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1.
Cell ; 166(4): 935-949, 2016 Aug 11.
Article in English | MEDLINE | ID: mdl-27477512

ABSTRACT

Clearance of misfolded and aggregated proteins is central to cell survival. Here, we describe a new pathway for maintaining protein homeostasis mediated by the proteasome shuttle factor UBQLN2. The 26S proteasome degrades polyubiquitylated substrates by recognizing them through stoichiometrically bound ubiquitin receptors, but substrates are also delivered by reversibly bound shuttles. We aimed to determine why these parallel delivery mechanisms exist and found that UBQLN2 acts with the HSP70-HSP110 disaggregase machinery to clear protein aggregates via the 26S proteasome. UBQLN2 recognizes client-bound HSP70 and links it to the proteasome to allow for the degradation of aggregated and misfolded proteins. We further show that this process is active in the cell nucleus, where another system for aggregate clearance, autophagy, does not act. Finally, we found that mutations in UBQLN2, which lead to neurodegeneration in humans, are defective in chaperone binding, impair aggregate clearance, and cause cognitive deficits in mice.


Subject(s)
Adaptor Proteins, Vesicular Transport/metabolism , Autophagy , Neurodegenerative Diseases/metabolism , Proteasome Endopeptidase Complex/metabolism , Adaptor Proteins, Signal Transducing , Animals , Autophagy-Related Proteins , Brain/metabolism , Brain/pathology , Disease Models, Animal , Gene Knock-In Techniques , HSP70 Heat-Shock Proteins/metabolism , Huntingtin Protein/metabolism , Male , Mice , Neurodegenerative Diseases/pathology , Protein Aggregates , Protein Folding , Proteolysis
2.
PLoS Genet ; 18(5): e1010222, 2022 05.
Article in English | MEDLINE | ID: mdl-35604931

ABSTRACT

Insertion of new material into the Escherichia coli peptidoglycan (PG) sacculus between the cytoplasmic membrane and the outer membrane requires a well-organized balance between synthetic and hydrolytic activities to maintain cell shape and avoid lysis. Since most bacteria carry multiple enzymes carrying the same type of PG hydrolytic activity, we know little about the specific function of given enzymes. Here we show that the DD-carboxy/endopeptidase PBP4 localizes in a PBP1A/LpoA and FtsEX dependent fashion at midcell during septal PG synthesis. Midcell localization of PBP4 requires its non-catalytic domain 3 of unknown function, but not the activity of PBP4 or FtsE. Microscale thermophoresis with isolated proteins shows that PBP4 interacts with NlpI and the FtsEX-interacting protein EnvC, an activator of amidases AmiA and AmiB, which are needed to generate denuded glycan strands to recruit the initiator of septal PG synthesis, FtsN. The domain 3 of PBP4 is needed for the interaction with NlpI and EnvC, but not PBP1A or LpoA. In vivo crosslinking experiments confirm the interaction of PBP4 with PBP1A and LpoA. We propose that the interaction of PBP4 with EnvC, whilst not absolutely necessary for mid-cell recruitment of either protein, coordinates the activities of PBP4 and the amidases, which affects the formation of denuded glycan strands that attract FtsN. Consistent with this model, we found that the divisome assembly at midcell was premature in cells lacking PBP4, illustrating how the complexity of interactions affect the timing of cell division initiation.


Subject(s)
Escherichia coli Proteins , Escherichia coli , ATP-Binding Cassette Transporters/metabolism , Amidohydrolases/metabolism , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Endopeptidases , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Lipoproteins/metabolism , N-Acetylmuramoyl-L-alanine Amidase/metabolism , Peptidoglycan/metabolism
3.
EMBO J ; 39(5): e102246, 2020 03 02.
Article in English | MEDLINE | ID: mdl-32009249

