Paclitaxel is a famous chemotherapeutic agent, but its microbial production poses a long-standing challenge due to its poor product selectivity. Taxadiene-5 alpha-hydroxylase (CYP725A4) plays a crucial role in the biosynthesis of paclitaxel, catalyzing the oxidation of taxadiene and iso-taxadiene. This process yields several products, including the byproducts 5(12)-oxa-3(11)-cyclotaxane (OCT) and 5(11)-oxa-3(11)-cyclotaxane (iso-OCT), as well as the target compound taxadien-5 alpha-ol (T5OH). Despite extensive studies, the molecular mechanism of CYP725A4-catalyzed transformations is still elusive, which could impede our understanding of further engineering of the paclitaxel biosynthetic pathway. In this study, the crystal structure of CYP725A4 in complex with taxadiene is elucidated. Through comprehensive computational analyses, the catalytic mechanisms of CYP725A4 in the biosynthesis of natural paclitaxel are deciphered. Our calculations indicate that the oxidation of taxadiene affords a zwitterion intermediate, which can undergo two competing transformation routes. One involves the formation of epoxide, which further undergoes the water-mediated rearrangement to form the T5OH product. In the alternative pathway, protonation of the oxygen in the zwitterion intermediate facilitates subsequent hydride transfer and carbon-oxygen coupling, resulting in the side products OCT/iso-OCT. Contrary to taxadiene, hydroxylation at C5 of iso-taxadiene directly yields the target product T5OH. These crystallographic studies and computational analyses have yielded valuable insights into the catalytic mechanisms of CYP725A4 and laid the foundation for the further engineering of CYP725A4.

Although cytochrome P450 enzymes are the most versatile biocatalysts in nature, there is insufficient comprehension of the molecular mechanism underlying their functional innovation process. Here, by combining ancestral sequence reconstruction, reverse mutation assay, and progressive forward accumulation, we identified 5 founder residues in the catalytic pocket of flavone 6-hydroxylase (F6H) and proposed a “3-point fixation” model to elucidate the functional innovation mechanisms of P450s in nature. According to this design principle of catalytic pocket, we further developed a de novo diffusion model (P450Diffusion) to generate artificial P450s. Ultimately, among the 17 non-natural P450s we generated, 10 designs exhibited significant F6H activity and 6 exhibited a 1.3- to 3.5-fold increase in catalytic capacity compared to the natural CYP706X1. This work not only explores the design principle of catalytic pockets of P450s, but also provides an insight into the artificial design of P450 enzymes with desired functions.

As the first member of the family with sequence similarity 3 (FAM3), FAM3A promotes synthesis of ATP in mitochondria of hepatic cells and cells from other organs. Dysregulations of FAM3A are involved in the development of diabetes and nonalcoholic fatty liver disease (NAFLD). So far, the molecule mechanism under the physiological and pathological functions of FAM3A is largely unexplored. Here, we determined the crystal structure of FAM3A at high resolution of 1.38Å, complexed with an unknown-source compound which was characterized through metabolomics and confirmed as methacholine by thermal shift assay and surface plasmon resonance (SPR). Exploration for natural ligands of FAM3A was conducted through the same molecular interaction assays. The observed binding of acyl-L-carnitine molecules indicated FAM3A participating in fatty acid beta-oxidation. Knockdown and rescue assays coupled with fatty acid oxidation determination confirmed the role of FAM3A in beta-oxidation. This investigation reveals the molecular mechanism for the biological function of FAM3A and would provide basis for identifying drug target for treatment of diabetes and NAFLD.

