Rpf蛋白：一种激活休眠状态放线菌的复苏促进因子

放线菌能产生多样性丰富的小分子化合物，但大多数放线菌因为处于“活的尚未培养”状态而无法分离培养。造成“活的尚未培养”状态的原因之一可能是由于一些环境因素，例如有机物、重金属、抗生素等胁迫使细胞处于休眠保护状态，直到遇到适宜的条件才能继续复苏生长。复苏促进因子（Resuscitation-Promoting Factor，Rpf）是由某些放线菌分泌的一类蛋白质，首次在藤黄微球菌（Micrococcus luteus）中发现，之后人们对Rpf蛋白的功能和分布给予了更多的关注。Rpf蛋白能促进一些休眠的革兰氏阳性细菌复苏，这为“活的尚未培养”放线菌的分离培养提供了可能性。同时，针对一些致病放线菌物种，开发Rpf蛋白抑制物为相关疾病的治疗也提供了一条新的途径。基于此，本文对Rpf蛋白的结构组成、特征功能、作用机制及应用前景进行了简要的概述。     

细菌复苏促进因子--Rpf

细菌复苏促进因子Rpf是第一个被发现的原核生物自分泌生长因子,该因子在放线菌门细菌中广泛存在,具有促进细菌休眠体复苏的作用.Rpf在细菌生长代谢过程中所发挥的重要调节作用,使其具有潜在的应用价值.     

藤黄微球菌Rpf活性蛋白的制取及其对红球菌VBNC菌体的复苏作用

【目的】克隆藤黄微球菌Micrococcus luteus IAM 14879(=NCIMB 13267)的复苏促进因子Rpf(resuscitation promoting factor)的基因,在大肠杆菌中表达获取基因重组蛋白,考察对近缘高GC革兰氏阳性菌红球菌Rhodococcus sp.DS471活的非可培养VBNC(viable but non-culturable)菌体的复苏促进生长能力。【方法】抽提制备藤黄微球菌的DNA,确定rpf基因引物进行PCR扩增,利用pET15b质粒载体并转化大肠杆菌DE3表达,以SDS-PAGE检验获取纯化重组蛋白;在培养基中添加Rpf,以MPN(most probable number)法计数、评价对VBNC状态菌体的复苏促进生长效果。【结果】基因测序证实获得藤黄微球菌的rpf基因并在大肠杆菌中表达;SDS-PAGE分析表明获得rpf基因的重组蛋白;该蛋白对处于VBNC状态的红球菌具有近100倍的复苏促进生长能力。【结论】成功克隆了藤黄微球菌的rpf基因,在大肠杆菌中获得了表达,表明了Rpf蛋白对处于VBNC状态的红球菌具有复苏促进生长效果。     

微生物VBNC状态形成及复苏机制

99%以上的微生物因处于活的但非可培养(viable but non-culturable,VBNC)状态而无法分离培养。复苏促进因子(resuscitation-promoting factors,Rpfs)是培养获取VBNC菌的最重要突破。结合课题组近十余年从环境功能视角利用Rpf复苏培养VBNC菌的研究,本文在阐述微生物VBNC状态的形成及复苏进展的基础上,从VBNC菌形成及复苏过程出发,探究"探索因子"与群体感应的内在关系。并总结了课题组利用Rpf所复苏培养的具有潜在环境功能的VBNC菌种。本论文将为揭示微生物VBNC状态的形成及复苏机制提供新的思路,并为认识和重新评价Rpf法复苏培养VBNC菌在污染环境微生物修复中的作用提供理论依据。     

结核分枝杆菌RPF样蛋白家族及其功能

上世纪末,Mukamolova等从藤黄微球菌（Micrococcus luteus）发现一种分泌蛋白-复苏促进因子（Rpf）.该因子在皮摩尔浓度下能促进休眠期的藤黄微球菌及其他数种高G＋C含量的革兰氏阳性菌复苏和生长.结核分枝杆菌全基因组发现和该因子同源性较高的5个基因,预测产物都是分泌蛋白,一级结构都含有一个转糖基域.5个基因有一个共同的功能未知的域,3级结构预测该保守结构域和溶菌酶同源.重组表达的Rpf对不同种均有活性.5个rpf在不同生长时期均有表达,但调控有差异.     

