Search

Two papers in this issue of Molecular Microbiology from Carol Gross and colleagues describe experiments that investigate how two alternative Escherichia coliσ proteins recognize target promoter −10 regions. A combination of genetics, biochemistry and bioinformatics is used to show that determinants in two adjacent domains of the σ proteins contact discrete sequence elements in the −10 regions. [ABSTRACT FROM AUTHOR]

In the present study, silver nanoparticles (AgNPs) were synthesised by adding 1 mM Ag nitrate solution to different concentrations (1%, 2.5%, 5%) of branch extracts of Eurycoma longifolia, a well known medicinal plant in South–East Asian countries. Characterisation of AgNPs was carried out using techniques such as ultraviolet–visible spectrophotometry, X‐ray diffractrometry, Fourier transform infrared–attenuated total reflection spectroscopy (FTIR–ATR), scanning electron microscopy. XRD analysis revealed face centre cubic structure of AgNPs and FTIR–ATR showed that primary and secondary amide groups in combination with the protein molecules present in the branch extract were responsible for the reduction and stabilisation of AgNPs. Furthermore, antioxidant [2,2‐diphenyl‐1‐picrylhydrazyl and 2,2′‐Azino‐bis(3‐ethylbenzthiazoline‐6‐sulphonic acid)], antimicrobial and anticancer activities of AgNPs were investigated. The highest bactericidal activity of these biogenic AgNPs was found against Escherichia coli with zone inhibition of 11 mm. AgNPs exhibited significant anticancer activity against human glioma cells (DBTRG and U87) and human breast adenocarcinoma cells (MCF‐7 and MDA‐MB‐231) with IC50 values of 33, 42, 60 and 38 µg/ml. [ABSTRACT FROM AUTHOR]

The primary structure of protein S8 from the 30-S ribosomal subunit of Escherichia coil was determined mainly by automatic Edman degradation using a modified Beckman protein sequenator and the solid-phase sequenator of Laursen. The complete sequence, containing 109 amino acids, was derived by analysing peptides from tryptic, chymotryptic, thermolysin, staphylococcal protease and cyanogen bromide digestion of the protein. The amino acid composition was found to be (aspartic acid)6, (asparagine)3, (threonine)5, (serine)5, (glutamic acid)7, (glutamine)6, (proline)5, (glycine)6, (alanine)11, (valine)9, (methionine)4, (isoleucine)7, (leucine)9, (tyrosine)3, (phenylalanine)3, (lysine)11, (arginine)8, (cysteine)1. S8 is a basic protein and binds to the 16-S RNA; knowledge of its sequence is necessary for a detailed study of its interaction with the ribosomal RNA. [ABSTRACT FROM AUTHOR]

The present study reports the synthesis of silver nanoparticles (AgNPs) using both biological and chemical routes to find out the best method for control of their size and activity. The fungal agent (Fusarium oxysporum) and the plant (Azadirachta indica) were found to be the best source for AgNPs synthesis. Both biosynthesis and chemosynthesis were achieved by challenging filtrate with AgNO3 (1 mM) solution. The synthesised nanoparticles were characterised by ultraviolet–visible spectroscopy, Fourier transform infrared spectroscopy, nanoparticle tracking analysis (LM20), zeta potential measurement and transmission electron microscopy. The biologically synthesised nanoparticles were spherical, polydispersed and in the range of 10–40 nm, while chemically synthesised nanoparticles were highly monodispersed with a size of 5 nm. The antimicrobial assay against Escherichia coli and Staphylococcus aureus proved biogenic AgNPs to be more potent antibacterial agents than chemically synthesised AgNPs. The possible antibacterial mechanism of AgNPs has also been discussed. Biogenic AgNPs have shown more activity because of the protein capping and their mode of entry into the bacterial cell. These findings may encourage the use of biosynthesis over the chemosynthesis method. [ABSTRACT FROM AUTHOR]

Penicillin-binding protein (pbp) 1b, the main DD-transpeptidase/transglycosylase of Escherichia coli, is normally present in the cell in three molecular forms α, β and γ, differenciated by their mobility in sodium dodecyl sulfate/polyacrylamide gel electrophoresis. The three molecular forms are enzymatically active in vitro and their relative amounts are kept fairly constant in most labelling experiments with radioactive β-lactam antibiotics. In this paper, we have analyzed the expression of ponB (mrcB), the structural gone for pbp 1b, and the relation among the three forms of pbp 1b in ponB strains lysogenyzed by λ540 (ponB+) recombinant bacteriophages. Our data indicate that ponB is transcribed anti-clockwise on the E. coli chromosome and suggest that pbp 1bx is the first membrane-bound form of pbp 1b able to bind labelled β-lactams, and is the precursor of pbp 1bβ which is, in turn, the precursor of pbp 1bγ. [ABSTRACT FROM AUTHOR]

