Dibenzothiophene biodesulfurization pathway improvement using diagnostic GFP fusions

The dibenzothiophene biodesulfurization pathway has shown significant potential for improving the processing of sulfur-containing fossil fuels. However, the rate of desulfurization is limited by the last enzyme in the pathway, DszB. Genetic constructs designed to produce increased DszB activity were not functional due to low production of DszB, even when using a consensus ribosome binding site. To increase DszB production, the untranslated region 5' of dszB was mutated using degenerate oligonucleotides and translational fusions with gfp to detect increased translation of dszB. After screening only 96 mutants, several showed increased green fluorescence and two showed increased DszB activity. When cotransformed with the full dszABC operon, the mutant dszB increased the rate of desulfurization ninefold relative to that using the native dszB.     

A scalable, GFP-based pipeline for membrane protein overexpression screening and purification

We describe a generic, GFP-based pipeline for membrane protein overexpression and purification in Escherichia coli. We exemplify the use of the pipeline by the identification and characterization of E. coli YedZ, a new, membrane-integral flavocytochrome. The approach is scalable and suitable for high-throughput applications. The GFP-based pipeline will facilitate the characterization of the E. coli membrane proteome and serves as an important reference for the characterization of other membrane proteomes.     

New transposons to generate GFP protein fusions in Candida albicans

Transposon elements are important tools for gene function analysis, for example they can be used to easily create genome-wide collections of insertion mutants. Transposons may also carry sequences coding for an epitope or fluorescent marker useful for protein expression and localization analysis. We have developed three new Tn5-based transposons that incorporate a GFP (green fluorescent protein) coding sequence to generate fusion proteins in the important fungal pathogen Candida albicans. Each transposon also contains the URA3 and Kan(R) genes for yeast and bacterial selection, respectively. After in vitro transposition, the insertional allele is transferred to the chromosomal locus by homologous recombination. Transposons Tn5-CaGFP and Tn5-CaGFP-URA3::FLIP can generate C-terminal truncated GFP fusions. A URA3 flipper recycling cassette was incorporated into the transposon Tn5-CaGFP-URA3::FLIP. After the induction of Flip recombinase to excise the marker, the heterozygous strain is transformed again in order to obtain a GFP-tagged homozygous strains. In the Tn5-CaGFP-FL transposon the markers are flanked by a rare-cutting enzyme. After in vitro transposition into a plasmid-borne target gene, the markers are eliminated by restriction digestion and religation, resulting in a construct coding for full-length GFP-fusion proteins. This transposon can generate plasmid libraries of GFP insertions in proteins where N- or C-terminal tagging may alter localization. We tested our transposon system by mutagenizing the essential septin CDC3 gene. The results indicate that the Cdc3 C-terminal extension is important for correct septin filament assembly. The transposons described here provide a new system to obtain global gene expression and protein localization data in C. albicans.     

Creating precise GFP fusions in plasmids using yeast homologous recombination

Using a combination of primer amplification, homologous recombination, and yeast genetics, we established a method for creating precise promoter and protein fusions in genes originating from organisms other than yeast. One major advantage of this new method is its versatility. Fusions can be produced within a target gene without constraints regarding the site of insertion. Thus, fusions can be generated within a target sequence exactly at the site desired, and all sequences upstream and downstream of the insertion site were preserved. To illustrate the general applicability of this technique, we fused the gene encoding GFP to a Caenorhabditis elegans homologue of the dishevelled gene, dsh-2. This approach is not restricted to GFP fusions but can be utilized to create fusions between almost any two sequences regardless of the source. Therefore, this method provides a flexible alternative to other PCR-mediated techniques.     

Overproduction and purification of the Tn10-specified inner membrane tetracycline resistance protein Tet using fusions to β-galactosidase