ABSTRACT

The peptidoglycan (PG) sacculus provides bacteria with the mechanical strength to maintain cell shape and resist osmotic stress. Enlargement of the mesh-like sacculus requires the combined activity of peptidoglycan synthases and hydrolases. In Escherichia coli, the activity of two PG synthases is driven by lipoproteins anchored in the outer membrane (OM). However, the regulation of PG hydrolases is less well understood, with only regulators for PG amidases having been described. Here, we identify the OM lipoprotein NlpI as a general adaptor protein for PG hydrolases. NlpI binds to different classes of hydrolases and can specifically form complexes with various PG endopeptidases. In addition, NlpI seems to contribute both to PG elongation and division biosynthetic complexes based on its localization and genetic interactions. Consistent with such a role, we reconstitute PG multi-enzyme complexes containing NlpI, the PG synthesis regulator LpoA, its cognate bifunctional synthase, PBP1A, and different endopeptidases. Our results indicate that peptidoglycan regulators and adaptors are part of PG biosynthetic multi-enzyme complexes, regulating and potentially coordinating the spatiotemporal action of PG synthases and hydrolases.


Subject(s)
Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Lipoproteins/metabolism , Multienzyme Complexes , N-Acetylmuramoyl-L-alanine Amidase/metabolism , Cell Wall/enzymology , Endopeptidases/genetics , Endopeptidases/metabolism , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Lipoproteins/genetics , N-Acetylmuramoyl-L-alanine Amidase/genetics , Peptidoglycan/metabolism
4.
Clin Sci (Lond) ; 137(16): 1333-1346, 2023 08 31.
Article in English | MEDLINE | ID: mdl-37593846

ABSTRACT

Weight loss in overweight or obese individuals with Type 2 diabetes (T2D) can normalize hepatic fat metabolism, decrease fatty acid oversupply to ß cells and restore normoglycaemia. One in six people has BMI <27 kg/m2 at diagnosis, and their T2D is assumed to have different aetiology. The Personal Fat Threshold hypothesis postulated differing individual thresholds for lipid overspill and adverse effects on ß-cell function. To test this hypothesis, people with Type 2 diabetes and body mass index <27kg/m2 (n = 20) underwent repeated 5% weight loss cycles. Metabolic assessments were carried out at stable weight after each cycle and after 12 months. To determine how closely metabolic features returned to normal, 20 matched normoglycemic controls were studied once. Between baseline and 12 months: BMI fell (mean ± SD), 24.8 ± 0.4 to 22.5 ± 0.4 kg/m2 (P<0.0001) (controls: 21.5 ± 0.5); total body fat, 32.1 ± 1.5 to 27.6 ± 1.8% (P<0.0001) (24.6 ± 1.5). Liver fat content and fat export fell to normal as did fasting plasma insulin. Post-meal insulin secretion increased but remained subnormal. Sustained diabetes remission (HbA1c < 48 mmol/mol off all glucose-lowering agents) was achieved by 70% (14/20) by initial weight loss of 6.5 (5.5-10.2)%. Correction of concealed excess intra-hepatic fat reduced hepatic fat export, with recovery of ß-cell function, glycaemic improvement in all and return to a non-diabetic metabolic state in the majority of this group with BMI <27 kg/m2 as previously demonstrated for overweight or obese groups. The data confirm the Personal Fat Threshold hypothesis: aetiology of Type 2 diabetes does not depend on BMI. This pathophysiological insight has major implications for management.


Subject(s)
Diabetes Mellitus, Type 2 , Humans , Diabetes Mellitus, Type 2/etiology , Body Mass Index , Overweight , Obesity/complications , Weight Loss
5.
Molecules ; 27(22)2022 Nov 10.
Article in English | MEDLINE | ID: mdl-36431855

ABSTRACT

The occurrence and distribution of antibiotics in the environment has received increasing attention due to their potential adverse effects on human health and ecosystems. Humic substances (HS) influence the mobility, reactivity, and bioavailability of antibiotics in the environment significantly due to their interaction. As a result, HS can affect the dissemination of antibiotic-resistance genes, which is one of the main problems arising from contamination with antibiotics. The review provides quantitative data on the binding of HS with fluoroquinolones, macrolides, sulfonamides, and tetracyclines and reports the proposed mechanisms of their interaction. The main issues of the quantification of antibiotic-HS interaction are discussed, which are a development of standard approaches and the accumulation of a dataset using a standard methodology. This would allow the implementation of a meta-analysis of data to reveal the patterns of the binding of antibiotics to HS. Examples of successful development of humic-based sorbents for fluoroquinolone and tetracycline removal from environmental water systems or polluted wastewaters were given. Data on the various effects of HS on the dissemination of antibiotic-resistance genes (ARGs) were summarized. The detailed characterization of HS properties as a key point of assessing the environmental consequences of the formation of antibiotic-HS complexes, such as the dissemination of antibiotic resistance, was proposed.


