Characterisation of the membrane-extrinsic domain of the TatB component of the twin arginine protein translocase

The twin arginine protein transport (Tat) system transports folded proteins across cytoplasmic membranes of bacteria and thylakoid membranes of plants, and in Escherichia coli it comprises TatA, TatB and TatC components. In this study we show that the membrane extrinsic domain of TatB forms parallel contacts with at least one other TatB protein. Truncation of the C-terminal two thirds of TatB still allows complex formation with TatC, although protein transport is severely compromised. We were unable to isolate transport-inactive single codon substitution mutations in tatB suggesting that the precise amino acid sequence of TatB is not critical to its function.

Structured summary

TatAphysically interacts with TatA by two hybrid(View interaction)TatB and TatCbind by molecular sieving(View interaction)TatBphysically interacts with TatB by two hybrid (View Interaction 1, 2)     

Probing binding site of bacteriochlorophyll a and carotenoid in the reconstituted LH1 complex from Rhodospirillum rubrum S1 by Stark spectroscopy

Stark spectroscopy is a powerful technique to investigate the electrostatic interactions between pigments as well as between the pigments and the proteins in photosynthetic pigment–protein complexes. In this study, Stark spectroscopy has been used to determine two nonlinear optical parameters (polarizability change Tr(Δα) and static dipole-moment change |Δμ| upon photoexcitation) of isolated and of reconstituted LH1 complexes from the purple photosynthetic bacterium, Rhodospirillum (Rs.) rubrum. The integral LH1 complex was prepared from Rs. rubrum S1, while the reconstituted complex was assembled by addition of purified carotenoid (all-trans-spirilloxanthin) to the monomeric subunit of LH1 from Rs. rubrum S1. The reconstituted LH1 complex has its Q_y absorption maximum at 878 nm. This is shifted to the blue by 3 nm in comparison to the isolated LH1 complex. The energy transfer efficiency from carotenoid to bacteriochlorophyll a (BChl a), which was determined by fluorescence excitation spectroscopy of the reconstituted LH1 complex, is increased to 40%, while the efficiency in the isolated LH1 complex is only 28%. Based on the differences in the values of Tr(Δα) and |Δμ|, between these two preparations, we can calculate the change in the electric field around the BChl a molecules in the two situations to be E _Δ ≈ 3.4 × 10⁵ [V/cm]. This change can explain the 3 nm wavelength shift of the Q_y absorption band in the reconstituted LH1 complex.     

Recognition of S-RNases by an S locus F-box like protein and an S haplotype-specific F-box like protein in the Prunus-specific self-incompatibility system

Key message

S-RNase was demonstrated to be predominantly recognized by an S locus F-box-like protein and an S haplotype-specific F-box-like protein in compatible pollen tubes of sweet cherry.

Abstract

Self-incompatibility (SI) is a reproductive barrier that rejects self-pollen and inhibits self-fertilization to promote outcrossing. In Solanaceae and Rosaceae, S-RNase-based gametophytic SI (GSI) comprises S-RNase and F-box protein(s) as the pistil and pollen S determinants, respectively. Compatible pollen tubes are assumed to detoxify the internalized cytotoxic S-RNases to maintain growth. S-RNase detoxification is conducted by the Skp1-cullin1-F-box protein complex (SCF) formed by pollen S determinants, S locus F-box proteins (SLFs), in Solanaceae. In Prunus, the general inhibitor (GI), but not pollen S determinant S haplotype-specific F-box protein (SFB), is hypothesized to detoxify S-RNases. Recently, SLF-like proteins 1–3 (SLFL1–3) were suggested as GI candidates, although it is still possible that other proteins function predominantly in GI. To identify the other GI candidates, we isolated four other pollen-expressed SLFL and SFB-like (SFBL) proteins PavSLFL6, PavSLFL7A, PavSFBL1, and PavSFBL2 in sweet cherry. Binding assays with four PavS-RNases indicated that PavSFBL2 bound to PavS^{1, 6}-RNase while the others bound to nothing. PavSFBL2 was confirmed to form an SCF complex in vitro. A co-immunoprecipitation assay using the recombinant PavS⁶-RNase as bait against pollen extracts and a mass spectrometry analysis identified the SCF complex components of PavSLFLs and PavSFBL2, M-locus-encoded glutathione S-transferase (MGST), DnaJ-like protein, and other minor proteins. These results suggest that SLFLs and SFBLs could act as predominant GIs in Prunus-specific S-RNase-based GSI.