PIASx结构与功能的研究进展

PIAS（protein inhibitor of activated STAT）蛋白家族能够与许多蛋白质发生相互作用,其中大部分为转录因子。PIASx是4个组成成员中的一种,其包括两个亚型。PIASx通过与不同种类的蛋白相互作用,影响它们的活性和功能。PIASx蛋白的调控机制主要有两种：一种是通过其自身所具有的SUMO（smallubiquitin-related modifiers）E3连接酶活性,促进对一些转录因子、转录辅因子的SUMO化修饰,从而调控它们的转录活性;另一种是作为构架蛋白,通过与雄激素受体的作用参与雄激素介导的基因转录调节。PIAS蛋白的上述两种作用机制并不是完全互相排斥的,这体现了PIASx蛋白功能的特异性和复杂性。     

植物复苏性状的分子机理研究进展

复苏性状是某些生物应对水分剧烈变化恶劣环境的一种特殊适应能力,在植物界广泛分布于苔藓和蕨类低等植物,一些高等植物也具有这种性状。复苏植物可以在损失体内95％以上的水分后,遇水而复苏,以此度过环境恶劣的时段。复苏性状的分子机制一直让人们着迷,但对其认知还十分有限。近年来的研究表明,一些小分子代谢物和特殊蛋白的大量积累在复苏植物脱水过程中对生物膜和大分子结构起保护作用;复苏性状中的信号转导与基因调控可能包括ABA在内的一系列信号分子和途径。随着“组学”技术的发展,更宽广角度的研究将会极大的促进人们对复苏性状的认知。对于复苏性状的深入研究,可能为农作物和蔬菜的改良提供一个全新的方向,具有很大的潜在应用价值。     

炎症因子相关基因在创伤失血性休克中的研究进展

近年来研究认为在创伤失血性休克的发生发展及液体复苏、缺血再关注过程中均伴随着炎症因子的变化,现将与炎症因子密切相关基因环氧化酶-2(COX-2)、核因子κB(NF-κB)、诱导型一氧化氮合酶(iNOS)、高迁移率族蛋白1(HMGB1)、低氧诱导因子1α(HIF1α)、血红素氧合酶-1(HO-1)、寒冷诱导的RNA结合蛋白(CIRBP)在创伤失血性休克中的作用机制方面的研究及进展作一综述,为创伤失血性休克临床救治提供思路。     

Smac与肿瘤的放化疗增敏

Smac(second mitochondria-derived activator of Caspase)是一种内源性促进细胞凋亡的蛋白,主要通过拮抗凋亡抑制因子(inhibitor of apoptosis proteins,IAPs)对Caspase的抑制,以及促进Caspase的催化活性从而促进凋亡,并可通过与IAPs的作用参与NF-кB的调控。IAPs在肿瘤的发生、迁移以及耐药、辐射抗性的形成中发挥重要的作用。肿瘤细胞中IAPs的高表达与其抵抗凋亡的作用相关。因此,探究Smac对IAPs的拮抗作用和对Caspase的激活机制,能够进一步阐明肿瘤细胞抗凋亡机制和其他死亡途径的逃逸机制。阐述了Smac蛋白的结构、与IAPs的相互作用以及Smac模拟物作为肿瘤放化疗增敏剂的研究。     

Id-1在恶性肿瘤发生中的作用及其机制

分化抑制因子-1(inhibitor of differentiation protein 1,Id-1)是Id转录调节蛋白家族成员之一,属于螺旋-环-螺旋蛋白超家族成员。早期对Id-1的研究认为其主要作用是负向调节正常细胞的分化。近年来研究表明,Id-1在多种肿瘤中过表达并通过多条信号通路促进肿瘤的发生,现就Id-1在肿瘤发生中的作用及其作用机制作一综述。     

Evaluation of Rpf protein of Micrococcus luteus for cultivation of soil actinobacteria

Rpf protein, a kind of resuscitation promoting factor, was first found in the culture supernatant of Micrococcus luteus. It can resuscitate the growth of M. luteus in “viable but non-culture, VBNC” state and promote the growth of Gram-positive bacteria with high G + C content. This paper investigates the resuscitating activity of M. luteus ACCC 41016^T Rpf protein, which was heterologously expressed in E. coli, to cells of M. luteus ACCC 41016^T and Rhodococcus marinonascens HBUM200062 in VBNC state, and examines the effect on the cultivation of actinobacteria in soil. The results showed that the recombinant Rpf protein had resuscitation effect on M. luteus ACCC 41016^T and R. marinonascens HBUM200062 in VBNC state. 83 strains of actinobacteria, which were distributed in 9 families and 12 genera, were isolated from the experimental group with recombinant Rpf protein in the culture medium. A total of 41 strains of bacteria, which were distributed in 8 families and 9 genera, were isolated from the control group without Rpf protein. The experimental group showed richer species diversity than the control group. Two rare actinobacteria, namely HBUM206391^T and HBUM206404^T, were obtained in the experimental group supplemented with Rpf protein. Both may be potential new species of Actinomadura and Actinokineospora, indicating that the recombinant expression of M. luteus ACCC 41016^T Rpf protein can effectively promote the isolation and culture of actinobacteria in soil.     