The many-banded krait, Bungarus multicinctus, has been recorded as the animal resource of JinQianBaiHuaShe in the Chinese Pharmacopoeia. Characterization of its venoms classified chief phyla of modern animal neurotoxins. However, the evolutionary origin and diversification of its neurotoxins as well as biosynthesis of its active compounds remain largely unknown due to the lack of its high-quality genome. Here, we present the 1.58 Gbp genome of B. multicinctus assembled into 18 chromosomes with contig/scaffold N50 of 7.53 Mbp/149.8 Mbp. Major bungarotoxin-coding genes were clustered within genome by family and found to be associated with ancient local duplications. The truncation of glycosylphosphatidylinositol anchor in the 3’-terminal of a LY6E paralog released modern three-finger toxins（3FTxs） from membrane tethering before the Colubroidea divergence. Subsequent expansion and mutations diversified and recruited these 3FTxs. After the cobra/krait divergence, the modern unit-B of β-bungarotoxin emerged with an extra cysteine residue. A subsequent point substitution in unit-A enabled theβ-bungarotoxin covalent linkage. The B. multicinctus gene expression, chromatin topological organization, and histone modification characteristics were featured by transcriptome, proteome, chromatin conformation capture sequencing, and ChIP-seq. The results highlighted that venom production was under a sophisticated regulation. Our findings provide new insights into snake neurotoxin research, meanwhile will facilitate antivenom development, toxin-driven drug discovery and the quality control of JinQianBaiHuaShe.

丹参在治疗心绞痛、冠心病和心肌梗死等疾病中具有广泛应用.CYP76AH3是其活性成分丹参酮合成途径中的关键P450酶,位于丹参酮复杂合成网络通路的分支处,其晶体结构解析及关键氨基酸分析对丹参酮的合成生物学具有重要意义.作为跨膜蛋白的Ⅱ型P450酶的蛋白质纯化、晶体培养和晶体结构解析的难度一贯较大.本研究通过构建原核表达重组质粒,纯化目的蛋白质,成功培养了 CYP76AH3晶体,解析了晶体结构.根据CavityPlus分析确定对接范围,采用分子对接程序Discovery Studio筛选出与底物相互作用的关键氨基酸,包括与底物有氢键相互作用的Gly298和Asp294,以及与底物有疏水相互作用的Phe479、Leu367和Leu293;通过点突变模拟进一步预测了关键氨基酸的突变对蛋白质结构稳定性的影响.本研究将为CYP76AH3的蛋白质工程提供目标,为丹参酮的合成生物学研究奠定了基础.

CYP76AH1 is the key enzyme in the biosynthesis pathway of tanshinones in Salvia miltiorrhiza, which are famous natural products with activities against various heart diseases and others. CYP76AH1 is a membrane-associated typical plant class II cytochrome P450 enzyme and its catalytic mechanism has not to be clearly elucidated. Structural determination of eukaryotic P450 enzymes is extremely challenging. Recently, we solved the crystal structures of CYP76AH1 and CYP76AH1 in complex with its natural substrate miltiradiene. The structure of CYP76AH1 complexed with miltiradiene is the first plant cytochrome P450 structure in complex with natural substrate. The studies revealed a unique array pattern of amino acid residues, which may play an important role in orienting and stabilizing the substrate for catalysis. This work would provide structural insights into CYP76AH1 and related P450s and the basis to efficiently improve tanshinone production by synthetic biology techniques.

Tanshinones are important diterpenoid secondary metabolites from Salvia miltiorrhiza, widely used as cardiovascular and cerebrovascular medicines. CYP76AH1 is a membrane-associated cytochrome P450 enzyme and plays a critical role in the biosynthetic pathway of tanshinones. To clarify the relationship between structure and function of CYP76AH1, we recently constructed the expression vector of CYP76AH1 and purified the enzyme. The engineered CYP76AH1 was expressed in E. coli Trans-blue cells and exhibited enhanced expression and solubility. The proper folding of the engineered CYP76AH1 was assessed by CO difference spectrum assay. Functional identification of the recombinant enzyme was performed by conducting enzymatic reaction with the purified CYP76AH1 in presence of substrate, the co-factor NADPH and the purified SmCPR1 (cytochrome P450 reductase from Salvia miltiorrhiza), and by subsequently analyzing the reaction extract through GC-MS. X-ray crystal complex structure of CYP76AH1 with inhibitor 4-phenylimmidazole (4-PI) was determined at the resolution of 2.6 Å. In the ligand-binding cavity of 4-PI bound CYP76AH1, the inhibitor 4-PI forms a hydrogen bound with a water molecule which coordinates with heme at the sixth coordination position. There are two open channels which substrate and product site may access and leave the active site. In the CYP76AH1/4-PI complex structure, the imidazole ring of 4-PI is parallel to helix I instead of perpendicular to helies I in most P450s bound imidazole. 4-PI may be work in the stability of CYP76AH1 crystal structure. These studies provide information on functional expression and purification of CYP76AH1, and overall structure of CYP76AH1 complexed with 4-PI.

