Quasi- and nonequivalence in the structure of bacterial flagellar filament

In supercoiled forms of flagellar filaments, which are thought to be produced by combinations of two distinct subunit lattices, the lattices are elastically deformed in 11 different ways, depending on their azimuthal positions on the circumference of a tube with 11 protofilaments. Those two interactions are nonequivalent as opposed to quasiequivalent ones in elastically deformed lattices of otherwise identical interactions. The term nonequivalence is defined to represent different bonding interactions, and quasiequivalent is used to describe deformed but conserved bonding interactions. By using two distinct lattices that were accurately determined by x-ray fiber diffraction, 10 possible supercoiled forms of flagellar filaments were simulated, based on a bistable-subunit packing model. Comparison to the observed forms showed good agreement, indicating that the model and determined lattice parameters effectively represent realistic features of the structure. The simulated quasiequivalent lattices have been compared to the two nonequivalent lattices, revealing an interesting feature: the maximum deviation in the intersubunit distance by elastic deformation is almost three-quarters of the difference between the two distinct lattices, demonstrating a balanced coexistence of a well-defined conformational distinction and extensive adaptability in the molecular structure of flagellin and its packing interactions.     

Kinetic characterization of phosphotransfer between CheA and CheY in the bacterial chemotaxis signal transduction pathway

Phosphorylation of the CheY protein is a crucial step in the chemotaxis signal transduction pathway of Escherichia coli. CheY becomes phosphorylated by acquiring a phosphoryl group from CheA, an autophosphorylating protein kinase. In this study, we utilized a rapid-quench instrument to investigate the kinetics of phosphotransfer in single-turnover experiments. Our results are consistent with a three-step mechanism for the CheA-to-CheY phosphotransfer reaction: (i) reversible binding of CheY to P-CheA; (ii) rapid, reversible phosphotransfer to CheY; (iii) reversible dissociation of the resulting CheA x CheY-P complex. Investigation of the effect of CheY concentration on the observed rate of phosphotransfer demonstrated saturation kinetics; the extrapolated limiting rate constant for phosphotransfer was 650 +/- 200 s(-1), while the Km value indicated from this work was 6.5 +/- 2 microM. We demonstrated that the CheA-CheY phosphotransfer reaction was reversible by observing partial transfer of [32P]phosphate from CheY-P to CheA and by observing the effect of high concentrations of unphosphorylated CheA on the equilibrium: P-CheA + CheY <--> CheA + CheY-P. We found that the rate of phosphotransfer from P-CheA to CheY can be inhibited by unphosphorylated CheA as well as by a fragment of CheA (CheA124-257) that contains the CheY binding site; these results suggest that the unphosphorylated form of CheA can effectively compete with P-CheA for available CheY (Kd approximately 1.5 +/- 0.6 microM for the CheY x CheA124-257 complex and for the CheY x CheA complex).     

Phosphotransfer between CheA, CheY1, and CheY2 in the chemotaxis signal transduction chain of Rhizobium meliloti

The soil bacterium Rhizobium meliloti responds to chemotactic stimuli by modulating the rotary speed of its flagella. Unlike in Escherichia coli, the signal transduction chain of R. meliloti contains two different response regulators, CheY1 and CheY2, but no CheZ phosphatase. Phosphorylation of CheY1 and CheY2 by the central ATP-dependent autokinase, CheA, is the crucial step in signal transduction. In vivo, phospho-CheY2 (CheY2-P) is the chief regulator of flagellar rotation, its action being modulated by CheY1 [Sourjik, V., and Schmitt, R. (1996) Mol. Microbiol. 22, 427-436]. In this study, we have investigated these phosphotransfer reactions in vitro using the radiolabeled recombinant proteins, CheA (labeled via [gamma-32P]ATP), CheY1, and CheY2 (labeled via acetyl [32P]phosphate). Our results are consistent with the following four-step phosphotransfer: (i) ATP-dependent autophosphorylation of CheA (with a limiting rate constant of 0.008 s-1 at saturating ATP concentrations); (ii) rapid phospho transfer from phospho-CheA to CheY1 and CheY2; (iii) autodephosphorylation of CheY1-P and CheY2-P with half-lives of 12 +/- 1 s and 10.5 +/- 1 s, respectively; and (iv) reversible phosphotransfer from CheY2-P to CheA. In the three-component mixture, CheA/CheY1/CheY2, we observed rapid phosphotransfer from CheY2-P via CheA to CheY1. Thus, CheY1 assumes the role of a "phosphatase" of CheY2-P by acting as a sink for phosphate, whenever unphosphorylated CheA is present. The intracellular concentrations of CheA/CheY1/CheY2 determined immunochemically were 1.5 microM:20 microM:20 microM, a range that was adopted for in vitro assays. The results reflect a unique control by CheY1 of the active, phosphorylated state of the main response regulator, CheY2-P. This mechanism appears to be a new twist to signal transduction among members of the alpha-subgroup of proteobacteria.     