Proteins of the Rpf (resuscitation promoting factor) family are peptidoglycan hydrolases

The secreted Micrococcus luteus protein, Rpf, is required for successful resuscitation of dormant "non-culturable" M. luteus cells and for growth stimulation in poor media. The biochemical mechanism of Rpf action remained unknown. Theoretical predictions of Rpf domain architecture and organization, together with a recent NMR analysis of the protein structure, indicate that the conserved Rpf domain has a lysozyme-like fold. In the present study, we found that both the secreted native protein and the recombinant protein lyse crude preparations of M. luteus cell walls. They also hydrolyze 4-methylumbelliferyl-beta-D-N,N',N'-triacetylchitotrioside, a synthetic substrate for peptidoglycan muramidases, with optimum activity at pH 6. The Rpf protein also has weak proteolytic activity against N-CBZ-Gly-Gly-Arg-beta-naphthylamide, a substrate for trypsin-like enzymes. Rpf activity towards 4-methylumbelliferyl-beta-D-N,N',N'-triacetylchitotrioside was reduced when the glutamate residue at position 54, invariant for all Rpf family proteins and presumably involved in catalysis, was altered. The same amino acid substitution resulted in impaired resuscitation activity of Rpf. The data indicate that Rpf is a peptidoglycan-hydrolyzing enzyme, and strongly suggest that this specific activity is responsible for its growth promotion and resuscitation activity. A possible mechanism of Rpf-mediated resuscitation is discussed.     

Resuscitation Promoting Factors: a Family of Microbial Proteins in Survival and Resuscitation of Dormant Mycobacteria

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is an extraordinarily successful pathogen of humankind. It has been estimated that up to one-third of the world’s population is infected with M. tuberculosis, and this population is an important reservoir for disease reactivation. Resuscitation promoting factor (Rpf) is a secretory protein, which was first reported in Micrococcus luteus. There are five functionally redundant Rpf-like proteins found in M. tuberculosis. Rpf promotes the resuscitation of dormant bacilli to yield normal, viable colony forming bacteria. All Rpfs share a conserved domain of about 70 amino acids and possess a lysozyme-like activity. The structural studies of the conserved domain suggest that Rpfs could be considered as a c-type lysozyme and lytic transglycosylases. Recently a novel class of nitrophenylthiocyanates (NPT) inhibitors of the muralytic activity of Rpf were reported which opens a new approach in the study of cell-wall hydrolyzing enzymes. This review describes molecular and structural studies conducted on Rpf proteins, their role in the resuscitation of dormant bacteria, in the reactivation of latent infection and identification of low molecular weight inhibitors of resuscitation promoting factors.     

The rpf gene of Micrococcus luteus encodes an essential secreted growth factor

Micrococcus luteus secretes a small protein called Rpf, which has autocrine and paracrine signalling functions and is required for the resuscitation of dormant cells. Originally isolated from the supernatant of actively growing cultures, Rpf was also detected on the surface of actively growing bacteria. Most molecules may be sequestered non-productively at the cell surface, as a truncated form of the protein, encompassing only the 'Rpf domain' is fully active. The C-terminal LysM module, which probably mediates binding to the cell envelope, is not required for biological activity. Rpf was essential for growth of M. luteus. Washed cells, inoculated at low density into a minimal medium, could not grow in its absence. Moreover, the incorporation of anti-Rpf antibodies into the culture medium at the time of inoculation also prevented bacterial growth. We were unable to inactivate rpf using a disrupted form of the gene, in which most of the coding sequence was replaced with a selectable thiostrepton resistance marker. Gene disruption was possible in the presence of a second, functional, plasmid-located copy of rpf, but not in the presence of a rpf derivative whose protein product lacked the secretory signal sequence. As far as we are aware, Rpf is the first example of a truly secreted protein that is essential for bacterial growth. If the Rpf-like proteins elaborated by Mycobacterium tuberculosis and other mycobacteria prove similarly essential, interference with their proper functioning may offer novel opportunities for protecting against, and treating, tuberculosis and other mycobacterial disease.     

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.     