The accuracy of Qβ translation by Escherichia coli extracts in polymix and a conventional Tris/Mg2+ system has been followed. Misinsertions of histidine and of tryptophan into the phage coat protein were less frequent in polymix than in Tris/Mg2+, as were errors leading to u change in the coat protein pI. Even the lowest Qβ error rates, however, were still an order of magnitude greater than those for poly(U) or poly(U-G) translation. Comparing Qβ translational errors made in vitro to those found in whole cells, histidine misinsertions were almost twice as frequent, errors leading to a coat protein charge change six times more frequent and tryptophan misinsertions at least 15 times more frequent in vitro. The relation of these findings to measurements of translational accuracy and to factors affecting fidelity is discussed. [ABSTRACT FROM AUTHOR]

The complete primary structure of elongation factor Tu from Escherichia coli has been elucidated. The protein, which is a mixture of two gene products, consists of a single polypeptide chain of 393 residues. After tryptic digestion of S-carboxymethylated protein, 50 tryptic peptides were isolated covering the complete protein chain. Their alignment was established with overlapping peptides obtained by chemical cleavage with cyanogen bromide and subsequent enzymic subdigestion with Staphylococcus aureus protease, chymotrypsin, elastase and thermolysin. Peptides were sequenced by manual dansyl-Edman and direct Edman degradation procedures. The N-terminal amino acid of EF-Tu is serine and is N-acetylated. The lysine residue at position 56, in the polypeptide chain is partly methylated. The C-terminal residue is a mixture of serine and glycine, and this was the only heterogeneity found in the EF-Tu preparation used in this study. [ABSTRACT FROM AUTHOR]

Biomimetic synthesis of metal nanoparticles (NPs) is safe and eco‐friendly; therefore, find diverse applications. Considering this, the soil fungi Penicillium chrysogenum strain Fungal germplasm collection centre/ BLS1 was isolated, characterized and explored to synthesize extracellular silver NPs (AgNPs) under optimised conditions. The synthesis of AgNPs was investigated using ultraviolet (UV)–visible spectroscopy, Fourier‐transform infra‐red spectroscopy (FTIR), transmission electron microscope (TEM) and dynamic light scattering (DLS) analysis. Process optimisation exhibited AgNPs synthesis within 8 h using 2 mM AgNO3 at pH 11 and temperature 70°C. TEM analysis revealed polydispersed ellipsoidal shaped AgNPs with average particle size 96.8 nm as measured by DLS. AgNPs showed negative zeta potential that confers surface stability in solution. FTIR spectra confirmed the presence of protein bound to AgNPs. Antibacterial activity against Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus by the AgNPs (100 ppm) was demonstrated by counting colony forming unit, disc diffusion, and growth kinetics assay. Additionally radial assay revealed antifungal activity of AgNPs (100 ppm) against phytopathogenic fungi Sclerotinia sclerotiorum Microbial type culture collection 8785. Furthermore, AgNPs (100 ppm) did not show any cytotoxic effects on human Red blood cells. Therefore, this novel fungal strain can be utilised for biofabrication of AgNPs under optimised conditions and have shown strong antimicrobial property. [ABSTRACT FROM AUTHOR]