Malaria is a worldwide epidemic that extensively endangers health of human beings. Before artemisinin was developed to treat with malaria, about 400 million person-time of malaria infections and at least 1 million deaths from malaria were reported in the world every year. Thus malaria has been listed as one of the world's three major death diseases by the WHO. The discovery of artemisinin by Chinese scientists created a novel therapy approach to treat with malaria effectively. Amorpha-4,11-diene oxidase is a plant cytochrome P450 enzymes, i.e. CYP71AV1, which catalyzes each of the three oxidation steps from amorpha-4,11-diene to form artemisinic acid, the intermediate of artemisinin. CYP71AV1 is the key enzyme in artemisinin biosynthesis. By constructing the prokaryotic expression vector pCWOri(+)-CYP71AV1, functional expression and purification of complementary CYP71AV1 were performed. The enzyme activity was monitored by CO differential spectrum assay and the heme-based activity analysis. The preliminary crystallization condition was obtained by crystallization screening. These studies provide basis for resolving the crystal structure of CYP71AV1 and for producing artemisinin in large scale through biosynthetic biology approach, and will provide references for over expression, purification and crystallization of other plant P450 enzymes.

Ginseng, which contains ginsenosides as bioactive compounds, has been regarded as an important traditional medicine for several millennia. However, the genetic background of ginseng remains poorly understood, partly because of the plant's large and complex genome composition. We report the entire genome sequence of Panax ginseng using next-generation sequencing. The 3.5-Gb nucleotide sequence contains more than 60% repeats and encodes 42 006 predicted genes. Twenty-two transcriptome datasets and mass spectrometry images of ginseng roots were adopted to precisely quantify the functional genes. Thirty-one genes were identified to be involved in the mevalonic acid pathway. Eight of these genes were annotated as 3-hydroxy-3-methylglutaryl-CoA reductases, which displayed diverse structures and expression characteristics. A total of 225 UDP-glycosyltransferases (UGTs) were identified, and these UGTs accounted for one of the largest gene families of ginseng. Tandem repeats contributed to the duplication and divergence of UGTs. Molecular modeling of UGTs in the 71st, 74th, and 94th families revealed a regiospecific conserved motif located at the N-terminus. Molecular docking predicted that this motif captures ginsenoside precursors. The ginseng genome represents a valuable resource for understanding and improving the breeding, cultivation, and synthesis biology of this key herb.

Flavonoids, natural products abundant in the model legume Glycine max, confer benefits to plants and to animal health. Flavonoids are present in soybean mainly as glycoconjugates. However, the mechanisms of biosynthesis of flavonoid glycosides are largely unknown in G. max. In the present study, 212 putative UDP-glycosyltransferase (UGT) genes were identified in G. max by genome-wide searching. The GmUGT genes were distributed differentially among the 20 chromosomes, and they were expressed in various tissues with distinct expression profiles. We further analyzed the enzymatic activities of 11 GmUGTs that are potentially involved in flavonoid glycosylation, and found that six of them (UGT72X4, UGT72Z3, UGT73C20, UGT88A13, UGT88E19 and UGT92G4) exhibited activity toward flavonol, isoflavone, flavone and flavanol aglycones with different kinetic properties. Among them, UGT72X4, UGT72Z3 and UGT92G4 are flavonol-specific UGTs, and UGT73C20 and UGT88E19 exhibited activity toward both flavonol and isoflavone aglycones. In particular, UGT88A13 exhibited activity toward epicatechin, but not for the flavonol aglycones kaempferol and quercetin. Overexpression of these six GmUGT genes significantly increased the contents of isoflavone and flavonol glucosides in soybean hairy roots. In addition, overexpression of these six GmUGT genes also affected flavonol glycoside contents differently in seedlings and seeds of transgenic Arabidopsis thaliana. We provide valuable information on the identification of all UGT genes in soybean, and candidate GmUGT genes for potential metabolic engineering of flavonoid compounds in both Escherichia coli and plants.

