dormancy cytokine properties, have been extensively investigated in the medical field. Although the Rpf from Micrococcus luteus has been successfully utilized to resuscitate and stimulate microbial populations for the degradation of polychlorinated biphenyls (PCBs), the presence of indigenous Rpf homologs in PCB-contaminated soils has not been established. In this study, the distribution characteristics of rpf-like genes and indigenous strain capable of producing Rpf in PCB-contaminated soils were explored. The results revealed the widespread presence of Rpf-like domains and their associated genes, particularly in close association with heavy metals and PCBs. The rpf-like genes were predominantly found in Proteobacteria and displayed a positive correlation with genes involved in PCB degradation and viable but non-culturable (VBNC) formation. Notably, the recombinant Rpf-Ac protein derived from the indigenous strain Achromobacter sp. HR2 exhibited muralytic activity and demonstrated significant efficacy in resuscitating the growth of VBNC cells, while also stimulating the growth of normal cells. These findings shed light on the prevalent presence of Rpf homologs in PCB-contaminated soils and their potential to resuscitate functional populations in the VBNC state, thereby enhancing in situ bioremediation.

Enhanced rhizoremediation of polychlorinated biphenyls by resuscitation-promoting factor stimulation linked to plant growth promotion and response of functional microbial populations

Rhizoremediation is acknowledged as a green technology for removing polychlorinated biphenyls (PCBs) in soil. However, rhizoremediation is limited because most soil microorganisms enter into a viable but non-culturable (VBNC) state under PCBs stress. This work was to study the effect of resuscitation-promoting factor (Rpf) on rhizoremediation efficiency of PCBs in alfalfa and rhizosphere microbiological communities. Results suggested that Rpf promoted alfalfa growth in PCB-contaminated soil by improving antioxidant enzymes and detoxification metabolites in alfalfa. After 40 d Rpf treatment, removal rate for five selected PCBs significantly increased by 0.5-2.2 times. Rpf enhanced relative abundances of bphA and bphC responsible for degrading PCBs, and enzymatic activities of metabolizing exogenous compounds in rhizosphere soil. High-throughput sequencing showed that Rpf did not change the dominant microbial population at phyla and genera levels, but caused variation of the bacterial community structures. The promoting function of Rpf was linked to the shift of various key populations having different functions depending on Rpf concentrations. Pseudomonas and Rhizobium spp. enrichment might stimulate PCB degradation and Streptomyces and Bacillus spp. primarily contributed to alfalfa growth. Predicted functions in rhizosphere soil bacterial community indicated Rpf facilitated soil nutrient cycling and environmental adaptation. This study indicated that Rpf was an active additive for strengthening rhizoremediation efficiency of PCB-contaminated soil and enhancing their in-situ remediation.

Single-cell-level microfluidics assisted with resuscitation-promoting factor technology (SMART) to isolate novel biphenyl-degrading bacteria from typical soils in eastern China

Soil microorganisms represent one of the largest biodiversity reservoirs. However, most low-abundance, slow-growing or dormant microorganisms in soils are difficult to capture with traditional enrichment culture methods. These types of microorganisms represent a valuable "microbial seed bank". To better exploit and utilize this "microbial dark matter", we developed a novel strategy that integrates single-cell-level isolation with microfluidics technology and culture with resuscitation-promoting factor (Rpf) to isolate biphenyl-degrading bacteria from four typical soils (paddy soil, red soil, alluvial soil and black soil) in eastern China. Multitudinous bacteria were successfully isolated and cultured; some of the identified clades have not been previously linked to biphenyl biodegradation, such as Actinotalea, Curtobacterium and Rothia. Soil microcosmic experiments validated that some bacteria are responsible for biphenyl degradation in soil. In addition, genomic sequencing and Illumina MiSeq sequencing of 16S rRNA genes indicated that exogenous Rpf mainly promotes the recovery and growth of bacteria containing endogenous Rpf-encoding genes. In summary, this study provides a novel strategy for capturing target functional microorganisms in soils, indicates potential bioresources for the bioremediation of contaminated soils, and enhances our current understanding of the mechanisms involved in the response to exogenous Rpf.

