FLP Site Research Articles

One-step conversion of methane and formaldehyde to ethanol over SA-FLP dual-active-site catalysts: A DFT study

One-step conversion of methane and formaldehyde into ethanol is a 100% atom-efficient process for carbon resources utilization and environment protection but still faces eminent challenges due to the lacking of efficient catalysts. Therefore, developing active and stable catalysts is crucial for the co-conversion of methane and formaldehyde. Herein, twelve kinds of “Single-Atom” - “Frustrated Lewis Pair” (SA-FLP) dual-active-site catalysts are designed for the direct conversion of methane and formaldehyde to ethanol based on density functional theory (DFT) calculations and microkinetic simulations. The results show that the SA-FLP dual active sites can simultaneously activate methane at the SA site and activate formaldehyde at the FLP site. Among the twelve designed SA-FLP catalysts, Fe1-FLP shows the best performance in the co-conversion of methane and formaldehyde to ethanol with the rate-determining barrier of 1.15 eV. Ethanol is proved as the main product with the turnover frequency of 1.32 × 10−4 s−1 at 573 K and 3 bar. This work provides a universal strategy to design dual active sites on metal oxide materials and offers new insights into the effective conversion of methane and formaldehyde to desired C2 chemicals.

Design of SA-FLP Dual Active Sites for Nonoxidative Coupling of Methane

Direct conversion of methane to value-added chemical products under nonoxidative conditions is one of the most effective routes but still faces eminent challenges due to thermodynamic constraints and the lack of efficient catalysts. Herein, we propose to construct “Single-Atom”-“Frustrated Lewis Pair” (SA-FLP) dual-active-site catalysts for nonoxidative coupling of methane (NOCM). The single-atom site is created by doping a Pt atom at the Ce site of the CeO2 surface. The FLP site is fabricated by removing oxygen atom(s) adjacent to Pt atoms. Density functional theory (DFT) calculations reveal that SA-FLP dual active sites can simultaneously activate two methane molecules and notably enhance the coupling of hydrocarbon species to generate C2 products. The SA-FLP sites with two oxygen vacancies show the best performance for methane activation with a low energy barrier of 0.32 and 0.71 eV at SA and FLP sites, respectively. The coupling of two methyl groups to further generate ethane and ethylene only needs to surpass the highest barrier of 1.31 eV. Microkinetic analysis demonstrates that on the designed SA-FLP sites, CH4 consumption can reach a high turnover frequency (TOF) of 0.3014 s–1 under the conditions of 1200 K and a CH3 partial pressure of 8.0 × 10–3 bar, which is nearly two orders of magnitude higher than the experimentally reported value (3.8 ∼ 5.5 × 10–3 s–1) on traditional Pt/CeO2 catalysts. Importantly, the main product on the SA-FLP sites is shown to be the desired ethane with a TOF of 0.2535 s–1 under the conditions mentioned above. This study not only provides a strategy for designing efficient catalysts for NOCM but also offers insights into C–C coupling to generate oriented C2 products.

Design of Single-Atom and Frustrated-Lewis-Pair dual active sites for direct conversion of CH4 and CO2 to acetic acid

Direct conversion of CH4 and CO2 into acetic acid is an emerging attractive process but remains a significant challenge due to the inherent stability of both molecules. Hence, developing active and stable catalysts is crucial for the simultaneous activation of CO2 and CH4. Herein, we designed the “Single-Atom” - “Frustrated-Lewis-Pair” (SA-FLP) dual-active-site catalysts for the co-conversion of CH4 and CO2 to acetic acid based on density functional theory (DFT) calculations. The SA sites were introduced by doping the transition-metal (TM) atoms (TM = Fe, Co, Ni, Cu; Ru, Rh, Pd, Ag; Os, Ir, Pt, Au) into CeO2(110) surface, and the FLP sites were constructed by the regulation of surface oxygen vacancies. Our results demonstrate the introduction of SA into CeO2 surface could facilitate the formation of oxygen vacancies, and thus promotes the formation of FLP sites. The SA-FLP dual active sites can concurrently activate CH4 and CO2 with CH4 preferentially activated at SA sites and CO2 preferentially activated at FLP sites. Among the twelve SA-FLP catalysts, Ag1-FLP catalyst exhibits the best performance in the reaction of CH4 and CO2 to acetic acid with a rate-determining barrier of 1.12 eV and a turnover frequency of 2.52 × 10–3 s−1 at 573 K and 2 bar. This work not only offers a novel catalyst prototype for the co-conversion of CH4 and CO2 to acetic acid but also provides insights into developing dual-active-site catalysts on earth-abundant metal oxide materials.