Flavonols are one of the largest groups of flavonoids that confer benefits for the health of plants and animals. Flavonol glycosides are the predominant flavonoids present in the model legume Lotus japonicus. The molecular mechanisms underlying the biosynthesis of flavonol glycosides as yet remain unknown in L. japonicus. In the present study, we identified a total of 188 UDP-glycosyltransferases (UGTs) in L. japonicus by genome-wide searching. Notably, 12 UGTs from the UGT72 family were distributed widely among L. japonicus chromosomes, expressed in all tissues, and showed different docking scores in an in silico bioinformatics docking analysis. Further enzymatic assays showed that five recombinant UGTs (UGT72AD1, UGT72AF1, UGT72AH1, UGT72V3, and UGT72Z2) exhibit activity toward flavonol, flavone, and isoflavone aglycones. In particular, UGT72AD1, UGT72AH1, and UGT72Z2 are flavonol-specific UGTs with different kinetic properties. In addition, the overexpression of UGT72AD1 and UGT72Z2 led to increased accumulation of flavonol rhamnosides in L. japonicus and Arabidopsis thaliana. Moreover, the increase of kaempferol 3-O-rhamnoside-7-O-rhamnoside in transgenic A. thaliana inhibited root growth as compared with the wild-type control. These results highlight the significance of the UGT72 family in flavonol glycosylation and the role of flavonol rhamnosides in plant growth.

Small heat shock proteins assemble as large oligomers in vitro and exhibit ATP-independent chaperone activities. Ile-X-Ile motif is essential in both the function and oligomer formation. AgsA of Salmonella enterica serovar Typhimurium has been demonstrated to adopt large oligomeric structure and possess strong chaperone activity. Size exclusion chromatography, non-denaturing pore gradient PAGE, and negatively stain electron microscopic analysis of the various C-terminal truncated mutants were performed to investigate the role of Ile-X-Ile motif in the oligomer assembly of AgsA. By measuring the ability to prevent insulin from aggregating induced by TCEP, the chaperone-like activity of AgsA and the C-terminal truncated mutants at room temperature were determined. We found that the truncated mutants with Ile-X-Ile motif partially or fully deleted lost the ability to form large oligomers. Contrast to wild type AgsA which displayed weak chaperone-like activity, those mutants shown significantly enhanced activities at room temperature. In summary, biochemical experiment, activity assay and electron microscopic analysis suggested that Ile-X-Ile motif is essential in oligomer assembly of AgsA and might take the role of an inhibitor for its chaperone-like activity at room temperature.

To obtain a comprehensive understanding of proteins involved in mitochondrion-sarcoplasmic reticulum (SR) linking, a catalog of proteins from mitochondrion-associated membrane (MAM) of New Zealand white rabbit skeletal muscle were analyzed by an optimized shotgun proteomic method. The membrane fractions were prepared by differential centrifugation and separated by 1D electrophoresis followed by a highly reproducible, automated LC-MS/MS on the hybrid linear ion trap (LTQ)-Orbitrap mass spectrometer. By integrating as low as 1% false discovery rate as one of the features for quality control method, 459 proteins were identified from both of the two independent MAM preparations. Protein pI value, molecular weight range, and transmembrane region were calculated using bioinformatics softwares. One hundred one proteins were recognized as membrane proteins. This protein database suggested that the MAM preparations composed of proteins from mitochondrion, SR, and transverse-tubule. This result indicated mitochondria physically linked with SR in rabbit skeletal muscle, voltage-dependent anion channel 1 (VDAC1), VDAC2, and VDAC3 might participate in formation of the tethers between SR and mitochondria.