Tetracycline resistance in the Enterobacteriaceae is mediated by a number of genetically related, usually plasmid-borne, determinants which specify an efflux system involving an inner membrane protein, Tet. Attempts to overproduce the Tn10 (Class B)-encoded Tet in Escherichia coli by cloning the structural gene tet downstream of the lambda PL promoter under regulation by temperature-sensitive lambda repressor cI857 were unsuccessful; induction at 42 degrees C resulted in filamentous, non-viable cells containing little detectable overproduction of the protein. However, cells containing tet fused to lacZ were resistant to tetracycline at 30 degrees C and synthesized modest amounts of a large fusion protein when induced at 42 degrees C. Fusion of the N-terminal half or the first 38 amino acids of tet to lacZ did lead to increased production of fusion proteins. Fusions could be purified by size or by LacZ immunoaffinity or substrate-affinity chromatography. In the latter method, selected detergents were required to counteract nonspecific binding of Tet to the adsorbant. Amino acid sequencing of the N-terminus of Tet-LacZ fusion proteins indicated that most molecules were blocked at this terminus. The sequence of an unblocked subpopulation was consistent with that expected from the nucleotide sequence. A collagen peptide linker, genetically placed between tet and lacZ, allowed recovery of purified Tet protein after collagenase treatment of the purified fusion protein.     

Rationalizing membrane protein overexpression

Functional and structural studies of membrane proteins usually require overexpression of the proteins in question. Often, however, the 'trial and error' approaches that are mainly used to produce membrane proteins are not successful. Our rapidly increasing understanding of membrane protein insertion, folding and degradation means that membrane protein overexpression can be more rationalized, both at the level of the overexpression host and the overexpressed membrane protein. This change of mindset is likely to have a significant impact on membrane protein research.     

Decoding signals for membrane protein assembly using alkaline phosphatase fusions.

We have used genetic methods to investigate the role of the different domains of a bacterial cytoplasmic membrane protein, MalF, in determining its topology. This was done by analyzing the effects of MalF topology of deleting various domains of the protein using MalF-alkaline phosphatase fusion proteins. Our results show that the cytoplasmic domains of the protein are the pre-eminent topogenic signals. These domains contain information that determines their cytoplasmic location and, thus, the orientation of the membrane spanning segments surrounding them. Periplasmic domains do not appear to have equivalent information specifying their location and membrane spanning segments do not contain information defining their orientation in the membrane. The strength of cytoplasmic domains as topogenic signals varies, correlated with the density of positively charged amino acids within them.     

A systematic assessment of mature MBP in membrane protein production: overexpression, membrane targeting and purification

Obtaining enough membrane protein in native or native-like status is still a challenge in membrane protein structure biology. Maltose binding protein (MBP) has been widely used as a fusion partner in improving membrane protein production. In the present work, a systematic assessment on the application of mature MBP (mMBP) for membrane protein overexpression and purification was performed on 42 membrane proteins, most of which showed no or poor expression level in membrane fraction fused with an N-terminal Histag. It was found that most of the small membrane proteins were overexpressed in the native membrane of Escherichia coli when using mMBP. In addition, the proteolysis of the fusions were performed on the membrane without solubilization with detergents, leading to the development of an efficient protocol to directly purify the target membrane proteins from the membrane fraction through a one-step affinity chromatography. Our results indicated that mMBP is an excellent fusion partner for overexpression, membrane targeting and purification of small membrane proteins. The present expression and purification method may be a good solution for the large scale preparation of small membrane proteins in structural and functional studies.     

Fast and efficient protein purification using membrane adsorber systems

The purification of proteins from complex cell culture samples is an essential step in proteomic research. Traditional chromatographic methods often require several steps resulting in time consuming and costly procedures. In contrast, protein purification via membrane adsorbers offers the advantage of fast and gentle but still effective isolation. In this work, we present a new method for purification of proteins from crude cell extracts via membrane adsorber based devices. This isolation procedure utilises the membranes favourable pore structure allowing high flow rates without causing high back pressure. Therefore, shear stress to fragile structures is avoided. In addition, mass transfer takes place through convection rather than diffusion, thus allowing very rapid separation processes. Based on this membrane adsorber technology the separation of two model proteins, human serum albumin (HSA) and immungluboline G (IgG) is shown. The isolation of human growth hormone (hGH) from chinese hamster ovary (CHO) cell culture supernatant was performed using a cation exchange membrane. The isolation of the enzyme penicillin acylase from the crude Escherichia coli supernatant was achieved using an anion exchange spin column within one step at a considerable purity. In summary, the membrane adsorber devices have proven to be suitable tools for the purification of proteins from different complex cell culture samples.     

The purification of recombinant proteins using C-terminal polyarginine fusions

Protein engineering was used to produce urogastrone with a polyarginine fusion. This fusion protein was designed to facilitate purification and illustrates a new approach to protein purification with considerable advantages over conventional techniques.     