A Pipeline for the Rapid Production and Dissemination of Mouse Intersectional Genetic Alleles for Functional, Molecular, and Anatomical Neural Circuit Mapping. (mouseintersectionalgenetics.org)

Here we describe an effort to build and distribute a community library, based on public input, of more than 100 mouse intersectional genetic alleles to facilitate developmental, anatomical, molecular, and functional characterizations of neural circuit organization in behavior and physiology. Even within narrowly defined cell types, significant diversity is found at multiple levels including genetic and molecular signatures, activity patterns, and synaptic connectivity. Current challenges now center on tools to identify, access, and study cell populations with increasing precision. Intersectional genetics offers exceptionally high resolution to consistently delineate distinct cell types in the embryo and adult mouse for functional, molecular and anatomical studies. Intersectional genetics utilizes a ubiquitously expressed conditional allele that is activated by Cre and Flp site specific recombinases. Upon activation, the intersectional genetic alleles may express any number of Genetically Encodable Effector Molecules (GEEMS), such as channelrhodopsins for neural activity perturbations or an L10‐GFP ribotrap fusion to affinity purify translating mRNAs. The intersectional allele is activated by overlapping expression of both Flp and Cre recombinases in the same cell. Traditionally, these recombinases have been deployed as gene knock‐in or transgenic alleles that are designed to express in a cell or gene specific fashion. The use of two selectors (Cre and Flp) to define a cellular population enables high specificity and modularity in combining any set of Cre, Flp, and intersectional alleles to fit an experiment. The number of Cre and Flp recombinase mouse lines are constantly growing, giving greater access to increasing numbers of cell types. Additionally, these recombinases are the focus of multiple efforts to deploy them in ways that select cells based on other unique properties such as neuronal activity and synaptic connectivity. To make this powerful genetic approach more accessible to as many research laboratories as possible, we are building a production pipeline to create a suite of resources for anyone to easily make their own intersectional mouse line, to produce over 100 targeted ES cell lines that can be developed into mouse lines, as well as 10–15 high demand mouse lines all for public distribution. Priority for the GEEMS to be intersectionally deployed will be based on a public input collected at mouseintersectionalgenetics.org. All plasmids, cell lines, and mouse lines developed under this effort will be distributed without restriction to non‐profit research organizations (Addgene and Mutant Mouse Resource and Research Center; MMRRC).Support or Funding InformationR21OD025327Figure 1

A Publicly Guided Effort to Rapidly Produce and Disseminate 100 Intersectional Genetic Alleles for the Study of Nervous System Circuit Development and Function in the Mouse