Distinct regions of U3 snoRNA interact at two sites within the 5' external transcribed spacer of pre-rRNAs in Trypanosoma brucei cells

U3 snoRNA is required for early pre-rRNA processing events that include cleavage of the 5' external transcribed spacer (5'ETS) and 18S rRNA maturation. Herein, psoralen RNA crosslinking has been used to indicate novel in vivo interactions between the minimally-sized Trypanosoma brucei U3 snoRNA and pre-rRNAs. Two discrete U3 crosslinks were mapped to 5'ETS sequences, then individually isolated by hybrid selection following digestion of pre-rRNAs. Crosslink positions within these U3-site1 and U3-site2 complexes were resolved by RNaseH digestion and primer extension analyses. Hinge bases of U3 contacted site1 bases U140 and U142 just 3' of the processed primary site. This is the first experimental evidence of a U3 RNA interaction adjacent to a major 5'ETS cleavage site and supports a critical role for U3 in its processing. Highly conserved box A bases contacted site2 base U945, 187 nt upstream of 18S-like rRNA sequences. Site2 sequences are not required for primary processing, thus, a U3 interaction here might have roles in subsequent downstream processing events. These results clearly demonstrated that distinct U3 snoRNA sequences crosslinked different regions of the 5'ETS and support a model for U3 as a multifunctional snoRNA.     

Distinct subclasses of small GTPases interact with guanine nucleotide exchange factors in a similar manner

The Ras-related GTPases are small, 20- to 25-kDa proteins which cycle between an inactive GDP-bound form and an active GTP-bound state. The Ras superfamily includes the Ras, Rho, Ran, Arf, and Rab/YPT1 families, each of which controls distinct cellular functions. The crystal structures of Ras, Rac, Arf, and Ran reveal a nearly superimposible structure surrounding the GTP-binding pocket, and it is generally presumed that the Rab/YPT1 family shares this core structure. The Ras, Rac, Ran, Arf, and Rab/YPT1 families are activated by interaction with family-specific guanine nucleotide exchange factors (GEFs). The structural determinants of GTPases required for interaction with family-specific GEFs have begun to emerge. We sought to determine the sites on YPT1 which interact with GEFs. We found that mutations of YPT1 at position 42, 43, or 49 (effector loop; switch I), position 69, 71, 73, or 75 (switch II), and position 107, 109, or 115 (alpha-helix 3-loop 7 [alpha3-L7]) are intragenic suppressors of dominant interfering YPT1 mutant N22 (YPT1-N22), suggesting these mutations prevent YPT1-N22 from binding to and sequestering an endogenous GEF. Mutations at these positions prevent interaction with the DSS4 GEF in vitro. Mutations in the switch II and alpha3-L7 regions do not prevent downstream signaling in yeast when combined with a GTPase-defective (activating) mutation. Together, these results show that the YPT1 GTPase interacts with GEFs in a manner reminiscent of that for Ras and Arf in that these GTPases use divergent sequences corresponding to the switch I and II regions and alpha3-L7 of Ras to interact with family-specific GEFs. This finding suggests that GTPases of the Ras superfamily each may share common features of GEF-mediated guanine nucleotide exchange even though the GEFs for each of the Ras subfamilies appear evolutionarily unrelated.     