Topology-informed strategies for the overexpression and purification of membrane proteins

Membrane proteins represent a significant fraction of all genomes and play key roles in many aspects of biology, but their structural analysis has been hampered by difficulties in large-scale production and crystallisation. To overcome the first of these hurdles, we present here a systematic approach for expression and affinity-tagging which takes into account transmembrane topology. Using a set of bacterial transporters with known topologies, we tested the efficacy of a panel of conventional and Gateway? recombinational cloning vectors designed for protein expression under the control of the tac promoter, and for the addition of differing N- and C-terminal affinity tags. For transporters in which both termini are cytoplasmic, C-terminal oligohistidine tagging by recombinational cloning typically yielded functional protein at levels equivalent to or greater than those achieved by conventional cloning. In contrast, it was not effective for examples of the substantial minority of proteins that have one or both termini located on the periplasmic side of the membrane, possibly because of impairment of membrane insertion by the tag and/or att-site-encoded sequences. However, fusion either of an oligohistidine tag to cytoplasmic (but not periplasmic) termini, or of a Strep-tag II peptide to periplasmic termini using conventional cloning vectors did not interfere with membrane insertion, enabling high-level expression of such proteins. In conjunction with use of a C-terminal Lumio? fluorescence tag, which we found to be compatible with both periplasmic and cytoplasmic locations, these findings offer a system for strategic planning of construct design for high throughput expression of membrane proteins for structural genomics projects.     

Topology-informed strategies for the overexpression and purification of membrane proteins

Membrane proteins represent a significant fraction of all genomes and play key roles in many aspects of biology, but their structural analysis has been hampered by difficulties in large-scale production and crystallisation. To overcome the first of these hurdles, we present here a systematic approach for expression and affinity-tagging which takes into account transmembrane topology. Using a set of bacterial transporters with known topologies, we tested the efficacy of a panel of conventional and Gateway recombinational cloning vectors designed for protein expression under the control of the tac promoter, and for the addition of differing N- and C-terminal affinity tags. For transporters in which both termini are cytoplasmic, C-terminal oligohistidine tagging by recombinational cloning typically yielded functional protein at levels equivalent to or greater than those achieved by conventional cloning. In contrast, it was not effective for examples of the substantial minority of proteins that have one or both termini located on the periplasmic side of the membrane, possibly because of impairment of membrane insertion by the tag and/or att-site-encoded sequences. However, fusion either of an oligohistidine tag to cytoplasmic (but not periplasmic) termini, or of a Strep-tag II peptide to periplasmic termini using conventional cloning vectors did not interfere with membrane insertion, enabling high-level expression of such proteins. In conjunction with use of a C-terminal Lumio fluorescence tag, which we found to be compatible with both periplasmic and cytoplasmic locations, these findings offer a system for strategic planning of construct design for high throughput expression of membrane proteins for structural genomics projects.     

重组N-乙酰鸟氨酸脱乙酰基酶的高效表达与纯化

利用质粒pET-22b( )为表达载体,成功构建了高效表达N-乙酰鸟氨酸脱乙酰基酶的基因工程菌BL21-pET-22b( )-argE。研究了该菌的最适超声破壁条件及硫酸铵分级沉淀的最适范围,并以金属螯合亲和层析法纯化含有6-His-Tag的目的蛋白。结果表明:26℃诱导表达的菌体,最佳超声破碎条件为功率200 W,超声时间为15min;目的蛋白主要存在于40%~50%硫酸铵沉淀中。通过Ni-NTA亲和层析柱纯化目的蛋白,可以达到SDS-PAGE电泳纯,并显示单亚基相对分子质量为43 000。纯化倍数为139倍,回收率为11.1%。     

Efficient purification of DNA fragments using a protein binding membrane

A novel and efficient method has been developed for isolation of correctly digested DNA fragments without the use of classic size-dependent electrophoretic separation methods. To achieve this, DNA fragments are end-labelled by haptens. After specific endonuclease digestion of the hapten-labelled DNA, the DNA is incubated with a protein that specifically binds to the hapten. The incubation mixture is then passed through a cartridge containing a protein-binding membrane that does not bind DNA. Undigested and partly digested DNA are retained on the membrane, while correctly digested DNA is selectively recovered for use in further downstream applications.     