Subject(s)
Anti-Bacterial Agents , Humic Substances , Humans , Ecosystem , Fluoroquinolones , Sulfanilamide
6.
Eur Biophys J ; 50(3-4): 597-611, 2021 May.
Article in English | MEDLINE | ID: mdl-33948690

ABSTRACT

Capsular antigen fragment 1 (Caf1) is an oligomeric protein consisting of 15 kDa monomeric subunits that are non-covalently linked through exceptionally strong and kinetically inert interactions into a linear polymer chain. It has been shown that after its thermal depolymerisation into unfolded monomeric subunits, Caf1 is able to efficiently repolymerise in vitro to reform its polymeric structure. However, little is known about the nature of the repolymerisation process. An improved understanding of this process will lead to the development of methods to better control the lengths of the repolymerised species, and ultimately, to better design of the properties of Caf1-based materials. Here we utilize small-angle X-ray scattering to estimate the size of Caf1 polymers during the first 24 h of the re-polymerisation process. Analytical ultracentrifugation measurements were also used to investigate the process post-24 h, where the rate of repolymerisation becomes considerably slower. Results show that in vitro polymerisation proceeds in a linear manner with no evidence observed for the formation of a lateral polymer network or uncontrolled aggregates. The rate of Caf1 in vitro repolymerisation was found to be concentration-dependent. Importantly, the rate of polymer growth was found to be relatively fast over the first few hours, before continuing at a dramatically slower rate. This observation is not consistent with the previously proposed step-growth mechanism of in vitro polymerisation of Caf1, where a linear increase in polymer length would be expected with time. We speculate how our observations may support the idea that the polymerisation process may be occurring at the ends of the chains with monomers adding sequentially. Our findings will contribute towards the development of new biomaterials for 3D cell culture and bio-printing.


Subject(s)
Fimbriae, Bacterial , Biocompatible Materials , Polymers , Ultracentrifugation , X-Rays
7.
Biochemistry ; 58(48): 4882-4892, 2019 12 03.
Article in English | MEDLINE | ID: mdl-31686499

ABSTRACT

Numerous bacterial toxins and other virulence factors use low pH as a trigger to convert from water-soluble to membrane-inserted states. In the case of colicins, the pore-forming domain of colicin A (ColA-P) has been shown both to undergo a clear acidic unfolding transition and to require acidic lipids in the cytoplasmic membrane, whereas its close homologue colicin N shows neither behavior. Compared to that of ColN-P, the ColA-P primary structure reveals the replacement of several uncharged residues with aspartyl residues, which upon replacement with alanine induce an unfolded state at neutral pH. Here we investigate ColA-P's structural requirement for these critical aspartyl residues that are largely situated at the N-termini of α helices. As previously shown in model peptides, the charged carboxylate side chain can act as a stabilizing helix N-Cap group by interacting with free amide hydrogen bond donors. Because this could explain ColA-P destabilization when the aspartyl residues are protonated or replaced with alanyl residues, we test the hypothesis by inserting asparagine, glutamine, and glutamate residues at these sites. We combine urea (fluorescence and circular dichroism) and thermal (circular dichroism and differential scanning calorimetry) denaturation experiments with 1H-15N heteronuclear single-quantum coherence nuclear magnetic resonance spectroscopy of ColA-P at different pH values to provide a comprehensive description of the unfolding process and confirm the N-Cap hypothesis. Furthermore, we reveal that, in urea, the single domain ColA-P unfolds in two steps; low pH destabilizes the first step and stabilizes the second.


Subject(s)
Colicins/chemistry , Colicins/metabolism , Amino Acid Motifs , Amino Acid Sequence , Circular Dichroism , Colicins/toxicity , Models, Molecular , Protein Denaturation , Protein Folding , Sequence Alignment
8.
Proc Natl Acad Sci U S A ; 113(34): E5034-43, 2016 08 23.
Article in English | MEDLINE | ID: mdl-27493217

ABSTRACT

The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin-LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin-LPS interactions and a bridging calcium ion.