Determination of regions in the dihydrofolate reductase structure that interact with the molecular chaperonin GroEL

Dihydrofolate reductase (DHFR) from Escherichia coli does not interact with the molecular chaperonin GroEL regardless of whether the interaction is initiated from the native or the unfolded state. In contrast, murine DHFR shows a strong interaction with GroEL. Using the structure of human DHFR as a model for the murine protein, a superimposition of the two structures shows that there are three distinct external loops in the eukaryotic DHFR that are not present in the E. coli protein. Removal of one loop (residues 99-108) from the eukaryotic murine DHFR has no effect on the interaction with GroEL. On the basis of the differences in structures, we inserted either of two surface loops of murine DHFR into the corresponding regions of E. coli DHFR. In the first mutant (EcDHFR-i(9)36), residues 36 and 37 (L-N) of E. coli DHFR were replaced with the nine amino acid sequence T-T-S-S-V-E-G-K-Q. In the second mutant (EcDHFR-i(7)136), residues 136-139 (V-F-S-E) of E. coli DHFR were replaced with the seven amino acid sequence L-P-E-Y-P-G-V. Both E. coli DHFR mutants formed a complex with GroEL starting from either the native or the unfolded states of DHFR. The binding was specific since the presence of MgATP caused the release of the proteins from GroEL. As with murine DHFR, nonnative conformations of EcDHFR-i(9)36 and EcDHFR-i(7)136 are bound to GroEL. Fluorescence titration techniques were used to quantitate the interaction between GroEL and these proteins. A simple chromatographic procedure was developed to remove contaminating tryptophan containing peptides from GroEL samples. The mutant EcDHFR-i(7)136 binds to GroEL with a stoichiometry of 4-5 mol of DHFR per mol of GroEL tetradecamer, while murine DHFR binds to GroEL with a stoichiometry of 2 mol of DHFR per mol of GroEL tetradecamer. Both murine DHFR and EcDHFR-i(7)136 bind to GroEL very tightly, with equilibrium dissociation constants of less than 85 nM.     

Absence of a barrier to backwards rotation of the bacterial flagellar motor demonstrated with optical tweezers

A cell of the bacterium Escherichia coli was tethered covalently to a glass coverslip by a single flagellum, and its rotation was stopped by using optical tweezers. The tweezers acted directly on the cell body or indirectly, via a trapped polystyrene bead. The torque generated by the flagellar motor was determined by measuring the displacement of the laser beam on a quadrant photodiode. The coverslip was mounted on a computer-controlled piezo-electric stage that moved the tether point in a circle around the center of the trap so that the speed of rotation of the motor could be varied. The motor generated approximately 4500 pN nm of torque at all angles, regardless of whether it was stalled, allowed to rotate very slowly forwards, or driven very slowly backwards. This argues against models of motor function in which rotation is tightly coupled to proton transit and back-transport of protons is severely limited.     

FlaA, a putative flagellar outer sheath protein, is not an immunodominant antigen associated with Lyme disease

FlaA was recently found to be associated with flagellar filaments of Borrelia burgdorferi. We tested whether antibodies to this protein are a good indicator of infection, as antibodies to FlaA proteins in other spirochetal infections show an increase in titer. Although overproduction of intact FlaA was highly toxic to Escherichia coli, truncated proteins which lacked the N-terminal signal sequence could be successfully overexpressed. Immunoblotting with sera from mammalian hosts infected with B. burgdorferi indicated that FlaA is not an immunodominant antigen in Lyme disease. However, sera from two patients reacted with both recombinant and native FlaA protein, suggesting that B. burgdorferi FlaA was antigenic and expressed in vivo.     

Distinct and specific functions of cGMP-dependent protein kinases

cGMP-dependent protein kinases I and II conduct signals from widespread signaling systems. Whereas the type I kinase mediates numerous effects of natriuretic peptides and nitric oxide in cardiovascular cells, the type II kinase transduces signals from the Escherichia coli heat-stable enterotoxin, STa, and from the endogenous intestinal peptide, guanylin, stimulating Cl- conductance of the cystic fibrosis transmembrane conductance regulator (CFTR). Although the two kinases may be interchangeable for several functions, CFTR regulation specifically requires the type II kinase.     