目的:从毛蚶软体部位中分离出具有一定抗癌活性的毛蚶蛋白组分,研究其对人乳腺癌细胞MCF-7的生长抑制作用.方法:以新鲜毛蚶软体部分为原材料,分离获得毛蚶抗癌蛋白组分(命名为NS);倒置相差显微镜观察不同浓度(50、100、200、400μg/mL)NS组分对MCF-7癌细胞生长的影响,将200 μg/mL NS组分作用MCF-7细胞不同时间(12、24、48 h)后,Giemsa染色观察癌细胞及核形态的变化,流式细胞术检测NS组分对MCF-7细胞周期及细胞凋亡的影响,Western blot检测细胞周期及细胞凋亡相关蛋白的表达.结果:与阴性对照组比较,各浓度NS组分对人乳腺癌MCF-7细胞生长均具有明显的抑制作用(P＜0.05或P＜0.01);倒置相差显微镜下可见200 μg/mL NS组分作用MCF-7细胞12 h后,部分细胞收缩变圆、脱落,24、48 h后细胞脱落现象更加明显;Giemsa染色发现,NS组分处理12h后细胞出现有丝分裂相增加,继而出现多核或核碎裂等现象;流式细胞术检测发现NS组分主要引起细胞G2-M期阻滞;NS处理组凋亡率均较对照组明显升高(P均＜0.01),且随着药物作用时间的延长,细胞凋亡比例逐渐增加.Western blot检测发现NS组分作用MCF-7细胞后p53及procaspase-3蛋白表达量均上调.结论:毛蚶抗癌蛋白NS组分体外对人乳腺癌MCF-7细胞的细胞毒作用主要通过引起细胞发生G2-M期阻滞、诱导细胞凋亡实现的,期间伴随p53及procaspase-3蛋白表达上调.

To obtain a comprehensive understanding of proteins involved in excitation–contraction coupling, a catalog of proteins from sarcoplasmic reticulum (SR) membrane fractions of New Zealand white rabbit skeletal muscle was analyzed by an optimized shotgun proteomic method. Light and heavy SR membrane fractions were obtained by nonlinear sucrose gradient centrifugation and separated by 1DE followed by a highly reproducible, automated LC‐MS/MS on the hybrid linear ion trap (LTQ) Orbitrap mass spectrometer. By integrating as low as 1% false discovery rate as one of the features for quality control method, 483 proteins were identified from both of the two independent SR preparations. Proteins involved in calcium release unit complex, including ryanodine receptor 1, dihydropyridine receptor, calmodulin, triadin, junctin, and calsequestrin, were all detected, which offered validation for this protein identification method. Rigorous bioinformatics analysis was performed. Protein pI value, molecular weight range, hydrophobicity index, and transmembrane region were calculated using bioinformatics softwares. Eighty‐three proteins were classified as hydrophobic proteins and 175 proteins were recognized as membrane proteins. Based on the proteomic analysis results, we found as the first time that not only transverse tubule but also mitochondrion physically connected to SR. The complete mapping of these proteomes may help in the elucidation of the process of excitation–contraction coupling and excitation–metabolism coupling.

Expression and crystallization of Cytochrome P450 from plants is difficult,and becomes the bottleneck of structural study for plant P450s.It was researched the expression and purification of AOS from guayule using E.coli expression system.In order to realize expression and purification of the AOS,its amino acid sequence was aligned with that of other CYP74A enzymes.Results showed that the AOS was the absence of the amino-terminal membrane anchor and the putative transit sequence.It could be expressed in E.coli as water-soluble form.Experimental purified recombinant AOS was an active octamer of molecular mass of 54.5 kD,it was milligram quantities of homogeneous,detergent-free AOS protein which would be used for crystallographic study.The reduced-CO difference spectrum of recombinant AOS had a characteristic band at 450 nm.Enzymatic activity assay was performed.Value of Km was 45.3 μmol/L,that is,the purified AOS exhibited high activity.