Background and Purpose: TAK-242, a novel synthetic small-molecule, suppresses production of multiple cytokines by inhibiting Toll-like receptor (TLR) 4 signalling. In this study, we investigated the target molecule of TAK-242 and examined its therapeutic effect in a mouse sepsis model.Experimental Approach: Binding assay with [(3)H]-TAK-242 and nuclear factor-kappaB reporter assay were used to identify the target molecule and binding site of TAK-242. Bacillus calmette guerin (BCG)-primed mouse sepsis model using live Escherichia coli was used to estimate the efficacy of TAK-242 in sepsis.Key Results: TAK-242 strongly bound to TLR4, but binding to TLR2, 3, 5, 9, TLR-related adaptor molecules and MD-2 was either not observed or marginal. Mutational analysis using TLR4 mutants indicated that TAK-242 inhibits TLR4 signalling by binding to Cys747 in the intracellular domain of TLR4. TAK-242 inhibited MyD88-independent pathway as well as MyD88-dependent pathway and its inhibitory effect was largely unaffected by lipopolysaccharide (LPS) concentration and types of TLR4 ligands. TAK-242 had no effect on the LPS-induced conformational change of TLR4-MD-2 and TLR4 homodimerization. In mouse sepsis model, although TAK-242 alone did not affect bacterial counts in blood, if co-administered with ceftazidime it inhibited the increases in serum cytokine levels and improved survival of mice.Conclusions and Implications: TAK-242 suppressed TLR4 signalling by binding directly to a specific amino acid Cys747 in the intracellular domain of TLR4. When co-administered with antibiotics, TAK-242 showed potent therapeutic effects in an E. coli-induced sepsis model using BCG-primed mice. Thus, TAK-242 may be a promising therapeutic agent for sepsis. [ABSTRACT FROM AUTHOR]

In Escherichia coli, rRNA operons are transcribed as 30S precursor molecules that must be extensively processed to generate mature 16S, 23S and 5S rRNA. While it is known that RNase III cleaves the primary transcript to separate the individual rRNAs, there is little information about the secondary processing reactions needed to form their mature 3′ and 5′ termini. We have now found that inactivation of the endoribonuclease RNase E slows down in vivo maturation of 16S RNA from the 17S RNase III cleavage product. Moreover, in the absence of CafA protein, a homolog of RNase E, formation of 16S RNA also slows down, but in this case a 16.3S intermediate accumulates. When both RNase E and CafA are inactivated, 5′ maturation of 16S rRNA is completely blocked. In contrast, 3′ maturation is essentially unaffected. The 5′ unprocessed precursor that accumulates in the double mutant can be assembled into 30S and 70S ribosomes. Precursors also can be processed in vitro by RNase E and CafA. These data indicate that both RNase E and CafA protein are required for a two step, sequential maturation of the 5′ end of 16S rRNA, and that CafA protein is a new ribonuclease. We propose that it be renamed RNase G. [ABSTRACT FROM AUTHOR]

To identify the ssDNA-binding domain of Escherichia coli RecA protein, we examined the ssDNA-binding capabilities of synthetic peptides, the sequences of which were derived from the C- and N-termini and from sequences within loops L1 and L2 of the RecA molecule identified from the crystal structure. Synthetic peptides derived from amino acid residues 185–219 of several bacterial RecA proteins, which include loop L2 of RecA, bound to ssDNA in filter-binding assays, whereas three separate synthetic peptides corresponding to single point mutants of E. coti RecA in this region did not. The binding of RecA to ssDNA examined using a gel-shill assay was inhibited by a synthetic peptide derived from this ssDNA-binding region, but not by synthetic peptides derived from amino acid residues 301–329 of the C-terminus or from N-terminal residues 6–39. A peptide corresponding to amino acid positions 152–169 of the RecA molecule and spanning loop L1 and its flanking regions did not bind ssDNA at peptide concentrations up to 250 μM. We have also defined a synthetic 20-amino-acid peptide that comprises amino acid residues 193–212 and includes loop L2 of RecA as the minimum unit that can bind to ssDNA from this region of RecA. Finally, two maltose-binding protein-RecA fusion proteins were made, one containing amino acid residues 185–224 of RecA and the other the last 51 C-terminal residues of RecA (amino acid residues 303–353). In contrast to the C-terminus-derived fusion protein, the fusion protein containing the putative DNA-binding site demonstrated significant binding to single-stranded oligonucleotides in both filter-binding and gel-shift assays. These findings suggest that a portion of the region extending from amino acid residues 193–212 is either part of or the whole ssDNA-binding domain of the RecA protein. [ABSTRACT FROM AUTHOR]

Focuses on [sup 1]H, [sup 13]C, [sup 15[N-NRM resonance assignments of oxidized thioredoxin h from the eukaryotic green alga Chlamydomonas reinhardtii using novel methods based on two-dimensional triple-resonance NRM spectroscopy and computer-assisted backbone assignment. Overexpression of cystolic thioredoxin h in E. coli; Secondary structure characteristics of thioredoxin h.