Subject(s)
Amino Acid Substitution , Calcium/chemistry , Escherichia coli/chemistry , Lipopolysaccharides/chemistry , Porins/chemistry , Amino Acid Motifs , Binding Sites , Calcium/metabolism , Cations, Divalent , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Lipopolysaccharides/metabolism , Models, Molecular , Mutation , Porins/genetics , Porins/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Folding , Protein Interaction Domains and Motifs , Protein Multimerization , Static Electricity
9.
Biophys J ; 113(8): 1673-1684, 2017 Oct 17.
Article in English | MEDLINE | ID: mdl-29045862

ABSTRACT

Intrinsically disordered regions within proteins are critical elements in many biomolecular interactions and signaling pathways. Antibacterial toxins of the colicin family, which could provide new antibiotic functions against resistant bacteria, contain disordered N-terminal translocation domains (T-domains) that are essential for receptor binding and the penetration of the Escherichia coli outer membrane. Here we investigate the conformational behavior of the T-domain of colicin N (ColN-T) to understand why such domains are widespread in toxins that target Gram-negative bacteria. Like some other intrinsically disordered proteins in the solution state of the protein, ColN-T shows dual recognition, initially interacting with other domains of the same colicin N molecule and later, during cell killing, binding to two different receptors, OmpF and TolA, in the target bacterium. ColN-T is invisible in the high-resolution x-ray model and yet accounts for 90 of the toxin's 387 amino acid residues. To reveal its solution structure that underlies such a dynamic and complex system, we carried out mutagenic, biochemical, hydrodynamic and structural studies using analytical ultracentrifugation, NMR, and small-angle x-ray scattering on full-length ColN and its fragments. The structure was accurately modeled from small-angle x-ray scattering data by treating ColN as a flexible system, namely by the ensemble optimization method, which enables a distribution of conformations to be included in the final model. The results reveal, to our knowledge, for the first time the dynamic structure of a colicin T-domain. ColN-T is in dynamic equilibrium between a compact form, showing specific self-recognition and resistance to proteolysis, and an extended form, which most likely allows for effective receptor binding.


Subject(s)
Colicins/metabolism , Amino Acid Sequence , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/metabolism , Colicins/chemistry , Colicins/genetics , Elasticity , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Hydrodynamics , Intrinsically Disordered Proteins/chemistry , Intrinsically Disordered Proteins/metabolism , Membrane Proteins , Models, Molecular , Mutation , Nuclear Magnetic Resonance, Biomolecular , Porins/chemistry , Porins/metabolism , Protein Conformation , Protein Domains , Saccharomyces cerevisiae Proteins , Scattering, Small Angle , Solutions/chemistry , Ultracentrifugation , X-Ray Diffraction
10.
Proc Natl Acad Sci U S A ; 111(22): 8197-202, 2014 Jun 03.
Article in English | MEDLINE | ID: mdl-24821816

ABSTRACT

Bacteria surround their cytoplasmic membrane with an essential, stress-bearing peptidoglycan (PG) layer. Growing and dividing cells expand their PG layer by using membrane-anchored PG synthases, which are guided by dynamic cytoskeletal elements. In Escherichia coli, growth of the mainly single-layered PG is also regulated by outer membrane-anchored lipoproteins. The lipoprotein LpoB is required for the activation of penicillin-binding protein (PBP) 1B, which is a major, bifunctional PG synthase with glycan chain polymerizing (glycosyltransferase) and peptide cross-linking (transpeptidase) activities. Here, we report the structure of LpoB, determined by NMR spectroscopy, showing an N-terminal, 54-aa-long flexible stretch followed by a globular domain with similarity to the N-terminal domain of the prevalent periplasmic protein TolB. We have identified the interaction interface between the globular domain of LpoB and the noncatalytic UvrB domain 2 homolog domain of PBP1B and modeled the complex. Amino acid exchanges within this interface weaken the PBP1B-LpoB interaction, decrease the PBP1B stimulation in vitro, and impair its function in vivo. On the contrary, the N-terminal flexible stretch of LpoB is required to stimulate PBP1B in vivo, but is dispensable in vitro. This supports a model in which LpoB spans the periplasm to interact with PBP1B and stimulate PG synthesis.


