A new bacterial mannosidase for the selective modification of ramoplanin and its derivatives

Ramoplanin is a lipoglycodepsipeptide produced by Actinoplanes sp. ATCC 33076 and active on bacterial cell wall biosynthesis by binding to Lipid II. A screening of an actinomycetes collection was performed to select enzymatic activities able to introduce specific modifications in the ramoplanin molecule. An extracellular mannosidase from Streptomyces GE 91081 was found to selectively remove one mannose unit from ramoplanin and tetrahydroramoplanin to give the corresponding mannosyl aglycones. These molecules show an improved microbiological activity versus some resistant staphylococci and streptococci, and are useful intermediates in the synthesis of novel ramoplanin-like antibiotics. The biotransformation of ramoplanin has been optimised to improve molar conversion and the transformation reaction rate.     

游动放线菌中orf20基因敲除对雷莫拉宁合成的影响

雷莫拉宁生物合成基因簇中orf20与已知的卤化酶基因高度同源.本研究在大肠杆菌中构建同框敲除质粒pSM-3,将其转入游动放线菌Actinoplanes sp.ATCC 33076,通过同源重组双交换的方法将orf20基因内部编码64个氨基酸的序列敲除,筛选得到双交换阻断突变株SIPI-A.2001 dorf20(Δor...     

Chemoenzymatic deacylation of ramoplanin

The chemoenzymatic deacylation of ramoplanin A2 is described for the first time: ramoplanin A2 was Boc-protected and hydrogenated to Boc-protected tetrahydroramoplanin, which was subsequently deacylated using an acylase from Actinoplanes utahensis NRRL 12052. The chemoenzymatic process proceeded with 80% overall yield, which favourably compares with the previously described chemical deacylation.     

The mechanism of action of ramoplanin and enduracidin

The lipoglycodepsipeptide antibiotic ramoplanin is proposed to inhibit bacterial cell wall biosynthesis by binding to intermediates along the pathway to mature peptidoglycan, which interferes with further enzymatic processing. Two sequential enzymatic steps can be blocked by ramoplanin, but there is no definitive information about whether one step is inhibited preferentially. Here we use inhibition kinetics and binding assays to assess whether ramoplanin and the related compound enduracidin have an intrinsic preference for one step over the other. Both ramoplanin and enduracidin preferentially inhibit the transglycosylation step of peptidoglycan biosynthesis compared with the MurG step. The basis for stronger inhibition is a greater affinity for the transglycosylase substrate Lipid II over the MurG substrate Lipid I. These results provide compelling evidence that ramoplanin's and enduracidin's primary cellular target is the transglycosylation step of peptidoglycan biosynthesis.     

In vitro activity of ramoplanin and comparator drugs against anaerobic intestinal bacteria from the perspective of potential utility in pathology involving bowel flora

Susceptibility of intestinal bacteria to various antimicrobial agents in vitro, together with levels of those agents achieved in the gut, provides information on the likely impact of the agents on the intestinal flora. Orally administered drugs that are poorly absorbed may be useful for treatment of intestinal infections and for certain other situations in which intestinal bacteria may play a role. The antimicrobial activity of ramoplanin (MDL 62,198) against 928 strains of intestinal anaerobic bacteria was determined using the NCCLS-approved Wadsworth brucella laked-blood agar dilution method. The activity of ramoplanin was compared with that of ampicillin, bacitracin, metronidazole, trimethoprim/sulfamethoxazole (TMP/SMX), and vancomycin. The organisms tested included Bacteroides fragilis group (n=89), other Bacteroides species (n=16), other anaerobic Gram-negative rods (n=56) anaerobic cocci (n=114), Clostridium species (n=426), and non-sporeforming anaerobic Gram-positive rods (n=227). The overall MIC(90)s of ramoplanin, ampicillin, bacitracin, metronidazole, and vancomycin were 256, 32, 128, 16, and 128 mcg/ml, respectively. Ramoplanin was almost always highly active vs. Gram-positive organisms and relatively poor in activity against Gram-negative organisms, particularly Bacteroides, Bilophila, Prevotella, and Veillonella. Vancomycin was quite similar to ramoplanin in its activity. Ampicillin was relatively poor in activity vs. organisms that often produce beta-lactamase, including most of the Gram-negative rods as well as Clostridium bolteae and C. clostridioforme. Bacitracin was relatively poor in activity against most anaerobic Gram-negative rods, but better vs. most Gram-positive organisms. Metronidazole was very active against all groups other than bifidobacteria and some strains of other types of non-sporeforming Gram-positive bacilli. TMP/SMX was very poorly active, with an MIC(90) of >2048 mcg/ml.     

