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author:("Lu, yuefeng")
1.  Hydrogen peroxide-independent production of α-alkenes by OleTJE P450 fatty acid decarboxylase 
Background
Cytochrome P450 OleTJE from Jeotgalicoccus sp. ATCC 8456, a new member of the CYP152 peroxygenase family, was recently found to catalyze the unusual decarboxylation of long-chain fatty acids to form α-alkenes using H2O2 as the sole electron and oxygen donor. Because aliphatic α-alkenes are important chemicals that can be used as biofuels to replace fossil fuels, or for making lubricants, polymers and detergents, studies on OleTJE fatty acid decarboxylase are significant and may lead to commercial production of biogenic α-alkenes in the future, which are renewable and more environmentally friendly than petroleum-derived equivalents.
Results
We report the H2O2-independent activity of OleTJE for the first time. In the presence of NADPH and O2, this P450 enzyme efficiently decarboxylates long-chain fatty acids (C12 to C20) in vitro when partnering with either the fused P450 reductase domain RhFRED from Rhodococcus sp. or the separate flavodoxin/flavodoxin reductase from Escherichia coli. In vivo, expression of OleTJE or OleTJE-RhFRED in different E. coli strains overproducing free fatty acids resulted in production of variant levels of multiple α-alkenes, with a highest total hydrocarbon titer of 97.6 mg·l-1.
Conclusions
The discovery of the H2O2-independent activity of OleTJE not only raises a number of fundamental questions on the monooxygenase-like mechanism of this peroxygenase, but also will direct the future metabolic engineering work toward improvement of O2/redox partner(s)/NADPH for overproduction of α-alkenes by OleTJE.
doi:10.1186/1754-6834-7-28
PMCID: PMC3937522  PMID: 24565055
Alkenes; Biofuels; Monooxygenase; P450 fatty acid decarboxylase; Peroxygenase
2.  The Gain-of-Function of p53 Cancer Mutant in Promoting Mammary Tumorigenesis 
Oncogene  2012;32(23):2900-2906.
Tumor suppressor p53 is critical to suppress all types of human cancers, including breast cancers. The p53 gene is somatically mutated in over half of all human cancers. The majority of the p53 mutations are missense mutations, leading to the expression of the full-length p53 mutants. Several hotspot mutations, including R175H, are frequently detected in human breast cancers. P53 cancer mutants not only lose tumor suppression activity, but more problematically, gain new oncogenic activities. Despite correlation of the expression of p53 cancer mutants and the poor prognosis of human breast cancer patients, the roles of p53 cancer mutants in promoting breast cancer remain unclear. We employed the humanized p53 cancer mutant knock-in (R175H) mice and MMTV-Wnt-1 transgenic (mWnt-1) mice to specifically address the gain of function of R175H in promoting breast cancer. While both R175H/R175HmWnt-1(R175HmWnt-1) and p53−/−mWnt-1 mice died from mammary cancers at the same kinetics, which was much earlier than mWnt-1 mice, most of the R175HmWnt-1 mice developed multiple mammary tumors per mouse, whereas p53−/−mWnt-1 and mWnt-1 mice mostly developed one tumor per mouse. The multiple mammary tumors arose in the same R175HmWnt-1 mouse exhibited different histological characters. Moreover, R175H gain-of-function mutant expands the mammary epithelial stem cells (MESCs) that give rise to the mammary tumors. Since ATM suppresses the expansion of MESCs, the inactivation of ATM by R175H in mammary epithelial cells could contribute to the expansion of MESCs in R175HmWnt-1 mice. These findings provide the basis for R175H to promote the initiation of breast cancer by expanding MESCs.
doi:10.1038/onc.2012.299
PMCID: PMC3586389  PMID: 22824795
3.  Mechanism of 4-Chlorobenzoate: Coenzyme A Ligase Catalysis# 
Biochemistry  2008;47(31):8026-8039.