Subject(s)
Apolipoproteins B/metabolism , Bacterial Outer Membrane Proteins/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/enzymology , Penicillin-Binding Proteins/metabolism , Peptidoglycan Glycosyltransferase/metabolism , Serine-Type D-Ala-D-Ala Carboxypeptidase/metabolism , Apolipoproteins B/chemistry , Bacterial Outer Membrane Proteins/chemistry , Escherichia coli Proteins/chemistry , Nuclear Magnetic Resonance, Biomolecular , Penicillin-Binding Proteins/chemistry , Peptidoglycan/biosynthesis , Peptidoglycan Glycosyltransferase/chemistry , Periplasm/metabolism , Protein Interaction Domains and Motifs , Protein Structure, Tertiary , Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry
11.
J Biol Chem ; 289(1): 53-64, 2014 Jan 03.
Article in English | MEDLINE | ID: mdl-24214982

ABSTRACT

The microbial degradation of the plant cell wall is an important biological process that is highly relevant to environmentally significant industries such as the bioenergy and biorefining sectors. A major component of the wall is glucuronoxylan, a ß1,4-linked xylose polysaccharide that is decorated with α-linked glucuronic and/or methylglucuronic acid (GlcA/MeGlcA). Recently three members of a glycoside hydrolase family, GH115, were shown to hydrolyze MeGlcA side chains from the internal regions of xylan, an activity that has not previously been described. Here we show that a dominant member of the human microbiota, Bacteroides ovatus, contains a GH115 enzyme, BoAgu115A, which displays glucuronoxylan α-(4-O-methyl)-glucuronidase activity. The enzyme is significantly more active against substrates in which the xylose decorated with GlcA/MeGlcA is flanked by one or more xylose residues. The crystal structure of BoAgu115A revealed a four-domain protein in which the active site, comprising a pocket that abuts a cleft-like structure, is housed in the second domain that adopts a TIM barrel-fold. The third domain, a five-helical bundle, and the C-terminal ß-sandwich domain make inter-chain contacts leading to protein dimerization. Informed by the structure of the enzyme in complex with GlcA in its open ring form, in conjunction with mutagenesis studies, the potential substrate binding and catalytically significant amino acids were identified. Based on the catalytic importance of residues located on a highly flexible loop, the enzyme is required to undergo a substantial conformational change to form a productive Michaelis complex with glucuronoxylan.


Subject(s)
Bacterial Proteins/chemistry , Bacteroides/enzymology , Glycoside Hydrolases/chemistry , Xylans/chemistry , Biomass , Crystallography, X-Ray , Humans , Plants/chemistry , Protein Structure, Secondary , Protein Structure, Tertiary , Substrate Specificity
12.
Proc Natl Acad Sci U S A ; 109(51): 20889-94, 2012 Dec 18.
Article in English | MEDLINE | ID: mdl-23213210

ABSTRACT

Noncatalytic carbohydrate binding modules (CBMs) are components of glycoside hydrolases that attack generally inaccessible substrates. CBMs mediate a two- to fivefold elevation in the activity of endo-acting enzymes, likely through increasing the concentration of the appended enzymes in the vicinity of the substrate. The function of CBMs appended to exo-acting glycoside hydrolases is unclear because their typical endo-binding mode would not fulfill a targeting role. Here we show that the Bacillus subtilis exo-acting ß-fructosidase SacC, which specifically hydrolyses levan, contains the founding member of CBM family 66 (CBM66). The SacC-derived CBM66 (BsCBM66) targets the terminal fructosides of the major fructans found in nature. The crystal structure of BsCBM66 in complex with ligands reveals extensive interactions with the terminal fructose moiety (Fru-3) of levantriose but only limited hydrophobic contacts with Fru-2, explaining why the CBM displays broad specificity. Removal of BsCBM66 from SacC results in a ~100-fold reduction in activity against levan. The truncated enzyme functions as a nonspecific ß-fructosidase displaying similar activity against ß-2,1- and ß-2,6-linked fructans and their respective fructooligosaccharides. Conversely, appending BsCBM66 to BT3082, a nonspecific ß-fructosidase from Bacteroides thetaiotaomicron, confers exolevanase activity on the enzyme. We propose that BsCBM66 confers specificity for levan, a branched fructan, through an "avidity" mechanism in which the CBM and the catalytic module target the termini of different branches of the same polysaccharide molecule. This report identifies a unique mechanism by which CBMs modulate enzyme function, and shows how specificity can be tailored by integrating nonspecific catalytic and binding modules into a single enzyme.