Functional identification of the gene encoding the enzyme involved in mannosylation in ramoplanin biosynthesis in Actinoplanes sp.

Ramoplanin is a lipopeptide antibiotic active against multi-drug-resistant, Gram-positive pathogens. Structurally, it contains a di-mannose moiety attached to the peptide core at Hpg¹¹. The biosynthetic gene cluster of ramoplanin has already been reported and the assembly of the depsipeptide has been elucidated but the mechanism of transferring sugar moiety to the peptide core remains unclear. Sequence analysis of the biosynthetic gene cluster indicated ramo-orf29 was a mannosyltransferase candidate. To investigate the involvement of ramo-orf29 in ramoplanin biosynthesis, gene inactivation and complementation have been conducted in Actinoplanes sp. ATCC 33076 by homologous recombination. Metabolite analysis revealed that the ramo-orf29 inactivated mutant produced no ramoplanin but the ramoplanin aglycone. Thus, ramo-orf29 codes for the mannosyltransferase in the ramoplanin biosynthesis pathway. This lays the foundation for further exploitation of the ramoplanin mannosyltransferase and aglycone in combinatorial biosynthesis.     

Production of ramoplanin analogues by genetic engineering of Actinoplanes sp.

Ramoplanins are lipopeptides effective against a wide range of Gram-positive pathogens. Ramoplanin A2 is in Phase III clinical trials. The structure–activity relationship of the unique 2Z,4E-fatty acid side-chain of ramoplanins indicates a significant contribution to the antimicrobial activities but ramoplanin derivatives with longer 2Z,4E-fatty acid side-chains are not easy to obtain by semi-synthetic approaches. To construct a strain that produces such analogues, an acyl-CoA ligase gene in a ramoplanin-producing Actinoplanes was inactivated and a heterologous gene from an enduracidin producer (Streptomyces fungicidicus) was introduced into the mutant. The resulting strain produced three ramoplanin analogues with longer alkyl chains, in which X1 was purified. The MIC value of X1 was ~0.12 μg/ml against Entrococcus sp. and was also active against vancomycin-resistant Staphylococcus aureus (MIC = 2 μg/ml).     

Studies on the biosynthesis of the lipodepsipeptide antibiotic Ramoplanin A2

Ramoplanin, a non-ribosomally synthesized peptide antibiotic, is highly effective against several drug-resistant Gram-positive bacteria, including vancomycin-resistant Enterococcus faecium (VRE) and methicillin-resistant Staphylococcus aureus (MRSA), two important opportunistic human pathogens. Recently, the biosynthetic cluster from the ramoplanin producer Actinoplanes ATCC 33076 was sequenced, revealing an unusual architecture of fatty acid and non-ribosomal peptide synthetase biosynthetic genes (NRPSs). The first steps towards understanding how these biosynthetic enzymes cooperatively interact to produce the depsipeptide product are expression and isolation of each enzyme to probe its specificity and function. Here we describe the successful production of soluble enzymes from within the ramoplanin locus and the confirmation of their specific role in biosynthesis. These methods may be broadly applicable to the production of biosynthetic enzymes from other natural product biosynthetic gene clusters, especially those that have been refractory to production in heterologous hosts despite standard expression optimization methods.     