The mob mutants in Escherichia coil are pleiotropically defective in all molybdoenzyme activities. They synthesise molybdopterin, the unique core of the molybdenum cofactor, but are unable to attach the GMP moiety to molybdopterin to form molybdopterin guanine dinucleotide, the functional molybdenum cofactor in Escherichia coli. A partially purified preparation termed protein FA (protein factor d'association), is able to restore molybdoenzyme activities to broken cell preparations of mob mutants. A fragment of DNA capable of complementing mob mutants has been isolated from an E. coli genomic library. Strains carrying this DNA in a multicopy plasmid, express 30-fold more protein FA activity than the wild-type bacterium. Protein FA has been purified to homogeneity by a combination of ion-exchange, affinity and gel-filtration chromatography. Protein FA consists of a single polypeptide of molecular mass 22 kDa and is monomeric in solution. N-terminal amino acid sequencing confirmed that protein FA is a product of the first gene at the mob locus. The purified protein FA was required in stoichiometric rather than catalytic amounts in the process that leads to the activation of the precursor of the molybdoenzyme nitrate reductase, which is consistent with the requirement of a further component in the activation. [ABSTRACT FROM AUTHOR]

The TlpA protein of Bradyrhizobium japonicum was previously identified genetically as a membrane-anchored, periplasmic thioredoxin-like protein. Here we describe the heterologous expression in Escherichia coli, subsequent purification and biochemical characterization of TlpA. A soluble form of TlpA, which lacks its N-terminal membrane anchor, was overexpressed in E. coli and purified by a two-step procedure. Pure TlpA was shown to be a monomer in solution and was active in reducing the disulfides of insulin and in reactivating reduced, denatured RnaseA. Evidence is presented that two non-active-site cysteine residues form an intramolecular disulfide bond, a feature that is not normally found in other prokaryotic thioredoxins. [ABSTRACT FROM AUTHOR]

We previously found a trypsin-like proteinase which momentarily appears immediately before DNA synthesis in the cell cycle of Escherichia coli synchronized by phosphate starvation and which is closely related to the initiation of DNA replication (Kato, M., Irisawa, T., Morimoto, Y. and Muramatu, M., unpublished results). The proteinase was named proteinase In. It was purified approximately 2880-fold with a recovery of 15%. The isolated enzyme appeared homogeneous by gel filtration and electrophoresis. Its molecular mass was estimated by analytical gel filtration and SDS/PAGE as approximately 66 kDa. The isoelectric point of proteinase In is 4.9 and its optimal pH is approximately 9. Although protein In hydrolyzes fluorogenic substrate for trypsin, its hydrolytic activity seems markedly affected by amino-acid sequence lying towards the N-terminal from the P1 (lysine, arginine) residue. The proteinase does not hydrolyze N2-benzoyl-D,L-arginine-4-nitronanilide and fluorogenic substrates for chymotrypsin and elastase. The proteinase activity is inhibited by leupeptin, antipain and 4-nitrophenyl 4-guanidinobenzoate, but the effects of tosyl-L-lysine chloromethane, diisopropylfluorophosphate, benzamidine and pentamidine isethionate on the proteinase activity are weak or not inhibitory. Its activity is strongly affected in the presence of NaCl and KCl, and at a concentration of 1.5 M, these increase the activity 14-fold and 13-fold, respectively, above that without salt. Proteinase In was strongly inhibited by various esters of trans-4-guanidinome-thylcyclohexanecarboxylic acid, and their inhibitory effects were roughly correlated with those on growth of E. coli. Proteinase activity was found in the cytoplasmic fraction. [ABSTRACT FROM AUTHOR]

We recorded several types of heteronuclear three-dimensional (3D) NMR spectra on 15N-enriched and 13C/15N-enriched histidine-containing phosphocarrier protein, HPr, to extend the backbone assignments [van Nuland, N. A. J., van Dijk, A.A., Dijkstra, K., van Hoesel, F. H. J., Scheek, R. M. & Robillard, G. T. (1992) Eur. J. Biochem. 203, 483–491] to the side-chain 1H,15N and 13C resonances. From both 3D heteronuclear 1H-NOE 1H-13C and 1H-NOE 1H-15N multiple-quantum coherence (3D-NOESY-HMQC) and two-dimensional (2D) homonuclear NOE spectra, more than 1200 NOE were identified and used in a step-wise structure refinement process using distance geometry and restrained molecular dynamics involving a number of new features. A cluster of nine structures, each satisfying the set of NOE restraints, resulted from this procedure. The average root-mean-square positional difference for the Cα atoms is less than 0.12 nm. The secondary structure topology of the molecule is that of an open-face β sandwich formed by four antiparallel β strands packed against three α helices, resembling the recently published structure of Bacillus subtilis HPr, determined by X-ray crystallography [Herzberg, O., Reddy, P., Sutrina, S., Saier, M. H., Reizer, J. & Kapafia, G. (1992) Proc. Natl. Acad. Sci. USA 89, 2499–2503). [ABSTRACT FROM AUTHOR]