Transmembrane neuregulins interact with LIM kinase 1, a cytoplasmic protein kinase implicated in development of visuospatial cognition

The neuregulins are receptor tyrosine kinase ligands that play a critical role in the development of the heart, nervous system, and breast. Unlike many extracellular signaling molecules, such as the neurotrophins, most neuregulins are synthesized as transmembrane proteins. To determine the functions of the highly conserved neuregulin cytoplasmic tail, a yeast two-hybrid screen was performed to identify proteins that interact with the 157-amino acid sequence common to the cytoplasmic tails of all transmembrane neuregulin isoforms. This screen revealed that the neuregulin cytoplasmic tail interacts with the LIM domain region of the nonreceptor protein kinase LIM kinase 1 (LIMK1). Interaction between the neuregulin cytoplasmic tail and full-length LIMK1 was demonstrated by in vitro binding and co-immunoprecipitation assays. Transmembrane neuregulins with each of the three known neuregulin cytoplasmic tail isoforms interacted with LIMK1. In contrast, the cytoplasmic tail of TGF-alpha did not interact with LIMK1. In vivo, neuregulin and LIMK1 are co-localized at the neuromuscular synapse, suggesting that LIMK1, like neuregulin, may play a role in synapse formation and maintenance. To our knowledge, LIMK1 is the first identified protein shown to interact with the cytoplasmic tail of a receptor tyrosine kinase ligand.     

Mammalian 5'-AMP-activated protein kinase non-catalytic subunits are homologs of proteins that interact with yeast Snf1 protein kinase

The 5'-AMP-activated protein kinase is responsible for the regulation of fatty acid synthesis by phosphorylation and inactivation of acetyl-CoA carboxylase. The porcine liver 5'-AMP-activated protein kinase 63-kDa catalytic subunit co-purifies 14,000-fold with a 38- and 40-kDa protein (Mitchelhill, K.I. et al. (1994) J. Biol. Chem. 269, 2361-2364). The 63-kDa subunit is homologous to the Saccharomyces cerevisiae Snf1 protein kinase, which regulates gene expression during glucose derepression. Peptide amino acid and polymerase chain reaction-derived partial cDNA sequences of both the pig and rat liver enzymes show that the 38-kDa protein is homologous to Snf4p (CAT3) and that the 40-kDa protein is homologous to the Sip1p/Spm/GAL83 family of Snf1p interacting proteins. Sucrose density gradient and cross-linking experiments with purified 5'-AMP-activated protein kinase suggest that both the 38- and 40-kDa proteins associate tightly with the 63-kDa catalytic polypeptide in either a heterotrimeric complex or in dimeric complexes. The 40-kDa subunit is autophosphorylated within the 63-kDa subunit complex. The sequence relationships between the mammalian 5'-AMP-activated protein kinase and yeast Snf1p extend to the subunit proteins consistent with conservation of the functional roles of these polypeptides in cellular regulation by this family of metabolite-sensing protein kinases.     

The b and delta subunits of the Escherichia coli ATP synthase interact via residues in their C-terminal regions

An affinity resin for the F1 sector of the Escherichia coli ATP synthase was prepared by coupling the b subunit to a solid support through a unique cysteine residue in the N-terminal leader. b24-156, a form of b lacking the N-terminal transmembrane domain, was able to compete with the affinity resin for binding of F1. Truncated forms of b24-156, in which one or four residues from the C terminus were removed, competed poorly for F1 binding, suggesting that these residues play an important role in b-F1 interactions. Sedimentation velocity analytical ultracentrifugation revealed that removal of these C-terminal residues from b24-156 resulted in a disruption of its association with the purified delta subunit of the enzyme. To determine whether these residues interact directly with delta, cysteine residues were introduced at various C-terminal positions of b and modified with the heterobifunctional cross-linker benzophenone-4-maleimide. Cross-links between b and delta were obtained when the reagent was incorporated at positions 155 and 158 (two residues beyond the normal C terminus) in both the reconstituted b24-156-F1 complex and the membrane-bound F1F0 complex. CNBr digestion followed by peptide sequencing showed the site of cross-linking within the 177-residue delta subunit to be C-terminal to residue 148, possibly at Met-158. These results indicate that the b and delta subunits interact via their C-terminal regions and that this interaction is instrumental in the binding of the F1 sector to the b subunit of F0.     