The goal of this project is to build and distribute a community library of more than 100 mouse intersectional genetic alleles to facilitate the developmental, anatomical, molecular, and functional characterization of neural circuit organization in behavior and physiology based on public input. Even within narrowly defined cell types, significant diversity is found at multiple levels including genetic and molecular signatures, activity patterns, and synaptic connectivity. Current challenges now center on tools to identify, access, and study cell populations with increasing precision. Intersectional genetics offers exceptionally high resolution to consistently delineate distinct cell types in the embryo and adult mouse for functional, molecular and anatomical studies. Intersectional genetics utilizes a ubiquitously expressed conditional allele that is activated by Cre and Flp site specific recombinases. Upon activation, the intersectional genetic alleles may express any number of Genetically Encodable Effector Molecules (GEEMS), such as channelrhodopsins for neural activity perturbations or an L10‐GFP ribotrap fusion to affinity purify translating mRNAs. The intersectional allele is activated by overlapping expression of both Flp and Cre recombinases in the same cell. Traditionally, these recombinases have been deployed as gene knock‐in or transgenic alleles that are designed to express in a cell or gene specific fashion. The use of two selectors (Cre and Flp) to define a cellular population enables high specificity and modularity in combining any set of Cre, Flp and intersectional alleles to fit an experiment. The number of Cre and Flp recombinase mouse lines are constantly growing, giving greater access to increasing numbers of cell types. Additionally, these recombinases are the focus of multiple efforts to deploy them in ways that select cells based on other unique properties such as neuronal activity and synaptic connectivity. To make this powerful genetic approach more accessible to as many research laboratories as possible, we are building a production pipeline to create a suite of resources for anyone to easily make their own intersectional mouse line, to produce over 100 targeted ES cell lines that can be developed into mouse lines, as well as 10–15 high demand mouse lines all for public distribution. Priority for the GEEMS to be intersectionally deployed will be based on a public input collected at mouseintersectionalgenetics.org. All plasmids, cell lines and mouse lines developed under this effort will be distributed without restriction to non‐profit research organizations.Support or Funding InformationMcNair Medical InstituteR01HL130249R01HL130249‐02S1This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Hydrogen activation enabled by the interfacial frustrated Lewis pairs on cobalt borate nanosheets

Precisely controlling the surface physicochemical properties of a solid is critical to construct novel catalytic sites for various heterogeneous catalytic reactions. Herein, the interfacial frustrated Lewis pairs on cobalt borate (CoBOx) nanosheets are constructed by the surface hydroxyl on the top of one surface Co atom as the independent Lewis basic site and adjacent interfacial cobalt ion as the independent Lewis acidic site, enabling the efficient hydrogen activation as well as subsequent hydrogenation activity. Theoretical calculations and isotope experiments show that such a FLP site triggers the heterolytic hydrogen dissociation with a low activation energy of 0.37 eV. The catalytic performance, computational results, kinetic analysis and in-situ Fourier transform infrared spectroscopy profiles indicate the abundance of the surface hydroxyl on the top of the surface Co atom is the key for the construction of the interfacial FLP sites and subsequent hydrogen activation on those sites. Such a strategy provides a feasible approach to design the heterogenized FLP catalysts by controlling the interfacial physicochemical properties in term of the surface hydroxyl groups.

The NDUFB6 subunit of the mitochondrial respiratory chain complex I is required for electron transfer activity: A proof of principle study on stable and controlled RNA interference in human cell lines

Molecular bases of inherited deficiencies of mitochondrial respiratory chain complex I are still unknown in a high proportion of patients. Among 45 subunits making up this large complex, more than half has unknown function(s). Understanding the function of these subunits would contribute to our knowledge on mitochondrial physiology but might also reveal that some of these subunits are not required for the catalytic activity of the complex. A direct consequence of this finding would be the reduction of the number of candidate genes to be sequenced in patients with decreased complex I activity. In this study, we tested two different methods to stably extinct complex I subunits in cultured cells. We first found that lentivirus-mediated shRNA expression frequently resulted in the unpredicted extinction of additional gene(s) beside targeted ones. This can be ascribed to uncontrolled genetic material insertions in the genome of the host cell. This approach thus appeared inappropriate to study unknown functions of a gene. Next, we found it possible to specifically extinct a CI subunit gene by direct insertion of a miR targeting CI subunits in a Flp site (HEK293 Flp-In cells). By using this strategy we unambiguously demonstrated that the NDUFB6 subunit is required for complex I activity, and defined conditions suitable to undertake a systematic and stable extinction of the different supernumerary subunits in human cells.

Characterization of the Lactococcus lactis transcription factor FlpA and demonstration of an in vitro switch.