The glycosylated cell surface protein Rpf2, containing a resuscitation-promoting factor motif,is involved in intercellular communication of <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis>

The genome of Corynebacterium glutamicum ATCC 13032 contains two genes, rpf1 and rpf2, encoding proteins with similarities to the essential resuscitation-promoting factor (Rpf) of Micrococcus luteus. Both the Rpf1 (20.4 kDa) and Rpf2 (40.3 kDa) proteins share the so-called Rpf motif, a highly conserved protein domain of approximately 70 amino acids, which is also present in Rpf-like proteins of other gram-positive bacteria with a high G+C content of the chromosomal DNA. Purification of the C. glutamicum Rpf2 protein from concentrated supernatants, SDS-PAGE and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identified modified Rpf2 variants with increased or reduced mobility when compared with the calculated size of Rpf2. A Western blot-based enzyme immunoassay demonstrated glycosylation of the Rpf2 variants with higher molecular masses. Galactose and mannose were identified as two components of the oligosaccharide portion of the Rpf2 glycoprotein by capillary gas chromatography coupled to mass spectrometry. The Rpf2 protein was localized on the surface of C. glutamicum with the use of immuno-fluorescence microscopy. C. glutamicum strains with defined deletions in the rpf1 or rpf2 gene or simultaneous deletions in both rpf genes were constructed, indicating that the rpf genes are neither individually nor collectively essential for C. glutamicum. The C. glutamicum rpf double mutant displayed slower growth and a prolonged lag phase after transfer of long-stored cells into fresh medium. The addition of supernatant from exponentially growing cultures of the rpf double mutant, the wild type or C. glutamicum strains with increased expression of the rpf1 or rpf2 gene significantly reduced the lag phase of long-stored wild-type and rpf single mutant strains, but addition of purified His-tagged Rpf1 or Rpf2 did not. In contrast, the lag phase of the C. glutamicum rpf double mutant was not affected upon addition of these culture supernatants.     

Structural Changes and Cellular Localization of Resuscitation-Promoting Factor in Environmental Isolates of Micrococcus luteus

Dormancy among nonsporulating actinobacteria is now a widely accepted phenomenon. In Micrococcus luteus, the resuscitation of dormant cells is caused by a small secreted protein (resuscitation-promoting factor, or Rpf) that is found in “spent culture medium.” Rpf is encoded by a single essential gene in M. luteus. Homologs of Rpf are widespread among the high G + C Gram-positive bacteria, including mycobacteria and streptomycetes, and most organisms make several functionally redundant proteins. M. luteus Rpf comprises a lysozyme-like domain that is necessary and sufficient for activity connected through a short linker region to a LysM motif, which is present in a number of cell-wall-associated enzymes. Muralytic activity is responsible for resuscitation. In this report, we characterized a number of environmental isolates of M. luteus, including several recovered from amber. There was substantial variation in the predicted rpf gene product. While the lysozyme-like and LysM domains showed little variation, the linker region was elongated from ten amino acid residues in the laboratory strains to as many as 120 residues in one isolate. The genes encoding these Rpf proteins have been characterized, and a possible role for the Rpf linker in environmental adaptation is proposed. The environmental isolates show enhanced resistance to lysozyme as compared with the laboratory strains and this correlates with increased peptidoglycan acetylation. In strains that make a protein with an elongated linker, Rpf was bound to the cell wall, rather than being released to the growth medium, as occurs in reference strains. This rpf gene was introduced into a lysozyme-sensitive reference strain. Both rpf genes were expressed in transformants which showed a slight but statistically significant increase in lysozyme resistance.     

A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis

Many cases of active tuberculosis are thought to result from the reactivation of dormant Mycobacterium tuberculosis from a prior infection, yet remarkably little is known about the mechanism by which these non-sporulating bacteria reactivate. A family of extracellular bacterial proteins, known as resuscitation-promoting factors (Rpfs), has previously been shown to stimulate growth of dormant mycobacteria. While Rpf proteins are clearly peptidoglycan glycosidases, the mechanism and role of Rpf in mediating reactivation remains unclear. Here we use a yeast two-hybrid screen to identify potential binding partners of RpfB and report the interaction between RpfB and a putative mycobacterial endopeptidase, which we named Rpf-interacting protein A (RipA). This interaction was confirmed by in vitro and in vivo co-precipitation assays. The interacting domains map to the C-termini of both proteins, near predicted enzymatic domains. We show that RipA is a secreted, cell-associated protein, found in the same cellular compartment as RpfB. Both RipA and RpfB localize to the septa of actively growing bacteria by fluorescence microscopy. Finally, we demonstrate that RipA is capable of digesting cell wall material and is indeed a peptidoglycan hydrolase. The interaction between these two peptidoglycan hydrolases at the septum suggests a role for the complex in cell division, possibly during reactivation.