Chemistry and biology of the ramoplanin family of peptide antibiotics

The peptide antibiotic ramoplanin factor A2 is a promising clinical candidate for treatment of Gram-positive bacterial infections that are resistant to antibiotics such as glycopeptides, macrolides, and penicillins. Since its discovery in 1984, no clinical or laboratory-generated resistance to this antibiotic has been reported. The mechanism of action of ramoplanin involves sequestration of peptidoglycan biosynthesis Lipid intermediates, thus physically occluding these substrates from proper utilization by the late-stage peptidoglycan biosynthesis enzymes MurG and the transglycosylases (TGases). Ramoplanin is structurally related to two cell wall active lipodepsipeptide antibiotics, janiemycin, and enduracidin, and is functionally related to members of the lantibiotic class of antimicrobial peptides (mersacidin, actagardine, nisin, and epidermin) and glycopeptide antibiotics (vancomycin and teicoplanin). Peptidomimetic chemotherapeutics derived from the ramoplanin sequence may find future use as antibiotics against vancomycin-resistant Enterococcus faecium (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and related pathogens. Here we review the chemistry and biology of the ramoplanins including its discovery, structure elucidation, biosynthesis, antimicrobial activity, mechanism of action, and total synthesis.     

The Bacillus subtilis GntR family repressor YtrA responds to cell wall antibiotics

The transglycosylation step of cell wall synthesis is a prime antibiotic target because it is essential and specific to bacteria. Two antibiotics, ramoplanin and moenomycin, target this step by binding to the substrate lipid II and the transglycosylase enzyme, respectively. Here, we compare the ramoplanin and moenomycin stimulons in the Gram-positive model organism Bacillus subtilis. Ramoplanin strongly induces the LiaRS two-component regulatory system, while moenomycin almost exclusively induces genes that are part of the regulon of the extracytoplasmic function (ECF) σ factor σ(M). Ramoplanin additionally induces the ytrABCDEF and ywoBCD operons, which are not part of a previously characterized antibiotic-responsive regulon. Cluster analysis reveals that these two operons are selectively induced by a subset of cell wall antibiotics that inhibit lipid II function or recycling. Repression of both operons requires YtrA, which recognizes an inverted repeat in front of its own operon and in front of ywoB. These results suggest that YtrA is an additional regulator of cell envelope stress responses.     

Role of lipid-bound peptidoglycan precursors in the formation of pores by nisin, epidermin and other lantibiotics

It is generally assumed that type A lantibiotics primarily kill bacteria by permeabilization of the cytoplasmic membrane. As previous studies had demonstrated that nisin interacts with the membrane-bound peptidoglycan precursors lipid I and lipid II, we presumed that this interaction could play a role in the pore formation process of lantibiotics. Using a thin-layer chromatography system, we found that only nisin and epidermin, but not Pep5, can form a complex with [¹⁴C]-lipid II. Lipid II was then purified from Micrococcus luteus and incorporated into carboxyfluorescein-loaded liposomes made of phosphatidylcholine and cholesterol (1:1). Liposomes supplemented with 0.05 or 0.1 mol% of lipid II did not release any marker when treated with Pep5 or epilancin K7 (peptide concentrations of up to 5 mol% were tested). In contrast, as little as 0.01 mol% of epidermin and 0.1 mol% of nisin were sufficient to induce rapid marker release; phosphatidylglycerol-containing liposomes were even more susceptible. Controls with moenomycin-, undecaprenol- or dodecaprenolphosphate-doped liposomes demonstrated the specificity of the lantibiotics for lipid II. These results were correlated with intact cells in an in vivo model. M. luteus and Staphylococcus simulans were depleted of lipid II by preincubation with the lipopeptide ramoplanin and then tested for pore formation. When applied in concentrations below the minimal inhibitory concentration (MIC) and up to 5–10 times the MIC, the pore formation by nisin and epidermin was blocked; at higher concentrations of the lantibiotics the protective effect of ramoplanin disappeared. These results demonstrate that, in vitro and in vivo , lipid II serves as a docking molecule for nisin and epidermin, but not for Pep5 and epilancin K7, and thereby facilitates the formation of pores in the cytoplasmic membrane.     