The commercially important bacterium Lactococcus lactis contains two FNR-like proteins (FlpA and FlpB) which have a high degree of identity to each other and to the FLP of Lactobacillus casei. FlpA was isolated from a GST-FlpA fusion protein produced in Escherichia coli. Like FLP, isolated FlpA is a homodimeric protein containing both Zn and Cu. However, the properties of FlpA were more like those of the E. coli oxygen-responsive transcription factor FNR than the FLP of L. casei. As prepared FlpA recognized an FNR site (TTGAT-N4-ATCAA) but not an FLP site (CCTGA-N4-TCAGG) in band-shift assays. In contrast to FLP, DNA binding by FlpA did not require the formation of an intramolecular disulphide bond. However, despite containing only two cysteine residues per monomer, FlpA was able to acquire an FNR-like, oxygen-labile [4Fe 4S] cluster. But, whereas the incorporation of a [4Fe 4S] cluster into FNR enhances interaction with target DNA, it abolished DNA binding by FlpA. An FlpA variant (FlpA') with an N-terminal region designed to be more FLP-like failed to incorporate an iron-sulphur cluster but could now form an intramolecular disulphide. This simple example of protein engineering, converting an oxygen-labile [4Fe 4S] containing FNR-like protein into a dithiol-disulphide FLP-like redox sensor demonstrates the versatility of the basic CRP structure. Attempts to demonstrate an FlpA-based aerobic-anaerobic switch in the heterologous host E. coli were unsuccessful. However, studies with a series of FNR-dependent lac reporter fusions in strains of E. coli expressing flpA or flpB revealed that both homologues were able to activate expression of FNR-dependent promoters in vivo but only when positioned 61 base pairs upstream of the transcription start.

A novel regulatory switch mediated by the FNR-like protein of Lactobacillus casei.

FNR (regulator for fumarate and nitrate reduction) and CRP (cAMP receptor protein) are global regulators which regulate the transcription of overlapping modulons of target genes in response to anaerobiosis and carbon source in Escherichia coli. An ORF, designated flp because it encodes an FNR-like protein of the FNR-CRP family, has been found in Lactobacillus casei. The product of the flp coding region (FLP) was overproduced in E. coli, purified and crystallized. FLP is a homodimeric protein in which each subunit can form an intramolecular disulphide bond. The isolated protein also contains non-stoichiometric amounts of Cu and Zn. Although the DNA recognition helix of FLP resembles that of FNR, the flp gene failed to complement the anaerobic respiratory deficiency of an fnr mutant when expressed in E. coli and it neither activated nor interfered with transcription from FNR- or CRP-dependent promoters in E. coli. Site-specific DNA binding by oxidized FLP (the form containing intrasubunit disulphide bonds) was abolished by reduction. The interconversion between disulphide and dithiol forms thus provides the basis for a novel redox-mediated transcriptional switch. Two non-identical FLP-binding sites, distinct from FNR- and CRP-binding sites, were identified in the meIR region of E. coli by gel-retardation analysis. A further eight FLP-binding sites were selected from a random library. A synthetic oligonucleotide conforming to a putative FLP site consensus, CA/CTGA-N4-TCAG/TG (the most significant bases are underlined), was retarded by FLP. Functional tests showed that FLP represses the aerobic transcription of a semi-synthetic promoter in E. coli. A C5S variant of FLP lacking the ability to form intramolecular disulphide bonds was unable to bind to FLP sites and failed to repress transcription in vivo.

Tyr60 variants of Flp recombinase generate conformationally altered protein-DNA complexes: Differential activity in full-site and half-site recombinations

The tyrosine at position 60 of the Flp recombinase of the Saccharomyces cerevisiae plasmid, 2 μ circle, is invariant among site-specific recombinases of the “yeast plasmid family”. Alterations of this residue give rise to Flp variants that show no recombination activity when assayed in vivo in Escherichia coli. Upon purification, they bind substrate, execute DNA cleavage and catalyze recombination. The efficiency of strand cleavage follows the order: Flp(Y60F) > Flp > Flp(Y60S) > Flp(Y60D); efficiency of recombination between Flp sites on a linear substrate and a circular one follows the order: Flp > Flp(Y60F) > Flp(Y60S) > Flp(Y60D). Methylation footprints of the DNA-protein complexes formed by two of the Flp variants, Flp(Y60S) and Flp(Y60D), do not show hypermethylation of the G residues within the substrate core that is characteristic of complexes formed by wild-type Flp. The third variant, Flp(Y60F), causes significant distortion (although less than wildtype Flp) of the substrate core, as indicated by enhanced G-methylation. Binding profiles with circularly permuted substrates indicate that Flp(Y60S) and Flp(Y60D), but not Flp(Y60F), are defective in bending substrate DNA. In recombination between two Flp half-sites, the variant proteins are significantly more active than in normal full-site recombination.