     

Coronin7 forms a novel E3 ubiquitin ligase complex to promote the degradation of the anti-proliferative protein Tob

Tob belongs to the anti-proliferative Tob/BTG family. The level of Tob throughout the cell cycle is regulated by the SCF (Skp1/Cullin/F-box protein)^Skp2 ubiquitin ligase (E3) complex. Here, we show that Coronin7 (CRN7) is also involved in Tob degradation. We identified CRN7 as a Tob-interacting molecule. A sequence containing two of the six WD motifs in the middle of CRN7 was responsible for the interaction. CRN7 enhanced the polyubiquitination of Tob in vitro, and overexpression of CRN7 promoted proteasome-dependent degradation of Tob. Furthermore, CRN7 interacted with Cullin1 and Roc1 to form a novel SCF-like E3 complex, suggesting that Tob protein is regulated by multiple ubiquitination machineries.

Structured summary

Cullin1physically interacts with CRN7: shown by anti tag coimmunoprecipitation (view interaction)Roc1physically interacts with CRN7: shown by anti tag coimmunoprecipitation (view interaction)CRN7physically interacts with Tob1: shown by anti tag coimmunoprecipitation (view interaction)CDC34physically interacts with CRN7: shown by anti tag coimmunoprecipitation (view interaction)Tob1 and CRN7colocalize: shown by fluorescence microscopy (view interaction)Elongin Bphysically interacts with CRN7: shown by anti tag coimmunoprecipitation (view interaction)Elongin Cphysically interacts with CRN7: shown by anti tag coimmunoprecipitation (view interaction)Tob1physically interacts with CRN7: shown by two hybrid (view interaction)     

The Escherichia coli metal-binding chaperone SlyD interacts with the large subunit of [NiFe]-hydrogenase 3

The multi-step biosynthesis of the [NiFe]-hydrogenase enzyme involves a variety of accessory proteins. To further understand this process, a Strep-tag II variant of the large subunit of Escherichia coli hydrogenase 3, HycE, was constructed to enable isolation of protein complexes. A complex with SlyD, a chaperone protein implicated in hydrogenase production through association with the nickel-binding accessory protein HypB, was observed. A SlyD–HycE interaction preceding both iron and nickel insertion to the enzyme was detected, mediated by the chaperone domain of SlyD, and independent of HypB. These results support a model of several roles for SlyD during hydrogenase maturation.

Structured summary

HycEphysically interacts with HypA, HypB and SlyD by cross linking study (view interaction)HycEphysically interacts with DnaK and GroEL by cross linking study (view interaction)HypBphysically interacts with SlyD by cross linking study (view interaction)HycEphysically interacts with SlyD by cross linking study (view interaction 1, 2)     

Assembly of Deletion Mutants of the Rieske Iron–Sulfur Protein into the Cytochrome bc 1 Complex of Yeast Mitochondria

The assembly of two deletion mutants of the Rieske iron-sulfur protein into the cytochrome bc ₁ complex was investigated after import in vitro into mitochondria isolated from a strain of yeast, JPJ1, from which the iron-sulfur protein gene (RIP) had been deleted. The assembly process was investigated by immunoprecipitation of the labeled iron-sulfur protein or the two deletion mutants from detergent-solubilized mitochondria with specific antisera against either the iron-sulfur protein or the bc ₁ complex (complex III) [Fu and Beattie (1991). J. Biol. Chem. 266, 16212–16218]. The deletion mutants lacking amino acid residues 55–66 or residues 161–180 were imported into mitochondria in vitro and processed to the mature form via an intermediate form. After import in vitro, the protein lacking residues 161–180 was not assembled into the complex, suggesting that the region of the iron-sulfur protein containing these residues may be involved in the assembly of the protein into the bc ₁ complex; however, the protein lacking residues 55–66 was assembled in vitro into the bc ₁ complex as effectively as the wild type iron-sulfur protein. Moreover, this mutant protein was present in the mitochondrial membrane fraction obtained from JPJ1 cells transformed with a single-copy plasmid containing the gene for this protein lacking residues 55–66. This deletion mutant protein was also assembled into the bc ₁ complex in vivo, suggesting that the hydrophobic stretch of amino acids, residues 55–66, is not required for assembly of the iron-sulfur protein into the bc ₁ complex; however, this association did not lead to enzymatic activity of the bc ₁ complex, as the Rieske FeS cluster was not epr detectable in these mitochondria.     