Subject(s)
Bacillus subtilis/metabolism , Carbohydrates/chemistry , Enzymes/chemistry , Bacteroides/metabolism , Biofuels , Calorimetry/methods , Catalysis , Crystallography, X-Ray/methods , Fructans/chemistry , Glycoside Hydrolases/chemistry , Hydrophobic and Hydrophilic Interactions , Kinetics , Lectins/chemistry , Ligands , Models, Chemical , Oligosaccharides/chemistry , Polysaccharides/chemistry , Protein Binding , Protein Structure, Tertiary
13.
J Biol Chem ; 287(1): 337-346, 2012 Jan 02.
Article in English | MEDLINE | ID: mdl-22081604

ABSTRACT

Proteins that translocate across cell membranes need to overcome a significant hydrophobic barrier. This is usually accomplished via specialized protein complexes, which provide a polar transmembrane pore. Exceptions to this include bacterial toxins, which insert into and cross the lipid bilayer itself. We are studying the mechanism by which large antibacterial proteins enter Escherichia coli via specific outer membrane proteins. Here we describe the use of neutron scattering to investigate the interaction of colicin N with its outer membrane receptor protein OmpF. The positions of lipids, colicin N, and OmpF were separately resolved within complex structures by the use of selective deuteration. Neutron reflectivity showed, in real time, that OmpF mediates the insertion of colicin N into lipid monolayers. This data were complemented by Brewster Angle Microscopy images, which showed a lateral association of OmpF in the presence of colicin N. Small angle neutron scattering experiments then defined the three-dimensional structure of the colicin N-OmpF complex. This revealed that colicin N unfolds and binds to the OmpF-lipid interface. The implications of this unfolding step for colicin translocation across membranes are discussed.


Subject(s)
Colicins/chemistry , Colicins/metabolism , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Neutron Diffraction , Porins/metabolism , Detergents/chemistry , Escherichia coli/cytology , Escherichia coli/metabolism , Models, Molecular , Phosphatidylglycerols/metabolism , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Protein Transport , Scattering, Small Angle , Surface Properties , Time Factors
14.
J Bacteriol ; 193(19): 5431-41, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21803996

ABSTRACT

The control of mRNA stability is an important component of regulation in bacteria. Processing and degradation of mRNAs are initiated by an endonucleolytic attack, and the cleavage products are processively degraded by exoribonucleases. In many bacteria, these RNases, as well as RNA helicases and other proteins, are organized in a protein complex called the RNA degradosome. In Escherichia coli, the RNA degradosome is assembled around the essential endoribonuclease E. In Bacillus subtilis, the recently discovered essential endoribonuclease RNase Y is involved in the initiation of RNA degradation. Moreover, RNase Y interacts with other RNases, the RNA helicase CshA, and the glycolytic enzymes enolase and phosphofructokinase in a degradosome-like complex. In this work, we have studied the domain organization of RNase Y and the contribution of the domains to protein-protein interactions. We provide evidence for the physical interaction between RNase Y and the degradosome partners in vivo. We present experimental and bioinformatic data which indicate that the RNase Y contains significant regions of intrinsic disorder and discuss the possible functional implications of this finding. The localization of RNase Y in the membrane is essential both for the viability of B. subtilis and for all interactions that involve RNase Y. The results presented in this study provide novel evidence for the idea that RNase Y is the functional equivalent of RNase E, even though the two enzymes do not share any sequence similarity.