One-carbon units derived from glycine and serine are transferred to tetrahydrofolic acid (THFA) for biosynthesis of THFA metabolites in plants. Quantitatively analysis of THFA metabolites in plant tissues is challenging because of their low level, complexity and general instability. Our study was to develop a reliable method for quantifying THFA metabolites and folic acid in plants which differ in demand for methyl groups, for example, spinach (an accumulator of glycine betaine) and Arabidopsis thaliana (a non-accumulator of glycine betaine), in preparation for investigation of one-carbon flux through folate pathway in those plants. Under gold fluorescent light, fresh spinach and Arabidopsis leaves were ground in liquid nitrogen and treated with crude preparation of rat plasma conjugase. The resulting extracts were applied to folate binding protein agarose columns for purification. After eluting from the affinity chromatography columns, THFA metabolites and folic acid were determined by reversed-phase HPLC with fluorescence and UV detection. In spinach and Arabidopsis leaves, the contents of monoglutamate of N5-methyl-tetrahydrofolate (N5-CH3-THFA) were 252 ng/g and 64 ng/g, respectively,while the contents of total N5-CH3-THFA were 370 ng/g and 199 ng/g, respectively. Small amounts of THFA, N5-formyl-tetrahydrofolate (N5-HCO-THFA) were also detected in samples of both plants, folic acid was detected in Arabidopsis leaves, but not in spinach leaves. These results indicate that spinach synthesizes significantly more mono-glutamate and poly-glutamate of N5-CH3-THFA than rabidopsis does. This method for sample preparation and HPLC analysis is suitable for quantifying THFA metabolites and folic acid in plants.

Plants possess very large numbers of biosynthetic cytochrome P450 enzymes. In spite of the importance of these enzymes for the synthesis of bioactive plant secondary metabolites, only two plant P450 structures has been obtained to date. Isoflavone synthase (IFS) is a membrane-associated cytochrome P450 enzyme catalyzing the entry-point reaction into isoflavonoid biosynthesis. IFS from the model legume Medicago truncatula (CYP93C20) was engineered by deleting the membrane-spanning domain and inserting a hydrophilic polypeptide in the N-terminus and a four histidine tag at the C-terminus. The truncated form exhibited dramatically enhanced expression and solubility. The engineered enzyme was expressed in Escherichia coli XL1-blue cells and was purified by Ni2+-NTA affinity chromatograph and size-exclusion chromatograph. The purified enzyme was characterized by enzyme assay, reduced carbon monoxide difference spectroscopy and peptide mass fingerprinting. The engineered soluble enzyme exhibited the same activity as the full length membrane-associated enzyme expressed in yeast. These studies suggest an approach for engineering plant membrane-associated P450s with enhanced expression and solubility for mechanistic and structural studies.

Oxylipins are oxygenated derivatives of fatty acids and pivotal signaling molecules in plants and animals. Allene oxide synthase (AOS) is a key cytochrome P450 CYP74 enzyme involved in the biosynthesis of plant oxylipin jasmonates to convert 13(S)-hydroperoxide to allene oxide. Guayule (Parthenium argentatum) AOS, CYP74A2, was expressed in Escherichia coli. Protein was purified using affinity chromatography and size exclusion chromatography, and then crystallized. Two different crystal forms were obtained from 0.2 M (NH(4))H(2)PO(4), 50% MPD, 0.1 M Tris, pH 8.5 at 277 K using the hanging-drop vapor-diffusion method. Preliminary X-ray analysis was carried out, and the crystals were found to belong to the tetragonal space group I422 with cell parameters a = b = 126.5, c = 163.9 A, and the monoclinic space group C2 with cell parameters a = 336.5, b = 184.2, c = 159.0 A, beta = 118.6 degrees . Diffraction data were collected to 2.4 A resolution from a tetragonal form of crystal using a home X-ray source.

Cytochrome P450s exist ubiquitously in all organisms and are involved in many biological processes. Allene oxide synthase (AOS) is a P450 enzyme that plays a key role in the biosynthesis of oxylipin jasmonates, which are involved in signal and defense reactions in higher plants. The crystal structures of guayule (Parthenium argentatum) AOS (CYP74A2) and its complex with the substrate analog 13(S)-hydroxyoctadeca-9Z,11E-dienoic acid have been determined. The structures exhibit a classic P450 fold but possess a heme-binding mode with an unusually long heme binding loop and a unique I-helix. The structures also reveal two channels through which substrate and product may access and leave the active site. The entrances are defined by a loop between β3–2 and β3–3. Asn-276 in the substrate binding site may interact with the substrate's hydroperoxy group and play an important role in catalysis, and Lys-282 at the entrance may control substrate access and binding. These studies provide both structural insights into AOS and related P450s and a structural basis to understand the distinct reaction mechanism.