Thylakoid polypeptide composition and light-independent phosphorylation of the chlorophyll a,b-protein in Prochloron, a prokaryote exhibiting oxygenic photosynthesis

Thylakoids of the prokaryote Prochloron, present as a symbiont in ascidians isolated from the Red Sea at Eilat (Israel), showed polypeptide electrophoretic patterns comparable to those of thylakoids from eukaryotic oxygen-evolving organisms. Low temperature, fluorescence spectroscopy of Prochloron, having a chlorophyll a/b ratio of 3.8–5, and frozen in situ, demonstrated the presence of Photosystem II chlorophyll-protein complex emitting at 686 and 696 nm, as well as the emission band of Photosystem I at 720 nm which was so far not observed in Prochloron species. The latter emission was absent, if the cells or thylakoids were isolated prior to freezing. Energy transfer from chlorophyll b to chlorophyll a could be demonstrated to occur in vivo. The chlorophyll a,b-protein complex of Photosystem II, isolated by non-denaturing polyacrylamide gel electrophoresis, contained one major polypeptide of 34 kDa. The polypeptide was phosphorylated in vitro by a membrane-bound protein kinase which was not stimulated by light. A light-independent protein kinase activity was also found in isolated thylakoids of another prokaryote, the cyanophyte Fremyella diplosiphon. State I–State II transition could not be demonstrated in Prochloron by measurements of modulated fluorescence intensity in situ. We suggest that the presence of a light-independent thylakoid protein kinase of Prochloron, collected in the Red Sea at not less than 30 m depth, might be the result of an evolutionary process whereby this organism has adapted to an environment in which light, absorbed preferentially by Photosystem II, prevails.     

巴尔通体在滇西南蝙蝠中高度流行并具有丰富的遗传变异特征

蝙蝠是很多病原微生物的自然宿主, 全球多项研究表明蝙蝠是巴尔通体(Bartonella species)的主要宿主。为了解滇西南地区蝙蝠中巴尔通体的流行特征, 我们于2015-2017年间在云南省4个地区应用网捕法捕获蝙蝠3种305只。经种类鉴定后采集肝脾组织, 提取核酸, 通过TaqMan实时荧光定量PCR方法检测巴尔通体的tmRNA基因ssrA, 并进行测序鉴定和系统发育分析。结果发现172只蝙蝠检出该基因, 总感染率为56.4%; 其中临沧、西双版纳、保山和瑞丽4个采样点的蝙蝠感染率分别为50.0% (22/44)、61.7% (29/47)、62.1% (18/29)和55.7% (103/185)。中菊头蝠(Rhinolophus affinis)、小菊头蝠(R. blythi)和棕果蝠(Rousettus leschenaultii)的感染率分别为50.0% (22/44)、62.1% (18/29)和56.9% (132/232), 差异没有统计学意义(χ² = 1.135, P = 0.567), 表明巴尔通体在云南当地的蝙蝠种群中高度流行。定量PCR扩增产物2次扩增后测序获得37个巴尔通体ssrA序列, 属于10个系统发育分支, 其中1个为伊丽莎白巴尔通体(B. elizabethae)、特利波契巴尔通体(B. tribocorum)和克拉斯诺夫巴尔通体(B. krasnovii)的近缘种。其余序列与已知巴尔通体距离较远, 与亚洲、欧洲和美洲等其他地域来源于蝙蝠的巴尔通体近缘。遗传多样性分析显示, ssrA基因的核苷酸多样性指数(π)为0.11381 ± 0.00928, 基因型多样性指数(Hd)为0.985 ± 0.010, 形成29个基因型(单倍型), 说明云南蝙蝠巴尔通体具有丰富的遗传多样性。通过对本研究标本与全球相关序列的系统发育网络重建, 分析全球蝙蝠巴尔通体的地理和宿主分布特征, 可以看出巴尔通体与蝙蝠之间存在显著的宿主特异性关联。因此可初步确定蝙蝠-巴尔通体具有协同进化特征, 同时受到地理隔离的影响。     