Within the accompanying paper (Reger, A. S, Wu, R., Dunaway-Mariano, D. and Gulick, A. M. (2008) Crystallographic trapping of a 140° domain movement in the two-step reaction catalyzed by 4 chlorobenzoate:CoA ligase. Biochemistry) we reported the X-ray structure of 4-chlorobenzoate: CoA ligase (CBL) bound with 4-chlorobenzoyl-adenylate (4-CB-AMP) and the X-ray structure of CBL bound with 4-chlorophenacyl-CoA (4-CP-CoA) (an inert analog of the product 4-chlorobenzoyl-coenzyme A (4-CB-CoA)) and AMP. These structures defined two CBL conformational states. In conformation 1, CBL is poised to catalyze the adenylation of 4-chlorobenzoate (4-CB) with ATP (partial reaction 1) and in conformation 2, CBL is poised to catalyze the formation of 4-CB-CoA from 4-CB-AMP and CoA (partial reaction 2). These two structures showed that, by switching from conformation 1 to conformation 2, the cap domain rotates about the domain linker and thereby changes its interface with the N-terminal domain. The present work was carried out to determine the contributions made by each of the active site residues in substrate/cofactor binding and catalysis, and also to test the role of domain alternation in catalysis. In this paper, we report the results of steady-state kinetic and transient state kinetic analysis of wild-type CBL and of a series of site-directed CBL active site mutants. The major findings are as follows. First, wild-type CBL is activated by Mg+2 (a 12 to 75-fold increase in activity is observed depending on assay conditions) and its kinetic mechanism (ping-pong) supports the structure-derived prediction that PPi dissociation must precede the switch from conformation 1 to conformation 2 and therefore, CoA binding. Also, transient kinetic analysis of wild-type CBL identified the rate-limiting step of the catalyzed reaction as one that follows the formation of 4-CB-CoA (viz. CBL conformational change and/or product dissociation). The single turnover rate of 4-CB and ATP to form 4-CB-AMP and PPi (k= 300 s−1) is not effected by the presence of CoA, and it is ~3-fold faster than the turnover rate of 4-CB-AMP and CoA to form 4-CB-CoA and AMP (k= 120 s−1). Second, the active site mutants screened via steady-state kinetic analysis, were ranked based on the degree of reduction observed in any one of the substrate kcat/Km values, and those scoring higher than a 50-fold reduction in kcat/Km value were selected for further evaluation via transient state kinetic analysis. The single-turnover time courses, measured for the first partial reaction, and then for the full reaction, were analyzed to define the microscopic rate constants for the adenylation reaction and the thioesterification reaction. Based on our findings we propose a catalytic mechanism that centers on a small group of key residues (some of which serve in more than one role) and that includes several residues that function in domain alternation.
doi:10.1021/bi800698m
PMCID: PMC3694354  PMID: 18620421
4-chlorobenzoate: CoA ligase; 4-chlorobenzoate; aromatic degradation; coenzyme A; 4-chlorobenzoyl-adenosine-5′-monophosphate; 4-chlorobenzoyl-CoA; adenylate-forming enzyme superfamily; acyl-adenylate; catalytic mechanism; rapid quench; transient kinetics; kinetic mechanism; domain alternation; separate site catalysis
4.  Conversion of fatty aldehydes into alk (a/e)nes by in vitro reconstituted cyanobacterial aldehyde-deformylating oxygenase with the cognate electron transfer system 
Background
Biosynthesis of fatty alk(a/e)ne in cyanobacteria has been considered as a potential basis for the sunlight-driven and carbon-neutral bioprocess producing advanced solar biofuels. Aldehyde-deformylating oxygenase (ADO) is a key enzyme involved in that pathway. The heterologous or chemical reducing systems were generally used in in vitro ADO activity assay. The cognate electron transfer system from cyanobacteria to support ADO activity is still unknown.
Results
We identified the potential endogenous reducing system including ferredoxin (Fd) and ferredoxin-NADP+ reductase (FNR) to support ADO activity in Synechococcus elongatus PCC7942. ADO (Synpcc7942_1593), FNR (SynPcc7942_0978), and Fd (SynPcc7942_1499) from PCC7942 were cloned, overexpressed, purified, and characterized. ADO activity was successfully supported with the endogenous electron transfer system, which worked more effectively than the heterologous and chemical ones. The results of the hybrid Fd/FNR reducing systems demonstrated that ADO was selective against Fd. And it was observed that the cognate reducing system produced less H2O2 than the heterologous one by 33% during ADO-catalyzed reactions. Importantly, kcat value of ADO 1593 using the homologous Fd/FNR electron transfer system is 3.7-fold higher than the chemical one.