Stereochemical Analysis of Interaction of Signal Peptide with Phospholipids at the Initiation of Protein Translocation Across the Membrane

Abstract

Stereochemical analysis of signal peptide interaction with E. coli membrane phospholipids revealed the structural complementarity of N-terminus of signal peptide α-helix and acid phospholipids. The formation of their complex leads to neutralization of charges and decrease in hydrophilicity of both components, and promotes insertion of peptide and phospholipid into the membrane, not separately but as a complex. Interaction of acid phospholipids with the E. coli alkaline phosphatase (AP) signal peptide was thoroughly analyzed, and it was shown that in this case a complex of signal peptide α-helix with phosphatidylglycerol is inserted into the membrane with the lowest energy expense. On the basis of the results of stereochemical analysis and the available experimental data, a molecular mechanism of protein translocation initiation across the membrane has been proposed, in which the key events are the formation of the complex “signal peptide α-helix-acid phospholipid”, the coupled insertion of hydrophobic peptide-lipid complex into a nonpolar membrane interior and translocation across the membranes.     

Azocasein assay for alkaline protease in complex fermentation broth

Summary An azocasein assay has been developed for determination of alkaline protease in fermentation broth from a complex substrate containing ca. 50 g/l protein which to a high degree interferes with azocasein. Methods described in the literature have been found inaccurate as results deviate ca. 50% from true activity, so one of the methods is modified in order to eliminate interference. Proportionality between the relative azocasein concentration and the deviation from true activity is found. An azocasein concentration of 350 mg azocasein per ml sample gives satisfactory results with an accuracy of ±5%. Application of a standard addition method also improves the accuracy, but is laborious and less precise.Abbreviations a true enzyme activity - a _s activity determined from standard curve - AU Anson unit - c _A/T relative azocasein concentration (mg azocasein per mg total protein) - r ratio between measured and true enzyme activity - RD relative deviation from true value (%) - RSD relative standard deviation (%) - TCA trichloroacetic acid     

乙酰化修饰降低Ku蛋白的DNA结合活性

【目的】研究乙酰化修饰对Ku蛋白活性的影响。【方法】利用耻垢分枝杆菌为表达菌株,转入Ku蛋白表达质粒,纯化具有乙酰化修饰的Ku蛋白和无乙酰化的Ku蛋白突变体,比较两类蛋白的生化活性;分析氧化压力和酸性环境下耻垢分枝杆菌细胞内Ku蛋白乙酰化水平的变化。【结果】Ku蛋白过量表达的耻垢分枝杆菌比转入空质粒的对照菌株生长缓慢;乙酰化Ku蛋白比未发生乙酰化Ku蛋白修复断裂DNA的活性降低、DNA结合活性降低;氧化压力和酸性压力环境下,耻垢分枝杆菌细胞内Ku蛋白数量降低,乙酰化Ku蛋白数量变化不大。【结论】乙酰化修饰能够调节Ku蛋白的DNA结合活性,从而调节非同源末端连接修复系统的活性;Ku蛋白乙酰化程度升高是耻垢分枝杆菌对不良生长环境的反应。     

Tandem photoaffinity labeling of a target protein using a linker with biotin,alkyne and benzophenone groups and a bioactive small molecule with an azide group