A fourth gene from the Candida albicans CDR family of ABC transporters

Using primers derived from a region of the Candida albicans CDR1 (Candida drug resistance) gene that is conserved in other ABC (ATP-binding cassette) transporters, a DNA fragment from a previously unknown CDR gene was obtained by polymerase chain reaction (PCR). After screening a C. albicans genomic library with this fragment as a probe, the complete CDR4 gene was isolated and sequenced. CDR4 codes for a putative ABC transporter of 1490 amino acids with a high degree of homology to Cdr1p, Cdr2p and Cdr3p from C. albicans (62, 59 and 57% amino acid sequence identity, respectively). Cdr4p has a predicted structure typical for cluster I.1 of yeast ABC transporters, characterized by two homologous halves, each comprising an N-terminal hydrophilic domain with consensus sequences for ATP binding and a C-terminal hydrophobic domain with six transmembrane helices. In contrast to the CDR1/CDR2 genes, the genetic structure of the CDR4 gene was conserved in 59 C. albicans isolates from six different patients. Northern hybridization analysis showed that the CDR4 gene was expressed in most isolates, but no correlation between CDR4 mRNA levels and the degree of fluconazole resistance of the isolates was found. In addition, a C. albicans mutant in which both copies of the CDR4 gene were disrupted by insertional mutagenesis was not hypersusceptible to fluconazole as compared to the parent strain. Unlike CDR1 and CDR2, CDR4 does not, therefore, seem to be involved in fluconazole resistance in C. albicans.     

Growth inhibition of the cereal root pathogens Rhizoctonia solani AG8, R. oryzae and Gaeumannomyces graminis var. tritici by a recombinant 42-kDa endochitinase from Trichoderma harzianum

The objective of this study was to determine the effectiveness of a 42-kDa endochitinase coded by the ThEn42 gene from Trichoderma harzianum as a potential source of transgenic resistance to Rhizoctonia root rot of barley caused by Rhizoctonia solani AG8 and/or R. oryzae. The gene cThEn42 was codon optimized (GC content increased from 53.3 to 65.1%) and then synthesized to produce the modified cThEn42GC in Pichia pastoris for in vitro tests. Two expression vectors were constructed: one with the fungal signal peptide and the fungal activation peptide [FSP-FAP-cThEn(GC)] and the other with barley chitinase 26 signal peptide followed by the fungal signal and activation peptides [SP(HVChi26)-FSP-FAP-cThEn(GC)]. N-terminal sequencing showed that, of two proteins secreted into liquid medium, FSP was cleaved off faithfully in one protein and both FSP and FAP were cleaved from the other protein. Purified endochitinase provided strong in vitro inhibition of both R. solani AG8 and R. oryzae. The enzyme had an intermediate inhibitory activity against Gaeumannomyces graminis var. tritici, and no inhibitory activity against Fusarium graminearum, F. pseudograminearum, and F. culmorum.     

Fed-batch production of (S)-flurbiprofen in lipase-catalyzed dispersed aqueous phase reaction system induced by succinyl β-cyclodextrin and its extractive purification

Optically active (S)-flurbiprofen was produced fed-batch-wisely in a lipase-catalyzed dispersed aqueous phase reaction system induced by succinyl β-cyclodextrin (suβ-CD). A highly concentrated 480 mM (S)-flurbiprofen, corresponding to 117.0 g/l, with an enantiomeric excess of 0.98 and conversion yield of 0.48 was obtained. (S)-Flurbiprofen produced in an inclusion complex form with suβ-CD was extractively purified using three-step procedures: decomplexation of (S)-flurbiprofen and residual (R)-flurbiprofen ethyl ester ((R)-FEE) using the ethyl acetate, dissolution of (S)-flurbiprofen from (R)-FEE using a sodium bicarbonate solution, and selective precipitation of (S)-flurbiprofen using 2-propanol. Consequently, an extremely high concentration of 420 mM (S)-flurbiprofen with an optical purity higher than 98% was recovered after purification.     

