Radical SAM‐Dependent Adenosylation Involved in Bacteriohopanepolyol Biosynthesis †

From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees

For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.

Changing Fates of the Substrate Radicals Generated in the Active Sites of the B12-Dependent Radical SAM Enzymes OxsB and AlsB

OxsB is a B₁₂-dependent radical SAM enzyme that catalyzes the oxidative ring contraction of 2'-deoxyadenosine 5'-phosphate to the dehydrogenated, oxetane containing precursor of oxetanocin A phosphate. AlsB is a homologue of OxsB that participates in a similar reaction during the biosynthesis of albucidin. Herein, OxsB and AlsB are shown to also catalyze radical mediated, stereoselective C2'-methylation of 2'-deoxyadenosine monophosphate. This reaction proceeds with inversion of configuration such that the resulting product also possesses a C2' hydrogen atom available for abstraction. However, in contrast to methylation, subsequent rounds of catalysis result in C-C dehydrogenation of the newly added methyl group to yield a 2'-methylidene followed by radical addition of a 5'-deoxyadenosyl moiety to produce a heterodimer. These observations expand the scope of reactions catalyzed by B₁₂-dependent radical SAM enzymes and emphasize the susceptibility of radical intermediates to bifurcation along different reaction pathways even within the highly organized active site of an enzyme.

Highly sensitive determination of three kinds of amanitins in urine and plasma by ultra performance liquid chromatography-triple quadrupole mass spectrometry coupled with immunoaffinity column clean-up

建立了超高效液相色谱-三重四极杆质谱高灵敏测定尿液和血浆中α-鹅膏毒肽、β-鹅膏毒肽和γ-鹅膏毒肽的方法。经过免疫亲和柱净化,尿液样品浓缩20倍、血浆样品浓缩10倍,以Kinetex Biphenyl色谱柱(100 mm×2.1 mm, 1.7 μm)作为分析柱,甲醇-0.005%(v/v)甲酸水溶液作为流动相进行梯度洗脱分离,电喷雾电离、负离子、多反应监测模式下检测,外标法定量。3种鹅膏毒肽的线性范围为0.1~200 ng/mL,相关系数(r)>0.999。尿液和血浆中3种鹅膏毒肽的基质效应和提取回收率分别为92%~108%和90%~103%,变异系数均小于13%。尿液中3种鹅膏毒肽的准确度为-9.4%~8.0%,重复性和中间精度分别为3.0%~14%和3.5%~18%,当取样量为2.00 mL时,方法的检出限均为0.002 ng/mL;血浆中3种鹅膏毒肽的准确度为-13%~8.0%,重复性和中间精度分别为3.9%~9.7%和5.5%~12%,当取样量为1.00 mL时,方法的检出限均为0.004 ng/mL。该法操作简单、灵敏、准确,已在中毒患者摄入野生蘑菇后138 h的尿液中检出0.0067 ng/mL α-鹅膏毒肽和0.0059 ng/mL β-鹅膏毒肽。该法已成功解决中毒患者尿液和血浆中超痕量鹅膏毒肽的检测难题,对于疑似中毒病人的早诊断、早治疗、降低死亡率都具有非常重要意义,也为今后开展此类毒素毒理作用及机体代谢规律的研究提供了可靠的技术支撑。

l-methionine Adenosylation: Radical Intermediates and the Catalytic Competence of the 5'-Deoxyadenosyl Radical

Radical S-adenosyl-l-methionine (SAM) enzymes employ a [4Fe-4S] cluster and SAM to initiate diverse radical reactions via either H-atom abstraction or substrate adenosylation. Here we use freeze-quench techniques together with electron paramagnetic resonance (EPR) spectroscopy to provide snapshots of the reaction pathway in an adenosylation reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme on a peptide substrate containing a dehydroalanine residue in place of the target glycine. The reaction proceeds via the initial formation of the organometallic intermediate Ω, as evidenced by the characteristic EPR signal with g_∥ = 2.035 and g_⊥ = 2.004 observed when the reaction is freeze-quenched at 500 ms. Thermal annealing of frozen Ω converts it into a second paramagnetic species centered at g_iso = 2.004; this second species was generated directly using freeze-quench at intermediate times (∼8 s) and unequivocally identified via isotopic labeling and EPR spectroscopy as the tertiary peptide radical resulting from adenosylation of the peptide substrate. An additional paramagnetic species observed in samples quenched at intermediate times was revealed through thermal annealing while frozen and spectral subtraction as the SAM-derived 5'-deoxyadenosyl radical (5'-dAdo•). The time course of the 5'-dAdo• and tertiary peptide radical EPR signals reveals that the former generates the latter. These results thus support a mechanism in which Ω liberates 5'-dAdo• by Fe-C5' bond homolysis, and the 5'-dAdo• attacks the dehydroalanine residue of the peptide substrate to form the adenosylated peptide radical species. The results thus provide a picture of a catalytically competent 5'-dAdo• intermediate trapped just prior to reaction with the substrate.