Immobilization and affinity purification of recombinant proteins using histidine peptide fusions

A gene fusion approach to simplify protein immobilization and purification is described. A gene encoding the protein of interest is fused to a gene fragment encoding the affinity peptide Ala-His-Gly-His-Arg-Pro. The expressed fusion proteins can be purified using immobilized metal affinity chromatography. A vector, designed to ensure obligate head-to-tail polymerization of oligonucleotide linkers was constructed by in vitro mutagenesis. A linker encoding the affinity peptide, was synthesized and polymerized to two, four and eight copies. These linkers were fused to the 3' end of a structural gene encoding a two-domain protein A molecule, ZZ, and to the 5' end of a gene encoding beta-galactosidase. Fusion proteins, of both types, with zero or two copies of the linker showed little or no binding to immobilized Zn2+, while a relatively strong interaction could be observed for the fusions based on four or eight copies of the linker. Using a pH gradient, the ZZ fusions were found to be eluted from the resin at different pHs depending on the number of the affinity peptide. These results demonstrate that genetic engineering can be used to facilitate purification and immobilization of proteins to immobilized Zn2+ and that the multiplicity of the affinity peptide is an important factor determining the binding characteristics.     

Plasmodesmata transport of GFP and GFP fusions requires little energy and transitions during leaf expansion