Cloning and characterization of femA and femB from Staphylococcus epidermidis

A DNA fragment was identified and cloned from Staphylococcus epidermidis (Se) using femA from S. aureus (Sa) as a heterologous hybridization probe. DNA sequence analysis of a portion of this clone revealed two complete ORFs highly related to femA and femB of Sa. The genomic arrangement of the Se femA/B complex was nearly identical to that observed in Sa. Intra- and interspecies relatedness of these genes and conservation of genomic organization were consistent with gene duplication of one of these genes in an ancestral organism. Recombinant FEMA, produced in Escherichia coli (Ec), was purified to near homogeneity. Identity of the purified protein was verified by N-terminal amino acid (aa) sequence analysis.     

Measuring seasonal dynamics of leaf area index in a mixed conifer-broadleaved forest with direct and indirect methods

利用光学仪器法能够快速、高效地测定森林生态系统的叶面积指数(leaf area index, LAI)。然而, 评估该方法测定针阔混交林LAI季节动态准确性的研究较少。该研究基于凋落物法测定了小兴安岭地区阔叶红松(Pinus koraiensis)林LAI的季节动态, 其结果可代表真实的LAI。参考真实的LAI, 对半球摄影法(digital hemispherical photography, DHP)和LAI-2000植物冠层分析仪测定的有效叶面积指数(effective LAI, L_e)进行了评估。首先对DHP测定LAI过程中采用的不合理曝光模式(自动曝光)进行了系统校正。同时, 测定了光学仪器法估测LAI的主要影响因素(包括木质比例(woody-to-total area ratio, α)、集聚指数(clumping index, Ω_E)和针簇比(needle-to-shoot area ratio, γ_E))的季节变化。结果表明: 3种不同方法测定的LAI均表现为单峰型的季节变化, 8月初达到峰值。从5月至11月, DHP测定的L_e比真实的LAI低估50%-59%, 平均低估55%; 而LAI-2000植物冠层分析仪测定的L_e比真实的LAI低估19%-35%, 平均低估27%。DHP测定的L_e 经过自动曝光, α、Ω_E和γ_E校正后, 精度明显提高, 但仍比真实的LAI低估6%-15%, 平均低估9%; 相对而言, LAI-2000植物冠层分析仪测定的L_e经过α、Ω_E和γ_E校正后, 精度明显提高, 各时期与真实的LAI的差异均小于9%。研究结果表明, 考虑木质部和集聚效应对光学仪器法的影响后, DHP和LAI-2000植物冠层分析仪均能相对准确地测定针阔混交林LAI的季节动态, 其中, DHP的测定精度高于85%, 而LAI-2000植物冠层分析仪的测定精度高于91%。     

Daily Rhythms of Body Temperature in Acornys russatus: The Response to Chemical Signals Released by Acomys cahirinus

Two species of spiny mice of the genus Acomys—the golden spiny A. russaturs and the common spiny A. cuhirinus—are syrnpatnc in the and and hot parts of the Rift Valley in Israel. The coexistence of these two species is due to exclusion of A. russatus mice by A. cuhirinus mice from nocturnal activity. The aim of this research was to study if odor signals released by A. cahirinus mice can play a role in the exclusion of A. russatus mice. A. russatus mice with an implanted transmitter recording body temperature (T_b) were kept alone in a metabolic chamber under constant conditions of ambient temperature (27°C) and photoperiod (12 h light: 12 h dark). After 5 days of recording, chemical signals from an A. cuhirinus mouse were added through the air tube going into the metabolic chamber of the A. russatus mice. This treatment caused a shift of ∼ 2 h inT_b daily rhythm of the naive tested A. russutus mice, whereas no shift was observed in A. russatus mice that had been kept in the same room with the A. cahirinus mouse before measurements. These results strongly support the idea that chemical signals released by A. cahirinus mice can entrain the T_b rhythms of A. russatus mice. Therefore, it may be assumed that the exclusion of A. russatus mice from nocturnal activity by A. cuhirinus mice could be achieved through the odor released by the latter.