Conclusions
The cognate electron transfer system from cyanobacteria to support ADO activity was identified and characterized. For the first time, ADO was functionally in vitro reconstituted with the endogenous reducing system from cyanobacteria, which supported greater activity than the surrogate and chemical ones, and produced less H2O2 than the heterologous one. The identified Fd/FNR electron transfer system will be potentially useful for improving ADO activity and further enhancing the biosynthetic efficiency of hydrocarbon biofuels in cyanobacteria.
doi:10.1186/1754-6834-6-86
PMCID: PMC3691600  PMID: 23759169
Biofuels; Fatty alk(a/e)ne; Synechococcus elongatus PCC7942; Aldehyde-deformylating oxygenase; Ferredoxin; Ferredoxin-NADP+ reductase; The cognate reducing system
5.  Engineering cyanobacteria to improve photosynthetic production of alka(e)nes 
Background
Cyanobacteria can utilize solar energy and convert carbon dioxide into biofuel molecules in one single biological system. Synechocystis sp. PCC 6803 is a model cyanobacterium for basic and applied research. Alkanes are the major constituents of gasoline, diesel and jet fuels. A two-step alkane biosynthetic pathway was identified in cyanobacteria recently. It opens a door to achieve photosynthetic production of alka(e)nes with high efficiency by genetically engineering cyanobacteria.
Results
A series of Synechocystis sp. PCC6803 mutant strains have been constructed and confirmed. Overexpression of both acyl-acyl carrier protein reductase and aldehyde-deformylating oxygenase from several cyanobacteria strains led to a doubled alka(e)ne production. Redirecting the carbon flux to acyl- ACP can provide larger precursor pool for further conversion to alka(e)nes. In combination with the overexpression of alkane biosynthetic genes, alka(e)ne production was significantly improved in these engineered strains. Alka(e)ne content in a Synechocystis mutant harboring alkane biosynthetic genes over-expressed in both slr0168 and slr1556 gene loci (LX56) was 1.3% of cell dry weight, which was enhanced by 8.3 times compared with wildtype strain (0.14% of cell dry weight) cultivated in shake flasks. Both LX56 mutant and the wildtype strain were cultivated in column photo-bioreactors, and the alka(e)ne production in LX56 mutant was 26 mg/L (1.1% of cell dry weight), which was enhanced by 8 times compared with wildtype strain (0.13% of cell dry weight).
Conclusions
The extent of alka(e)ne production could correlate positively with the expression level of alkane biosynthetic genes. Redirecting the carbon flux to acyl-ACP and overexpressing alkane biosynthetic genes simultaneously can enhance alka(e)ne production in cyanobacteria effectively.
doi:10.1186/1754-6834-6-69
PMCID: PMC3679977  PMID: 23641684
Cyanobacteria; Synechocystis sp. PCC6803; Alka(e)ne; Fatty acid; Metabolic engineering
6.  Interplay between the Westerlies and Asian monsoon recorded in Lake Qinghai sediments since 32 ka 
Scientific Reports  2012;2:619.
Two atmospheric circulation systems, the mid-latitude Westerlies and the Asian summer monsoon (ASM), play key roles in northern-hemisphere climatic changes. However, the variability of the Westerlies in Asia and their relationship to the ASM remain unclear. Here, we present the longest and highest-resolution drill core from Lake Qinghai on the northeastern Tibetan Plateau (TP), which uniquely records the variability of both the Westerlies and the ASM since 32 ka, reflecting the interplay of these two systems. These records document the anti-phase relationship of the Westerlies and the ASM for both glacial-interglacial and glacial millennial timescales. During the last glaciation, the influence of the Westerlies dominated; prominent dust-rich intervals, correlated with Heinrich events, reflect intensified Westerlies linked to northern high-latitude climate. During the Holocene, the dominant ASM circulation, punctuated by weak events, indicates linkages of the ASM to orbital forcing, North Atlantic abrupt events, and perhaps solar activity changes.
doi:10.1038/srep00619
PMCID: PMC3431539  PMID: 22943005
7.  Effects of fatty acid activation on photosynthetic production of fatty acid-based biofuels in Synechocystis sp. PCC6803 
Background
Direct conversion of solar energy and carbon dioxide to drop in fuel molecules in a single biological system can be achieved from fatty acid-based biofuels such as fatty alcohols and alkanes. These molecules have similar properties to fossil fuels but can be produced by photosynthetic cyanobacteria.