The mechanism of loading of the FLP recombinase onto its DNA target sequence

The FLP recombinase interacts with its target sequence with the formation of three distinct DNA-protein complexes. The first complex leaves neither a DNase footprint nor is the DNA protected from methylation by dimethyl sulfate. We have found, however, that the FLP protein is bound predominantly to only one of the three 13 base-pair (bp) symmetry elements. This asymmetric loading of the FLP site seems to require the presence of an adjacent directly repeated 13 bp element. We speculate that this asymmetric filling of the target site may be accompanied by the unique order of cleavage and exchange of DNA strands.

Mutations that improve the binding of yeast FLP recombinase to its substrate.

When yeast FLP recombinase is expressed from the phage lambda PR promoter in a Salmonella host, it cannot efficiently repress an operon controlled by an operator/promoter region that includes a synthetic, target FLP site. On the basis of this phenotype, we have identified four mutant FLP proteins that function as more efficient repressors of such an operon. At least two of these mutant FLP proteins bind better to the FLP site in vivo and in vitro. One mutant changes the presumed active site tyrosine residue of FLP protein to phenylalanine, is blocked in recombination, and binds the FLP site about five-fold better than the wild-type protein. A second mutant protein that functions as a more efficient repressor retains catalytic activity. We conclude that the eukaryotic yeast FLP recombinase, when expressed in a heterologous prokaryotic host, can function as a repressor, and that mutant FLP proteins that bind DNA more tightly may be selected as more efficient repressors.

Mating type-like conversion promoted by the 2 micrograms circle site-specific recombinase: implications for the double-strand-gap repair model.

Double-strand breaks in DNA are known to promote recombination in Saccharomyces cerevisiae. Yeast mating type switching, which is a highly efficient gene conversion event, is apparently initiated by a site-specific double-strand break. The 2 micrograms circle site-specific recombinase, FLP, has been shown to make double-strand breaks in its substrate DNA. By using a hybrid 2 micrograms circle::Tn5 plasmid, a portion of which resembles, in its DNA organization, the active (MAT) and the silent (HML) yeast mating type loci, it is shown that FLP mediates a conversion event analogous to mating type switching. Whereas the FLP site-specific recombination is not dependent on the RAD52 gene product, the FLP-induced conversion is abolished in a rad52 background. The FLP-promoted conversion in vivo can be faithfully reproduced by making a double-stranded gap in vitro in the vicinity of the FLP site and allowing the gap to be repaired in vivo.

Mating type-like conversion promoted by the 2 micrograms circle site-specific recombinase: implications for the double-strand-gap repair model.

Double-strand breaks in DNA are known to promote recombination in Saccharomyces cerevisiae. Yeast mating type switching, which is a highly efficient gene conversion event, is apparently initiated by a site-specific double-strand break. The 2 micrograms circle site-specific recombinase, FLP, has been shown to make double-strand breaks in its substrate DNA. By using a hybrid 2 micrograms circle::Tn5 plasmid, a portion of which resembles, in its DNA organization, the active (MAT) and the silent (HML) yeast mating type loci, it is shown that FLP mediates a conversion event analogous to mating type switching. Whereas the FLP site-specific recombination is not dependent on the RAD52 gene product, the FLP-induced conversion is abolished in a rad52 background. The FLP-promoted conversion in vivo can be faithfully reproduced by making a double-stranded gap in vitro in the vicinity of the FLP site and allowing the gap to be repaired in vivo.

The minimal duplex DNA sequence required for site-specific recombination promoted by the FLP protein of yeast in vitro.