Plasmodesmata (Pd) are symplastic channels between neighboring plant cells and are key in plant cell-cell signaling. Viruses of proteins, nucleic acids, and a wide range of signaling macromolecules move across Pd. Protein transport Pd is regulated by development and biotic signals. Recent investigations utilizing the Arrhenius equation or Coefficient of conductivity showed that fundamental energetic measurements used to describe transport of proteins across membrane pores or the nuclear pore can also apply to protein movement across Pd. As leaves continue to expand, Pd transport of proteins declines which may result from changes in cell volume, Pd density or Pd structure.Key words: plasmodesmata, diffusion, GFP, viral transport, PVX, triple gene blockResearchers have argued for the last decade that movement of proteins and other macromolecules across Pd is regulated by development, stress and biotic signals. There are four current models describing different mechanisms of Pd transport. First is the non cell autonomous protein (NCAP) pathway that carries ribonucleoprotein complexes across Pd. NCAPs often carry RNA in a ribonucleoprotein complex to the Pd.^1–4 This mode of transport involved targeted movement, meaning that a set of proteins must dock within the Pd to gate it open to enable transfer between cells. Proteins which are normally too large to move across Pd can gate open Pd to enable its own transfer into neighboring cells. This is contrasted by nontargetted movement, which is passive movement of proteins that are sufficiently small enough to pass between cells.^5,6 The green fluorescent protein (GFP) has been described as a protein whose movement is non-targeted, meaning that it can diffuse across Pd. Reasons that we do not see continuous movement of small proteins between cells include protein compartmentalization or subcellular targeting signals. For example proteins may be synthesized and modified via the ER and Golgi networks and then transferred into vesicles and transported within cells to their destination. These proteins would not be free in the cytosol for diffusion across Pd. Alternatively, proteins which have dominant subcellular targeting signals which direct them to certain organelles such as the nucleus, peroxisome, or other destination would not be free to move across Pd.^5,6 A third model represents proteins in the ER that move laterally along the membrane or through the ER lumen into neighboring cells. This transport is quite rapid and investigations are ongoing to determine how this is regulated.^7–11 Finally, there is vesicle transport which deliver cargo to Pd.^12,13 The origin of these vesicles is still under investigation. Much more research has been accomplished toward defining non-targeted movement and the NCAP pathway while the ER and vesicle transport pathways are only recently described and very little is known about the regulatory mechanisms underlying these pathways.Pd permeability is governed in part by architecture, but also by key regulatory factors that determine Pd conductivity. Factors such as mysoin VIII, actin and calreticulin were identified in Pd which likely regulate expansion and contraction.^14–19 In addition calcium, ATP and plant hormones can downregulate Pd permeability during development and stress.^20,21 The tools for measuring Pd permeability has been to study the transport of fluorescently tagged proteins, fluorescent dextran beads, GFP or GFP fusions following microinjection or biolistic delivery to the cytoplasm of one cell.^22–26 Then video imaging or captured still images at select time intervals are used to characterize Pd transport. Until recently researchers quantified movement by the frequency they observed a certain type of movement. Therefore our ability to describe Pd permeability has been limited.Evidence that ATP impacts Pd conductivity has led investigations to explore the energy requirements for macromolecular transport across Pd. By understanding the energy requirements for transport of various proteins and nucleic acids we can better characterize passive or active transport processes. Toward this end two recent studies detailed quantitative approaches that can be employed to describe the developmental and energy requirements cell-to-cell transport of cytosolic proteins. Both papers used biolistic bombardment to deliver plasmids expressing GFP or GFP fusions to tobacco leaf epidermal cells and then captured still images of GFP fluorescence in neighboring cells. We employed the Arrhenius equation to characterize transport of GFP or GFP fused to the Potato virus X (PVX) TGBp1 movement protein. PVX TGBp1 was selected to compare with GFP alone since it is known to gate open Pd and has ATPase activity.⁴⁵ We predicted that the abilities of GFP alone and GFP-TGBp1 to move across Pd might be different and were surprised to learn that the energy for transport of both proteins was similar. This project established the principle that GFP and GFP-TGBp1 transport is temperature dependent showing a linear relationship between protein movement and the temperatures at which leaves were incubated.Green fluorescent sites on bombarded leaves were scored for the movement or no movement. Movement is defined as evidence of fluorescence in 2 or more cells at 24 h and no movement is when fluorescence is in single cells. These were then presented as a percentage of the total. So by digitizing the representation of movement we were able to represent a linear relationship between movement and temperature. Representing movement in this way also enabled us to represent movement values on a logarithm scale necessary for a classic Arrhenius plot. The activation energy (Ea) was calculated by fitting the data to the Arrhenius equation:% movement = A exp(-Ea/RT); and the Ea for GFP and GFP-TGBp1 was approximately 38 kJ/mol and 29 kJ/mol. These low activation energies are comparable to the reported 30 kJ/mol calculated for temperature dependence of protein transport through the cytosol. Evidence that GFP movement across Pd requires slightly more energy than through the cytoplasm suggests there may be some resistance within the pore. The lower energy for GFP-TGBp1 suggests that movement is facilitated, which likely reflects Pd gating by TGBp1, enabling greater transfer between cells.Liarzi and Epel define a new coefficient of conductivity of Pd.⁴² This study also concluded that cell-to-cell transport of GFP in nontransgenic or transgenic N. benthamiana plants expressing the Tobacco mosaic virus (TMV) movement protein (MP) is temperature dependent. The method was to measure the exponential decay, which is a measure of the impedance to diffusion driven cell-to-cell movement of fluorescence. The exponential decay factor? was determined by calculating the ratio of GFP fluorescence in bombarded cell 0 and neighboring cells. This was presented as a measure of fluorescence transfer from cell 0 to cell 1 to cell 2. A coefficient for conductivity C(Pd), 1/? for GFP was reflective of diffusion. Interestingly the (TMV) MP did not increase conductivity of GFP between neighboring leaf epidermal cells indicating that movement was already maximal. Considering prior reports that the TMV MP shows preferential spread into mesophyll rather than epidermal tissues during virus infection, it is possible that preferential spread into mesophyll cells would prevent experimental efforts to achieve improved conductivity of GFP between epidermal cells.