A novel linker containing biotin, alkyne and benzophenone groups (1) was synthesized to identify target proteins using a small molecule probe. This small molecule probe contains an azide group (azide probe) that reacts with an alkyne in 1 via an azide–alkyne Huisgen cycloaddition. Cross-linking of benzophenone to the target protein formed a covalently bound complex consisting of the azide probe and the target protein via 1. The biotin was utilized via biotin–avidin binding to identify the cross-linked complex. To evaluate the effectiveness of 1, it was applied in a model system using an allene oxide synthase (AOS) from the model moss Physcomitrella patens (PpAOS1) and an AOS inhibitor that contained azide group (3). The cross-linked complex consisting of PpAOS1, 1 and 3 was resolved via SDS–PAGE and visualized using a chemiluminescent system. The method that was developed in this study enables the effective identification of target proteins.     

Functional reconstitution and osmoregulatory properties of the ProU ABC transporter from Escherichia coli

Abstract

The ATP-binding cassette (ABC) transporter ProU from Escherichia coli translocates a wide range of compatible solutes and contributes to the regulation of cell volume, which is particularly important when the osmolality of the environment fluctuates. We have purified the components of ProU, i.e., the substrate-binding protein ProX, the nucleotide-binding protein ProV and the transmembrane protein ProW, and reconstituted the full transporter complex in liposomes. We engineered a lipid anchor to ProX for surface tethering of this protein to ProVW-containing proteoliposomes. We show that glycine betaine binds to ProX with high-affinity and is transported via ProXVW in an ATP-dependent manner. The activity ProU is salt and anionic lipid-dependent and mimics the ionic strength-gating of transport of the homologous OpuA system.     

The Structure,Role, and Regulation of Type 1 Protein Phosphatases

Abstract

Type 1 protein phosphatases (PP-1) comprise a group of widely distributed enzymes that specifically dephosphorylate serine and threonine residues of certain phosphoproteins. They all contain an isoform of the same catalytic subunit, which has an extremely conserved primary structure. One of the properties of PP-1 that allows one to distinguish them from other serine/threonine protein phosphatases is their sensitivity to inhibition by two proteins, termed inhibitor 1 and inhibitor 2, or modulator. The latter protein can also form a 1:1 complex with the catalytic subunit that slowly inactivates upon incubation. This complex is reactivated in vitro by incubation with MgATP and protein kinase F_A/GSK-3. In the cell the type 1 catalytic subunit is associated with noncatalytic subunits that determine the activity, the substrate specificity, and the subcellular location of the phosphatase. PP-1 plays an essential role in glycogen metabolism, calcium transport, muscle contraction, intracellular transport, protein synthesis, and cell division. The activity of PP-1 is regulated by hormones like insulin, glucagon, α- and β-adrenergic agonists, glucocorticoids, and thyroid hormones.     

Spin-Labeled Nucleotide Mobility in the Boundary of the EcoRI Endonuclease Binding Site

Abstract

A complex consisting of the EcoRI endonuclease site-specifically bound to spin-labeled DNA 26mers was prepared to provide a model system for studying possible conformational changes resulting from protein binding. EPR was used to monitor the mobility of the spin labels that were strategically placed in position 6, 9, or 11 with respect to the dyad axis of the 26mer. These positions are located within the flanking region on either side of the EcoRI hexamer binding site. This allows the monitoring of potential distal structural changes in the DNA helix caused by protein binding. The spectral line shapes indicate that the spin label closest to the EcoRI endonuclease binding site, i.e., in position 6, is most influenced by the binding event. The EPR data are analyzed according to a model that distinguishes between spectral effects due to a change in the hydrodynamic shape of the complex and those resulting from local variations in the spin-label mobility as characterized by a local order parameter S. S reflecting the motional restriction of the spin-labeled base is 0.20 ± 0.01 for all three oligomers as well as for the two complexes with the label in position 9 or 11, while the position 6 labeled complex yields S=0.25. To further evaluate the origin of the slightly larger EPR effect observed with position 6 labeled material, molecular dynamics (MD) simulations were used to explore the space accessible to the probes in positions 6, 9, and 11. MD results gave similar nitroxide trajectories for all three labeled 26mers in the absence or presence of EcoRI. Thus, the small position 6 effect is attributed to a structural distortion in the major groove of the DNA at this location possibly corresponding to a bend induced by protein binding. The observation that the spectral changes are small indicates the absence of any significant structural disruption being propagated along the helix as a result of protein binding. Also, the fact that the line shape of the 26mers did not change as expected from hydrodynamic theory in view of the significant increase in molecular volume upon protein binding suggests that there are additional relaxation processes involving the protein and nucleic acid.     