The 2-micron plasmid of the yeast Saccharomyces cerevisiae codes for a site-specific recombinase ('FLP') that efficiently catalyses recombination across the plasmid's two 599 bp repeats both in vivo and in vitro. We have used the partially purified FLP protein to define the minimal duplex DNA sequence required for intra- and intermolecular recombination in vitro. Previous DNase footprinting experiments had shown that FLP protected 50 bp of DNA around the recombination site. We made BAL31 deletions and synthetic FLP sites to show that the minimal length of the site that was able to recombine with a wild-type site was 22 bp. The site consists of two 7 bp inverted repeats surrounding an 8 bp core region. We also showed that the deleted sites recombined with themselves and that one of three 13 bp repeated elements within the FLP target sequence was not necessary for efficient recombination in vitro. Mutants lacking this redundant 13 bp element required a lower amount of FLP recombinase to achieve maximal yield of recombination than the wild type site. Finally, we discuss the structure of the FLP site in relation to the proposed function of FLP recombination in copy number amplification of the 2-micron plasmid in vivo.

The FLP recombinase of the Saccharomyces cerevisiae 2 microns plasmid attaches covalently to DNA via a phosphotyrosyl linkage.

The FLP recombinase, encoded by the 2 micron plasmid of Saccharomyces cerevisiae, promotes efficient recombination in vivo and in vitro between its specific target sites (FLP sites). It was previously determined that FLP interacts with DNA sequences within its target site (B. J. Andrews, G. A. Proteau, L. G. Beatty, and P. D. Sadowski. Cell 40:795-803, 1985), generates a single-stranded break on both DNA strands within the FLP site, and remains covalently attached to the 3' end of each break. We now show that the FLP protein is bound to the 3' side of each break by an O-phosphotyrosyl residue and that it appears that the same tyrosyl residue(s) is used to attach to either DNA strand within the FLP site.

The FLP Recombinase of the Saccharomyces cerevisiae 2μm Plasmid Attaches Covalently to DNA via a Phosphotyrosyl Linkage

The FLP recombinase, encoded by the 2 micron plasmid of Saccharomyces cerevisiae, promotes efficient recombination in vivo and in vitro between its specific target sites (FLP sites). It was previously determined that FLP interacts with DNA sequences within its target site (B. J. Andrews, G. A. Proteau, L. G. Beatty, and P. D. Sadowski. Cell 40:795-803, 1985), generates a single-stranded break on both DNA strands within the FLP site, and remains covalently attached to the 3' end of each break. We now show that the FLP protein is bound to the 3' side of each break by an O-phosphotyrosyl residue and that it appears that the same tyrosyl residue(s) is used to attach to either DNA strand within the FLP site.

Determination of DNA sequences essential for FLP-mediated recombination by a novel method.

The yeast 2-micron circle plasmid encodes a protein, FLP, that mediates site-specific recombination across the two FLP-binding sites of the plasmid. We have used a novel technique, "exonuclease-treated substrate analysis," to determine the minimal duplex DNA sequence needed for this recombination event. A linear DNA containing two FLP sites in a direct orientation was treated with the double-strand specific 3'-exonuclease, exonuclease III, to generate molecules with a nested set of single-strand deletions that extended into one of the FLP sites. The DNA was then end-labeled at the sites of the deletions and used as a substrate for recombination in vitro. FLP-mediated recombination between two FLP sites excised a restriction endonuclease cleavage site from the DNA. Comparison of the fragments produced by restriction enzyme digestion of untreated and FLP-treated DNA showed to the nucleotide the duplex DNA sequence required for FLP-mediated recombination. To examine essential sequences in the opposite DNA strand, similar experiments were done using the 5'-exonuclease encoded by phage T7. The minimal essential duplex DNA sequence lies within the region of the FLP site that was previously shown to be protected from nuclease digestion in the presence of FLP. A modified form of this technique can be used to study the minimal sequence requirements of site-specific DNA binding proteins.

Two-micrometer circle site-specific recombination: the minimal substrate and the possible role of flanking sequences.

The 2-mum circle DNA of yeast encodes a site-specific recombination system (FLP recombination). The recombination region had been mapped earlier to a 65-base-pair (bp) segment within the 599-bp-long inverted repeats of the molecule. I have shown that the "minimal" FLP substrate resides in a 13-bp dyad symmetry plus an 8-bp core located within the 65-bp recombination region. Further, as determined by different in vivo assays, sequences extraneous to the minimal FLP site and the 65-bp recombination region can affect the efficiency of the recombination reaction.