Subject(s)
Bacillus subtilis/enzymology , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Endoribonucleases/chemistry , Endoribonucleases/metabolism , Amino Acid Sequence , Bacterial Proteins/genetics , Computational Biology , Endoribonucleases/genetics , Escherichia coli/enzymology , Molecular Sequence Data , Multienzyme Complexes/metabolism , Polyribonucleotide Nucleotidyltransferase/metabolism , Protein Binding/genetics , Protein Structure, Tertiary , RNA Helicases/metabolism , Sequence Homology, Amino Acid , Two-Hybrid System Techniques
15.
Article in English | MEDLINE | ID: mdl-21505242

ABSTRACT

The antibiotic bacillaene is biosynthesized in Bacillus subtilis by a hybrid type 1 modular polyketide synthase/nonribosomal peptide synthetase of the trans-acyltransferase (trans-AT) class. Within this system, the essential acyl-group loading activity is provided by the action of three free-standing trans-acting acyltransferases. Here, the recombinant expression, purification and crystallization of the bacillaene synthase trans-acting acyltransferase PksC are reported. A diffraction data set has been collected from a single PksC crystal to 1.44 Šresolution and the crystal was found to belong to the orthorhombic space group P2(1)2(1)2(1).


Subject(s)
Acyltransferases/chemistry , Bacillus subtilis/enzymology , Crystallization , Crystallography, X-Ray
16.
Nucleic Acids Res ; 37(13): 4453-63, 2009 Jul.
Article in English | MEDLINE | ID: mdl-19474347

ABSTRACT

DNA mismatch repair (MMR) and very-short patch (VSP) repair are two pathways involved in the repair of T:G mismatches. To learn about competition and cooperation between these two repair pathways, we analyzed the physical and functional interaction between MutL and Vsr using biophysical and biochemical methods. Analytical ultracentrifugation reveals a nucleotide-dependent interaction between Vsr and the N-terminal domain of MutL. Using chemical crosslinking, we mapped the interaction site of MutL for Vsr to a region between the N-terminal domains similar to that described before for the interaction between MutL and the strand discrimination endonuclease MutH of the MMR system. Competition between MutH and Vsr for binding to MutL resulted in inhibition of the mismatch-provoked MutS- and MutL-dependent activation of MutH, which explains the mutagenic effect of Vsr overexpression. Cooperation between MMR and VSP repair was demonstrated by the stimulation of the Vsr endonuclease in a MutS-, MutL- and ATP-hydrolysis-dependent manner, in agreement with the enhancement of VSP repair by MutS and MutL in vivo. These data suggest a mobile MutS-MutL complex in MMR signalling, that leaves the DNA mismatch prior to, or at the time of, activation of downstream effector molecules such as Vsr or MutH.


Subject(s)
Adenosine Triphosphatases/metabolism , DNA Mismatch Repair , Endodeoxyribonucleases/metabolism , Escherichia coli Proteins/metabolism , Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/radiation effects , Cross-Linking Reagents , DNA Repair Enzymes/metabolism , DNA-Binding Proteins/metabolism , Endodeoxyribonucleases/chemistry , Endodeoxyribonucleases/radiation effects , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/radiation effects , MutL Proteins , MutS DNA Mismatch-Binding Protein/metabolism , Photochemical Processes , Protein Structure, Tertiary , Ultracentrifugation
17.
Eur Biophys J ; 39(3): 469-80, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19290517

ABSTRACT

Adhesion of the serotype M1 Streptococcus pyogenes strain SF370 to human tonsil explants and cultured keratinocytes requires extended polymeric surface structures called pili. In this important human pathogen, pili are assembled from three protein subunits: Spy0125, Spy0128 and Spy0130 through the action of sortase enzymes. For this study, the structural properties of these pili proteins have been investigated in solution. Spy0125 and Spy0128 display characteristics of globular, folded proteins. Circular dichroism suggests a largely beta-sheet composition for Spy0128 and Spy0125; Spy0130 appears to contain little secondary structure. Each of the proteins adopts a monodisperse, monomeric state in solution as assessed by analytical ultracentrifugation. Further, small-angle X-ray scattering curves for Spy0125, Spy0128 and Spy0130 suggest each protein adopts an elongated shape, likely comprised of two domains, with similar maximal dimensions. Based on the scattering data, dummy atom models of each of the pili subunits have been reconstructed ab initio. This study provides the first insights into the structure of Streptococcus pyogenes minor pili subunits, and possible implications for protein function are discussed.