Development of oxidovanadium and oxido-peroxido vanadium-based artificial DNA nucleases via multi spectroscopic investigations and theoretical simulation of DNA binding

Benzimidazole is a neutral ligand which is often used to synthesize bioactive compounds. Two transition metal benzimidazole-based complexes, namely, vanadium (IV) dioxido complex (complex 1) and vanadium (V) oxido-peroxido complex (complex 2) with tridentate benzimidazole ligand, 2,6-di (1H-benzo[d]imidazol-2-yl) pyridine (Byim) have been designed with the intention of developing potential DNA nuclease. Different studies involving biochemical and biophysical techniques along with molecular docking suggest that both the complexes interact with DNA, while the mode of binding is intercalation. The complexes were further used for DNA cleavage activity. Both of them were found to have substantial DNA nuclease activity, but complex 2 was more potent than complex 1 in exhibiting such activity.     

Localization and translation control of slam in Drosophila cellularization

ABSTRACT

In this extra view, we comment on our recent work concerning the mRNA localization of the gene slow as molasses (slam). slam is a gene essential for the polarized invagination of the plasma membrane and separation of basal and lateral cortical domains during cellularization as well as for germ cell migration in later embryogenesis. We have demonstrated an intimate relationship between slam RNA and its encoded protein. Slam RNA co-localizes and forms a complex with its encoded protein. Slam mRNA localization not only is required for reaching full levels of functional Slam protein but also depends on Slam protein. The translation of slam mRNA is subject to tight spatio-temporal regulation leading to a rapid accumulation of Slam protein and zygotic slam RNA at the furrow canal. In this extra view, we first discuss the mechanism controlling localization and translation of slam RNA. In addition, we document in detail the maternal and zygotic expression of slam RNA and protein and provide data for a function in membrane stabilization. Furthermore, we mapped the region of Slam protein mediating cortical localization in cultured cells.     

Structural Interaction Between DsrE-DsrF-DsrH Proteins Involved in the Transport of Electrons in the dsr Operon

Abstract

Biological redox reactions of inorganic sulfur compounds are important for the proper maintenance of environmental sulfur balance. These reactions are mediated by phylogeneticaly diverse set of microorganisms. The protein complex that is involved in such redox reactions of sulfur compounds is the complex encoded by dsr operon. The ecological and industrial importance of these microorganisms led us to investigate the structural details of the mechanism of the process of electron transport during such redox reactions performed by the dsr operon. Among the gene products of the operon, the proteins DsrE, DsrF, and DsrH are small soluble cytoplasmic proteins acting as α₂β₂γ₂ heterohexamer and are involved in the process of electron transport in these ecologically as well as industrially important microorganisms.

Since no structural details of the proteins were available we employed homology modeling to construct the three-dimensional structures of the DsrE, DsrF, and DsrH from Chlorobium tepidum. The putative three dimensional structures of the proteins were predicted from the models. Since DsrE, DsrF, and DsrH proteins act as a hetero-hexameric complex, the modeled proteins were subjected to molecular docking analyses to generate the model of the biochemically active complex. This allowed us to predict the probable binding modes of the proteins as well as the biochemical and the structural basis of the mechanism of the electron transport process by this complex. The hexamerization of the proteins would help to bring the Cys residues in close proximity, which enables the complex to actively take part electron transport process.     

Revisión del complejo de <Emphasis Type="Italic">Lonchocarpus cruentus</Emphasis> (Leguminosae: Papilionoideae: Millettieae), con descripciónes de cinco especies nuevas

The Lonchocarpus cruentus complex, within sect. Lonchocarpus, is described. This complex is characterized by the presence of a keeled vexillary margin on the pod. Five of the six species described and illustrated are new to science: Lonchocarpus aequatorialis, L. alternifoliolatus, L. guianensis, L. septentrionalis and L. trinitensis. A pronounced flower size difference in the north-south distribution of this complex is shown.     