^27,28 In which case the absence of a trans effect of TMV MP on GFP conductivity in the epidermis may not be surprising. In fact, prior investigations of TMV MP gating activities were conducted in mesophyll cells.^29,30 The best explanation for the combined studies is that cytosolic GFP can diffuse across Pd , however viral proteins which gate Pd enable their own low energy transfer into neighboring cells without allowing other proteins to flood into neighboring cells. Therefore viral movement proteins, such as PVX TGBp1 and TMV MP, which gate Pd provide themselves with an energetic advantage for transport into neighboring cells which is essential for rapid dissemination of virus into further tissues.These studies provide an interesting contrast between PVX TGBp1 and TMV MP. Both proteins gate open Pd for virus cell-to-cell transport, but there seems to be differences in how these proteins function in epidermal cells. This is likely due to their different roles in promoting virus cell-to-cell movement. PVX TGBp1 protein is also a suppressor of RNA silencing. We recently proposed a model in which TGBp1 rapidly moves from cell-to-cell ahead of virus infection, to suppress the cell''s RNA degradation machinery, as a means to promote infection.³¹ The TMV MP on the other hand is reported to bind viral RNA for transfer into neighboring cells.^32,33 Therefore, the different observations of PVX TGBp1 and TMV MP transport between epidermal cells likely reflect their functional differences. Both proteins are required for virus cell-to-cell movement, but their exact roles in virus movement are not identical.As mentioned earlier, Pd permeability is downregulated during plant development. Research tracking GFP diffusion through Pd in embryonic cells, in young emerging leaves, and in fully expanded leaves showed that fluorescence is highly mobile between cells in young tissues but is restricted during maturation. Viral movement proteins such as Cucumber mosaic virus 3a, and PVX TGBp1 remain highly mobile in mature leaves because they gate open Pd under conditions that normally restrict movement of GFP.^34,35 Schoenknecht et al., undertook a straightforward investigation of leaf maturation describing Pd transport in relationship to leaf area expansion. The outcome of this study was evidence that GFP movement between cells declines as leaves expand.It is reasonable to consider that simultaneous changes in gene expression and physiology is reflected in a downward trend in Pd conductivity and an increased requirement for Pd gating to enable selected transport of macromolecules between cells. In Arabidopsis embryos there is an obvious transition between developmental stages which are also represented by a decline in the ability for GFP to diffuse across Pd.^36,37 A detailed analysis of Pd structure in source and sink tissues revealed that Pd are simple single channeled structures in sink tissues while source tissues contain predominantly “H” shaped branching Pd structures. The change in Pd structure has been correlated with changes in conductivity and is often correlated with changes in sink to source metabolism.^38,39 The sink-to-source transition in leaf development is typically monitored using phloem loading of carboxyfluorescein diacetate. Leaves where CF dye unloads are defined as sink leaves and leaves that were restricted in dye unloading were defined as source leaves. Then biolistic bombardment of GFP expressing plasmids to sink and source leaves revealed that GFP readily diffuses across Pd in sink leaves but is more often restricted in source leaves.^{26,34,40–42}Leaf development is typically defined as a transition from juvenile to adult which is represented by homeotic transformations as well as vegetative phase changes.^43,44 Source and sink regions of a leaf have been shown to correlate with changes in Pd structure and conductivity during leaf expansion. However, in our study we found that N. tabacum leaves identified as source during week 2 or 3 would continue to expand over an 8 week period to twice or three times the leaf area which provides a real indication that the source designation may not entirely reflect final leaf maturation or completion of leaf development.⁴⁵> For example, as cells transition from sink to source physiology it is suggested that the frequency of single channeled Pd declines while the frequency of branched Pd increases.³⁹ It is possible that even after leaves transition into photosynthetic sources that Pd architecture continues to change and there is a further decline in the proportion of single channel to branched channels. Therefore either the change in cell volume or Pd architecture or both can slow-down diffusion of GFP between cells.Researchers often point to the ER continuity between cells as a driving force for Pd formation and function. During cell division the cell wall is laid down and forms around the ER creating Pd channels.⁴⁶ However, it is also worth noting that the actin cytoskeleton is also present in Pd and is central to organ and reproductive development.^19,47 Actin and actin binding proteins are necessary for a number of plant processes determining the cell division plane, cell polarity, cell elongation, cytoplasmic streaming, transporting mRNAs and proteins, and defense.^48–51 Overexpression of ACT1 in Arabidopsis leaves can lead to changes in epidermal leaf shape and cause dwarfism in plants.⁵² Actin binding proteins are also necessary for organizing and remodeling the F-actin network which drives normal development of specific cell types and organs.⁵³ Actin filament bundling and remodeling are also seen in nonhost defense responses.⁵⁴ We do not know the effects of overexpressing certain actin homologues or actin remodeling on Pd formation or conductivity. Because the F-actin network is also central to Pd trafficking of proteins and macromolecules between cells it is worth considering F-actin as an early factor contributing to Pd formation which may be necessary to ensure cell-to-cell communication when cell polarity and elongation as well as defense machinery are being established.In summary, the novel quantitative tools developed for measuring protein movement across Pd reveal the temperature dependence of protein trafficking. Both the use of Arrhenius equation and C(Pd) provide new opportunities to measure the energy requirements for protein transport. These tools will enable researchers to quantify effects of environmental and developmental conditions on Pd conductivity, as well as comparing differences in Pd conductivity between plant species or induced by genetic mutations.     