Subject(s)
Fimbriae Proteins/chemistry , Algorithms , Circular Dichroism , Computer Simulation , Fimbriae Proteins/genetics , Fimbriae, Bacterial/chemistry , Fimbriae, Bacterial/genetics , Models, Chemical , Models, Molecular , Protein Structure, Secondary , Scattering, Small Angle , Software , Solutions , Streptococcus pyogenes , Ultracentrifugation , Ultraviolet Rays , Water/chemistry , X-Ray Diffraction
18.
Nat Commun ; 10(1): 3056, 2019 07 11.
Article in English | MEDLINE | ID: mdl-31296869

ABSTRACT

Lamin A is a nuclear intermediate filament protein critical for nuclear architecture and mechanics and mutated in a wide range of human diseases. Yet little is known about the molecular architecture of lamins and mechanisms of their assembly. Here we use SILAC cross-linking mass spectrometry to determine interactions within lamin dimers and between dimers in higher-order polymers. We find evidence for a compression mechanism where coiled coils in the lamin A rod can slide onto each other to contract rod length, likely driven by a wide range of electrostatic interactions with the flexible linkers between coiled coils. Similar interactions occur with unstructured regions flanking the rod domain during oligomeric assembly. Mutations linked to human disease block these interactions, suggesting that this spring-like contraction can explain in part the dynamic mechanical stretch and flexibility properties of the lamin polymer and other intermediate filament networks.


Subject(s)
Intermediate Filament Proteins/metabolism , Lamin Type A/metabolism , Nuclear Matrix/metabolism , Protein Multimerization/physiology , Amino Acid Sequence/physiology , Animals , Cardiomyopathy, Dilated/genetics , Cross-Linking Reagents/chemistry , Elasticity , Humans , Intermediate Filament Proteins/chemistry , Intermediate Filament Proteins/genetics , Intermediate Filament Proteins/isolation & purification , Lamin Type A/chemistry , Lamin Type A/genetics , Lamin Type A/isolation & purification , Mass Spectrometry/methods , Muscular Dystrophies/genetics , Mutation , Nuclear Envelope/metabolism , Protein Domains/genetics , Protein Structure, Secondary/physiology , Rats , Rats, Sprague-Dawley , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism
19.
ACS Appl Nano Mater ; 1(7): 3590-3599, 2018 Jul 27.
Article in English | MEDLINE | ID: mdl-30101217

ABSTRACT

Functional protein-gold nanoparticle (AuNP) conjugates have a wide variety of applications including biosensing and drug delivery. Correct protein orientation, which is important to maintain functionality on the nanoparticle surface, can be difficult to achieve in practice, and dedicated protein scaffolds have been used on planar gold surfaces to drive the self-assembly of oriented protein arrays. Here we use the transmembrane domain of Escherichia coli outer membrane protein A (OmpATM) to create protein-AuNP conjugates. The addition of a single cysteine residue into a periplasmic loop, to create cysOmpATM, drives oriented assembly and increased equilibrium binding. As the protein surface concentration increases, the sulfur-gold bond in cysOmpATM creates a more densely populated AuNP surface than the poorly organized wtOmpATM layer. The functionalization of AuNP improved both their stability and homogeneity. This was further exploited using multidomain protein chimeras, based on cysOmpATM, which were shown to form ordered protein arrays with their functional domains displayed away from the AuNP surface. A fusion with protein G was shown to specifically bind antibodies via their Fc region. Next, an in vitro selected single chain antibody (scFv)-cysOmpATM fusion protein, bound to AuNP, detected influenza A nucleoprotein, a widely used antigen in diagnostic assays. Finally, using the same scFv-cysOmpATM-AuNP conjugates, a prototype lateral flow assay for influenza demonstrated the utility of fully recombinant self-assembling sensor layers. By simultaneously removing the need for both animal antibodies and a separate immobilization procedure, this technology could greatly simplify the development of a range of in vitro diagnostics.

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