Enzymatic properties and biological activity of resuscitation-promoting factor B of Rhodococcus sp. (GX12401)

Resuscitation-promoting factor B (RpfB) is one of the five members of Rpf-like family in Mycobacteriales, which have the resuscitation-promoting activity. Most strains of Rhodococcus also have RpfB gene, but the study of rpfB gene in Rhodococcus is not thorough. Here, we amplified the rpfB gene of intact Rhodococcus sp. (GX12401) and cloned it into pET30a (+) expression vector. Then a recombinant form of soluble RpfB was expressed in Escherichia coli BL21. The soluble recombinant RpfB was purified by Ni–Sepharose affinity chromatography and molecular weight of the protein was 55 kDa, determined by 12% SDS–PAGE stained with Coomassie brilliant blue R-250. When 4-methylumbelliferyl-β-D-N,N′,N″-triacetylchitoside was used as enzyme substrate to test lysozyme activity, the recombinant protein RpfB had good stability and enzyme activity, and the lysozyme activity was low (4.74 U), among which Mg²⁺, Na⁺, Al³⁺ and DMSO could significantly increase the activity of RpfB. The purified recombinant protein was added to Rhodococcus VBNC cells, and the VBNC cells were resuscitated at the concentration of 1 picomolar concentrations, which increased by 18% compared with the control, while the cell resuscitation was inhibited at the concentration of 1,000 picomolar concentrations. Therefore, RpfB can improve the survival ability of Rhodococcus in extreme or harsh environment and enhance the corresponding biological activity.

Promoting effect of the recombinant resuscitation promoting factors-2 of Rhodococcus erythropolis on petroleum degradation and cultivable bacterial diversities of the oil-contaminated soils

Resuscitation-promoting factors (Rpfs) belong to peptidoglycan hydrolases, which participate in recovery of dormant cells and promoting bacteria growth. In this study, the resuscitation promoting factor rpf2 gene of Rhodococcus erythropolis KB1 was expressed in Escherichia coli and purified by Ni²⁺ affinity chromatography. The purified recombinant fusion protein Rpf2 showed a closely 50 kDa band on sodium dodecyl sulphate polyacrylamide gel electrophoresis. The protein showed muralytic activity, with a specific activity of 1503 ± 123 U mg^-1 when determined with 4-methylumbelliferyl-β-d-N, N',N″-triacetotri-ylchitoside as substrate. It also showed protease activity when measured with azocasein as substrate, with a specific activity of 1528 ± 411 U mg^-1 . The addition of the recombinant Rpf2 protein significantly increased petroleum degradation efficiency of the indigenous micro-organisms and the petroleum degradation rates increased from 30·86 to 43·45%, 45·20 and 49·23% in the treatment groups. The recombinant protein also increased the petroleum-degrading bacterial diversities enriched from the contaminated soils. The cultivable bacterial flora of the treatment groups supplemented with different concentrations of Rpf2 increased from 82 genera in 9 phyla to 116 genera in 16 phyla and 138 genera in 16 phyla respectively. Thirteen extra petroleum-degrading bacteria strains were isolated from the petroleum-contaminated soils in the groups containing the recombinant Rpf2.

Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms

Culturing has been the cornerstone of microbiology since Robert Koch first successfully cultured bacteria in the late nineteenth century. However, even today, the majority of microorganisms in the marine environment remain uncultivated. There are various explanations for the inability to culture bacteria in the laboratory, including lack of essential nutrients, osmotic support or incubation conditions, low growth rate, development of micro-colonies, and the presence of senescent or viable but nonculturable (VBNC) cells. In the marine environment, many bacteria have been associated with dormancy, as typified by the VBNC state. VBNC refers to a state where bacteria are metabolically active, but are no longer culturable on routine growth media. It is apparently a unique survival strategy that has been adopted by many microorganisms in response to harsh environmental conditions and the bacterial cells in the VBNC state may regain culturability under favorable conditions. The resuscitation of VBNC cells may well be an important way to cultivate the otherwise uncultured microorganisms in marine environments. Many resuscitation stimuli that promote the restoration of culturability have so far been identified; these include sodium pyruvate, quorum sensing autoinducers, resuscitation-promoting factors Rpfs and YeaZ, and catalase. In this review, we focus on the issues associated with bacterial culturability, the diversity of bacteria entering the VBNC state, mechanisms of induction into the VBNC state, resuscitation factors of VBNC cells and implications of VBNC resuscitation stimuli for cultivating these otherwise uncultured microorganisms. Bringing important microorganisms into culture is still important in the era of high-throughput sequencing as their ecological functions in the marine environment can often only be known through isolation and cultivation.