谷物蛋白对白酒发酵过程中微生物群落及其代谢多样性的调控

[背景] 在白酒发酵过程中,原料中的谷物蛋白可为微生物的生长提供氮源等营养物质,进而形成多种代谢产物。谷物蛋白可分为清蛋白、球蛋白、醇溶蛋白和谷蛋白。然而,谷物蛋白对微生物多样性及其代谢产物多样性的调控尚不明确。[目的] 揭示白酒发酵过程中与微生物多样性及其代谢产物多样性显著相关的关键谷物蛋白种类及其调控作用。[方法] 通过Osborne法测定不同品种高粱中谷物蛋白的组成;采用多组学联用技术解析4种高粱在发酵过程中的微生物菌群多样性及代谢产物多样性;通过模拟发酵揭示原料中影响微生物群落及其代谢多样性的关键蛋白。[结果] 4种高粱中的谷物蛋白组成存在显著差异（ANOSIM：R=0.85,P=0.001）;4种高粱在发酵第5天时,S4高粱的细菌多样性显著（P<0.05）高于其他3种高粱,S3高粱中微生物的代谢产物多样性显著（P<0.05）高于其他3种高粱;清蛋白和球蛋白含量与发酵第5天的优势细菌多样性（R²=0.34,P<0.05;R²=0.58,P<0.05）和代谢产物多样性呈显著正相关（R²=0.58,P<0.05;R²=0.36,P<0.05）,被定义为关键蛋白;模拟发酵实验验证了优势细菌多样性和代谢产物多样性可随着2种关键蛋白即清蛋白和球蛋白含量的升高而升高。当清蛋白含量在3.0 g/L时,优势细菌多样性及代谢产物多样性可分别达到0.72和0.65;当球蛋白含量在3.0 g/L时,优势细菌多样性及代谢产物多样性可分别达到0.66和0.81。[结论] 研究揭示了酿造原料中的清蛋白和球蛋白对发酵过程中细菌多样性及代谢产物多样性的调控作用,为提高白酒发酵的可控性及质量提供了依据。     

重组细菌多药外排泵AcrAB-TolC的转运功能和动态组装

【背景】多药外排泵多以膜蛋白复合体形式存在,是导致细菌耐药性的重要原因。外排泵的转运功能和组装过程对于细菌耐药性和药物研发具有重要意义。【目的】以多药外排泵耐药结节细胞分化家族(resistance-nodulation-division family, RND)的重要成员AcrAB-TolC复合体为对象,研究其转运活性和体外组装特性。【方法】基于大肠杆菌AcrAB-TolC复合体基因序列,分别构建含有acrA、acrB、tolC基因的重组质粒,表达和纯化复合体各亚基,利用荧光光谱、等温滴定量热法(isothermal titration calorimetry,ITC)等技术分析复合体及亚基的转运功能、亚基与底物的相互作用,以及亚基间的相互作用和动态装配。【结果】实现了AcrAB-TolC复合体各组分的表达和纯化(纯度>98%),证实表达有各组分的活细胞提高了对于溴化乙锭(ethidium bromide,EB)的转运活性,并发现群体感应效应信号分子N-hexanoyl-L-homoserine lactone (C6-HSL)能够抑制AcrB、TolC对于EB的转运活性。ITC结果进一步证实了C6-HSL与AcrB、TolC的相互作用。ITC结果还显示AcrA分别与AcrB、TolC之间存在明显的相互作用,而AcrB与TolC之间无明显的相互作用。在体外装配实验中观测到AcrAB-TolC亚基的单分子荧光强度随时间增加,证实了复合体亚基在膜上的动态组装过程。【结论】实现了AcrAB-TolC外排泵及亚基的表达和纯化,证实了AcrAB-TolC对底物的转运活性及与底物的相互作用,观察到AcrAB-TolC的动态组装过程。以上结果为研究多药外排泵导致的细菌耐药性及抗菌策略具有重要意义。