Results
Synechocystis sp. PCC6803 mutant strains containing either overexpression or deletion of the slr1609 gene, which encodes an acyl-ACP synthetase (AAS), have been constructed. The complete segregation and deletion in all mutant strains was confirmed by PCR analysis. Blocking fatty acid activation by deleting slr1609 gene in wild-type Synechocystis sp. PCC6803 led to a doubling of the amount of free fatty acids and a decrease of alkane production by up to 90 percent. Overexpression of slr1609 gene in the wild-type Synechocystis sp. PCC6803 had no effect on the production of either free fatty acids or alkanes. Overexpression or deletion of slr1609 gene in the Synechocystis sp. PCC6803 mutant strain with the capability of making fatty alcohols by genetically introducing fatty acyl-CoA reductase respectively enhanced or reduced fatty alcohol production by 60 percent.
Conclusions
Fatty acid activation functionalized by the slr1609 gene is metabolically crucial for biosynthesis of fatty acid derivatives in Synechocystis sp. PCC6803. It is necessary but not sufficient for efficient production of alkanes. Fatty alcohol production can be significantly improved by the overexpression of slr1609 gene.
doi:10.1186/1754-6834-5-17
PMCID: PMC3366867  PMID: 22433663
Biofuel; Fatty alcohol; Fatty alkane; Cyanobacteria; Synechocystis sp. PCC6803; Fatty acid activation
8.  De novo Biosynthesis of Biodiesel by Escherichia coli in Optimized Fed-Batch Cultivation 
PLoS ONE  2011;6(5):e20265.
Biodiesel is a renewable alternative to petroleum diesel fuel that can contribute to carbon dioxide emission reduction and energy supply. Biodiesel is composed of fatty acid alkyl esters, including fatty acid methyl esters (FAMEs) and fatty acid ethyl esters (FAEEs), and is currently produced through the transesterification reaction of methanol (or ethanol) and triacylglycerols (TAGs). TAGs are mainly obtained from oilseed plants and microalgae. A sustainable supply of TAGs is a major bottleneck for current biodiesel production. Here we report the de novo biosynthesis of FAEEs from glucose, which can be derived from lignocellulosic biomass, in genetically engineered Escherichia coli by introduction of the ethanol-producing pathway from Zymomonas mobilis, genetic manipulation to increase the pool of fatty acyl-CoA, and heterologous expression of acyl-coenzyme A: diacylglycerol acyltransferase from Acinetobacter baylyi. An optimized fed-batch microbial fermentation of the modified E. coli strain yielded a titer of 922 mg L−1 FAEEs that consisted primarily of ethyl palmitate, -oleate, -myristate and -palmitoleate.
doi:10.1371/journal.pone.0020265
PMCID: PMC3100327  PMID: 21629774
9.  The Mechanism of Domain Alternation in the Acyl-Adenylate Forming Ligase Superfamily Member 4-Chlorobenzoate 
Biochemistry  2009;48(19):4115-4125.
4-Chlorobenzoate:CoA ligase (CBL) belongs to the adenylate-forming family of enzymes that catalyze a two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site is located at the interface of a large N-terminal domain and a smaller C-terminal domain. Crystallographic structures have been determined at multiple steps along the reaction pathway and form the basis for a proposal that the C-terminal domain rotates by ∼140° between the two states that catalyze the adenylation and thioester-forming half-reactions. The domain rotation is accompanied by a change in the main chain torsional angles of Asp402, a conserved residue located at the inter-domain hinge position. We have mutated the Asp402 residue to Pro in order to test the impact of reduced main chain flexibility at the putative hinge position. The crystal structure of the D402P mutant shows that the enzyme adopts the proposed adenylate-forming conformation with very little change to the overall structure. To examine the impact of this mutation on the ability of the enzyme to catalyze the complete reaction, single turnover kinetic experiments were performed. Whereas the ability of this mutant to catalyze the adenylate-forming half-reaction is reduced by ∼3-fold, catalysis of the second half-reaction is reduced by four orders of magnitude. The impact of the alanine replacement of Asp402 on the thioester-forming reaction is significant, although not as dramatic as the proline mutation, and provides evidence that the Asp402 carboxylate group, through ion pair formation with N-terminal domain residue Arg400, assists in the transition to the thioester-forming conformer. Together these results support the domain alternation hypothesis.
doi:10.1021/bi9002327
PMCID: PMC2680940  PMID: 19320426
domain alternation; domain linker; adenylation; thioesterification; 4-chorobenzoate; coenzyme A; ligase; thioester; acyl-adenylate; adenylate-forming enzyme superfamily; synthetase; protein hinge; 4-chlorobenzoyl-CoA; 4-chlorobenzoyl-adenosine-5′-monophosphate; transient kinetics; X-ray structure; site-directed mutation; separate site catalysis

Results 1-9 (9)