Biochemical and Mutational Analysis of Radical S-Adenosyl-L-Methionine Adenosylhopane Synthase HpnH from Zymomonas mobilis Reveals that the Conserved Residue Cysteine-106 Reduces a Radical Intermediate and Determines the Stereochemistry

Adenosylhopane is a crucial precursor of C₃₅ hopanoids, which are believed to modulate the fluidity and permeability of bacterial cell membranes. Adenosylhopane is formed by a crosslinking reaction between diploptene and a 5'-deoxyadenosyl radical that is generated by the radical S-adenosyl-L-methionine (SAM) enzyme HpnH. We previously showed that HpnH from Streptomyces coelicolor A3(2) (ScHpnH) converts diploptene to (22R)-adenosylhopane. However, the mechanism of the stereoselective C-C bond formation was unclear. Thus, here, we performed biochemical and mutational analysis of another HpnH, from the ethanol-producing bacterium Zymomonas mobilis (ZmHpnH). Similar to ScHpnH, wild-type ZmHpnH afforded (22R)-adenosylhopane. Conserved cysteine and tyrosine residues were suggested as possible hydrogen sources to quench the putative radical reaction intermediate. A Cys106Ala mutant of ZmHpnH had one-fortieth the activity of the wild-type enzyme and yielded both (22R)- and (22S)-adenosylhopane along with some related byproducts. Radical trapping experiments with a spin-trapping agent supported the generation of a radical intermediate in the ZmHpnH-catalyzed reaction. We propose that the thiol of Cys106 stereoselectively reduces the radical intermediate generated at the C22 position by the addition of the 5'-deoxadenosyl radical to diploptene, to complete the reaction.

[Determination of amanita peptide toxins in human urine by TurboFlow online clean-up-liquid chromatography-tandem mass spectrometry]

鹅膏肽类毒素是一类环状多肽类蘑菇毒素,中毒后会造成急性肝损伤,病死率非常高。我国因误食野生毒蘑菇导致的中毒事件常有发生,测定人尿中鹅膏肽类毒素的浓度,可为临床早期诊断和救治提供有价值的信息。该研究建立了TurboFlow (TF)在线净化-液相色谱-三重四极杆质谱快速定量检测尿液中5种鹅膏肽类毒素(α-鹅膏毒肽、β-鹅膏毒肽、γ-鹅膏毒肽、羧基二羟鬼笔毒肽和二羟鬼笔毒肽)的新方法。尿液样品经高速离心后,直接注入TurboFlow在线净化-液相色谱-串联质谱进行分析。对影响TF在线净化的参数如TF净化柱、上样溶剂、洗脱溶剂、转移流速、转移时间等进行了优化。在优化后的实验条件下,以TurboFlow^TMCyclone柱(50 mm×0.5 mm)为净化柱,Hypersil GOLD C₁₈柱(100 mm×2.1 mm)为分析柱,甲醇和4 mmol/L乙酸铵为流动相进行梯度洗脱,电喷雾正离子选择反应监测(SRM)模式下进行检测,基质匹配外标法定量。结果表明,鹅膏肽类毒素在1.0~50.0 μg/L范围内呈现良好的线性关系,相关系数均可达到0.997以上。方法的检出限为0.15~0.3 μg/L,定量限为0.5~1.0 μg/L。在2.0、5.0和10.0 μg/L的加标水平下,5种鹅膏肽类毒素的日内和日间回收率分别为87.0%~108.6%和86.8%~112.7%,日内、日间相对标准偏差(RSD)均小于14.5%。该检测方法准确、快速、灵敏度高、易操作,适用于公共卫生应急检测或临床中毒病因识别检测。

Characterization and Mechanistic Study of the Radical SAM Enzyme ArsS Involved in Arsenosugar Biosynthesis

Arsenosugars are a group of arsenic-containing ribosides that are found predominantly in marine algae but also in terrestrial organisms. It has been proposed that arsenosugar biosynthesis involves a key intermediate 5'-deoxy-5'-dimethylarsinoyl-adenosine (DDMAA), but how DDMAA is produced remains elusive. Now, we report characterization of ArsS as a DDMAA synthase, which catalyzes a radical S-adenosylmethionine (SAM)-mediated alkylation (adenosylation) of dimethylarsenite (DMAs^III ) to produce DDMAA. This radical-mediated reaction is redox neutral, and multiple turnover can be achieved without external reductant. Phylogenomic and biochemical analyses revealed that DDMAA synthases are widespread in distinct bacterial phyla with similar catalytic efficiencies; these enzymes likely originated from cyanobacteria. This study reveals a key step in arsenosugar biosynthesis and also a new paradigm in radical SAM chemistry, highlighting the catalytic diversity of this superfamily of enzymes.