Construction, bacterial expression, and characterization of hapten-specific single-chain Fv and alkaline phosphatase fusion protein

Immature airways are highly compliant compared to the adult, suggesting that trachea and bronchi from immature animals may be easily compressed. Although tracheal compression has been extensively studied, the effect of transmural pressure on occlusion of immature bronchi has been neglected. The transmural pressure at which the lumen closed was determined from the transmittance of pressure along the lumen of isolated bronchi from late-term foetal, 1 and 4 week old pigs. Bronchi from eight cases of sudden infant death syndrome (SIDS) were also studied. In several experiments, smooth muscle tone was produced either by electrical field stimulation or carbachol challenge, and the relationship between active muscle tone and resting transmural pressure was studied. Bronchi from foetal, 1 and 4 week old pigs were occluded by intraluminal pressures of -4, -5 and -24 cmH2O. SIDS bronchi closed at -11 cmH2O. Histological and endoscopic investigations showed that closure of the bronchi occurred along a plane and was not uniform along the bronchus. Carbachol precontraction increased the transmural pressure required to close bronchi by approximately 5 cmH2O. The relationship between muscle tone and resting pressure was the same in all age groups, except when transmural pressure was at or below closing pressure. Bronchi from immature animals and human infants are vulnerable to collapse by small changes in transmural pressure. Bronchial closure is partly dependent on smooth muscle tone, particularly in younger animals.     

Identification of proteins that interact with a protein of interest: applications of the yeast two-hybrid system

Colorectal cancer remains a major health problem. Few therapies are effective apart from surgery, and survival has increased little in recent years. This is despite the fact that screening by colonoscopy can potentially remove nearly all colorectal tumours before they become malignant. Molecular genetics has identified some inherited mutations (such as at APC and the mismatch repair loci) that predispose to colon cancer and some somatic mutations (such as at APC and p53) that cause sporadic colon tumours. We review the likely role of these and other genes in colorectal tumorigenesis. We also highlight areas of relative ignorance in colon cancer and emphasise that many important genes, especially those that cause invasion and metastasis, remain to be identified. Colorectal cancer is, however, a well characterised tumour, as regards both its natural history and its histopathology; there are consequently good prospects for advances in colon cancer genetics, with probable benefits for its treatment. We anticipate: (a) that new genes predisposing to colon tumours, including those conferring relatively minor risks, will be characterised; (b) genes and proteins important in invasion and metastasis will be identified; (c) the network of protein interactions in which molecules such as APC are involved will be elucidated; (d) large-scale studies of somatic mutations in tumours will provide accurate predictions of prognosis and suggest optimal therapeutic regimens; and (e) new potential targets for therapy will be identified. Whilst molecular genetics is by no means sufficient for progress in preventing and treating colon cancer, it is a necessary and central part of such advances.     

Characterization of early induced genes in Arabidopsis thaliana responding to bacterial inoculation: identification of centrin and of a novel protein with two regions related to kinase domains

It is well known that significant differences exist in the anthropometric data of different races and ethnic groups. This is a cross-sectional study on segmental bone length based on 3,647 Chinese children of equal sex distribution aged 3-18 years. The measurements included standing height, weight, arm span, foot length, and segmental bone length of the humerus, radius, ulna, and tibia. A normality growth chart of all the measured parameters was constructed. Statistical analysis of the results showed a very high linear correlation of height with arm span, foot length, and segmental bone lengths with a correlation coefficient of 0.96-0.99 for both sexes. No differences were found between the right and left side of all the segmental bone lengths. These Chinese children were found to have a proportional limb segmental length relative to the trunk.     

Serum and ascitic concentration of C3, C4 and protein in cirrhotic patients with spontaneous bacterial peritonitis

BACKGROUND: Lower concentration of ascitic or serum complement (C3, C4) or protein has been reported to participate in the development of spontaneous bacterial peritonitis (SBP). In Taiwan, the etiology of hepatic cirrhosis is mainly post-hepatic and SBP is the common complication. This study aims to determine the role of protein and complements in the pathogenesis of SBP. METHODS: 119 cirrhotic patients were divided into two groups, 30 SBP and 89 non-SBP. The concentrations of ascitic and serum complement and protein were measured for comparison. RESULTS: The ascitic and serum C3, C4 and protein levels were significantly lower (P < 0.05) in patients with SBP than in non-SBP patients. No significant differences were noted in the ascites/serum ratio of C3, C4 and protein in patient with or without SBP. CONCLUSIONS: Low levels of ascitic and serum protein and complements, C3 and C4, may be prone to develop SBP in our patients mostly with post-hepatitic cirrhosis.