Revolutionizing membrane protein overexpression in bacteria

The bacterium Escherichia coli is the most widely used expression host for overexpression trials of membrane proteins. Usually, different strains, culture conditions and expression regimes are screened for to identify the optimal overexpression strategy. However, yields are often not satisfactory, especially for eukaryotic membrane proteins. This has initiated a revolution of membrane protein overexpression in bacteria. Recent studies have shown that it is feasible to (i) engineer or select for E. coli strains with strongly improved membrane protein overexpression characteristics, (ii) use bacteria other than E. coli for the expression of membrane proteins, (iii) engineer or select for membrane protein variants that retain functionality but express better than the wild-type protein, and (iv) express membrane proteins using E. coli-based cell-free systems.     

Tabtoxin-resistant protein: overexpression, purification, and characterization

One of the self-protection mechanisms in Pseudomonas syringae pv. tabaci, a pathogen of tobacco wildfire, is thought to be due to its tabtoxin-resistance gene (ttr). In this study, the ttr gene was inserted into an expression vector, pQE30, and successfully expressed in Escherichia coli M15 at high levels. The purified recombinant tabtoxin-resistant protein (TTR) had an apparent molecular mass of about 21 kDa on SDS-PAGE as well as by mass spectroscopy and had a pI of 6.6 on isoelectric focusing-PAGE. Spectral analysis showed that TTR possesses a maximum fluorescence wavelength (lambda(max)) of 325 nm upon excitation at 282 nm and a positive band with a maximum at 195 nm and a broad negative band with a minimum at 215 nm in the far-UV CD spectrum. The spectrophotometric assay demonstrated the strong detoxification activity of TTR. These results are the first report of the characterization of the purified tabtoxin-resistant protein. Its capacity to detoxify tabtoxinine-beta-lactam shows that it must be one of the self-protection mechanisms in pv. tabaci.     

Optimization of expression and the purification by organic extraction of the integral membrane protein EmrE

EmrE is a member of the small multidrug resistance family of proteins and functions as a efflux transporter of lipophilic cations. This integral membrane protein is composed of 110 amino acids and is very hydrophobic with small loops exposed to the aqueous environment. This protein has been purified in a variety of ways including extraction with chloroform:methanol mixtures. This study explored culture growth and induction conditions, the parameters of organic solvent extraction, running conditions of a lipophilic column for lipid removal, as well as solubilization conditions. Optimal expression and purification protocols are crucial to the characterization goals of this protein. The experiments presented here led to an improvement in the yield of pure EmrE obtained by organic solvent extraction methods at a level of 0.9+/-0.2mg/L of culture. This is on the order of a 60% improvement over previous reports.     

Consequences of membrane protein overexpression in Escherichia coli

Overexpression of membrane proteins is often essential for structural and functional studies, but yields are frequently too low. An understanding of the physiological response to overexpression is needed to improve such yields. Therefore, we analyzed the consequences of overexpression of three different membrane proteins (YidC, YedZ, and LepI) fused to green fluorescent protein (GFP) in the bacterium Escherichia coli and compared this with overexpression of a soluble protein, GST-GFP. Proteomes of total lysates, purified aggregates, and cytoplasmic membranes were analyzed by one- and two-dimensional gel electrophoresis and mass spectrometry complemented with flow cytometry, microscopy, Western blotting, and pulse labeling experiments. Composition and accumulation levels of protein complexes in the cytoplasmic membrane were analyzed with improved two-dimensional blue native PAGE. Overexpression of the three membrane proteins, but not soluble GST-GFP, resulted in accumulation of cytoplasmic aggregates containing the overexpressed proteins, chaperones (DnaK/J and GroEL/S), and soluble proteases (HslUV and ClpXP) as well as many precursors of periplasmic and outer membrane proteins. This was consistent with lowered accumulation levels of secreted proteins in the three membrane protein overexpressors and is likely to be a direct consequence of saturation of the cytoplasmic membrane protein translocation machinery. Importantly accumulation levels of respiratory chain complexes in the cytoplasmic membrane were strongly reduced. Induction of the acetate-phosphotransacetylase pathway for ATP production and a down-regulated tricarboxylic acid cycle indicated the activation of the Arc two-component system, which mediates adaptive responses to changing respiratory states. This study provides a basis for designing rational strategies to improve yields of membrane protein overexpression in E. coli.