Murine interleukin-6 (IL-6), when expressed in Escherichia coil using the pUC9 vector, accumulated as insoluble aggregates or ‘inclusion bodies’. After selective urea washing of the inclusion bodies, to remove extraneous proteins, murine IL-6 was sohibilized with 8 M guanidine hydrochloride and then rapidly purified to homogeneity by gel-permeation chromatography followed by reversed-phase HPLC. It was demonstrated that complete disulfide bond formation in murine IL-6 occurred during the early urea washing/guanidine hydrochloride extraction steps, so no refolding step was required. When fully reduced murine IL-6 was dissolved in 8 M guanidine hydrochloride and allowed to air-oxidize, complete disulfide bond formation, monitored by analytical reversed-phase HPLC, was shown to occur within 13 h at 6°C. About 25 mg pure protein was obtained from 37 g wet cells. This recombinant murine 1L-6 had a specific activity in the hybridoma growth factor assay of 2×108 U/mg, which is equivalent to that of native murine IL-6. During the purification procedure, a number of variant forms of murine IL-6 were isolated and partially characterized. Two of these forms, T1 and T3, were C-terminal deletants of murine IL-6 lacking about 60 and 20 amino acids from the C-terminus, respectively, while the other form, T2, was an N-terminal deletant lacking 37 amino acids from the N-terminus. None of these variant forms of murine IL-6 bound to the murine IL-6 receptor and, consequently, all were inachve in the hybridoma growth factor assay. [ABSTRACT FROM AUTHOR]

The sequence of the tufA gene from the extreme thermophilic eubacterium Thermus aquaticus EP 00276 was determined. The GC content in third positions of codons is 89.5%, with an unusual predominance of guanosine (60.7%). The derived protein sequence differs from tufA- and tufB- encoded sequences for elongation factor Tu (EF-Tu) of Thermus thermophilus HB8, another member of the genus Thermus, in 10 of the 405 amino acid residues. Three exchanges are located in the additional loop of ten amino acids (182–191 ). The loop, probably involved in nucleotide binding, is absent in EF-Tu of the mesophile Escherichia coli. Since EF-Tu from E. coil is quite unstable, the protein is well-suited for analyzing molecular changes that lead to thermostabilization. Comparison of the EF-Tu domain I from E. coli and Thermus strains revealed clustered amino acid exchanges in the C-terminal part of the first helix and in adjacent residues of the second loop inferred to interact with the ribosome. Most other exchanges in the guanine nucleotide binding domain are located in loops or nearest vicinity of loops suggesting their importance for thermostability. The T. aquaticus EF-Tu was overproduced in E. coil using the tac expression system. Identity of the recombinant T. aquaticus EF-Tu was verified by Western blot analysis, N-terminal sequencing and GDP binding assays. [ABSTRACT FROM AUTHOR]

Wild-type recombinant horseradish peroxidase isoenzyme C and two protein variants, Phe41→ Val and Arg38→Lys, have been characterised using both one- and two-dimensional NMR spectroscopy. Proton NMR spectra recorded in both resting and cyanide-ligated states of the proteins were compared with those of the corresponding plant peroxidase. The latter contains 18% carbohydrate in eight N-linked oligosaccharide side chains whereas the recombinant proteins are expressed in non-glycosylated form. The spectra of the plant enzyme and refolded recombinant protein are essentially identical with the exception of carbohydrate-linked resonances in the former, indicating that their solution structures are highly similar. This comparison also identifies classes of carbohydrate resonances in the plant enzyme which provides new information on the local environment and mobility of the oligosaccharide side chains. Comparison of the spectra of the cyanide-ligated states of the two variants and those of plant horseradish peroxidase C indicated that there were significant differences with respect to haem and haem-linked resonances. These could not be rationalised simply on the basis of the local perturbation expected from a single-site substitution. The two substitutions made to residues on the distal side of the haem apparently influenced the degree of imidazolate character of the proximal His170 imidazole ring thus perturbing the magnetic environment of the haem group. Inspection of the spectra of the Phe41 → Val variant also showed that the resonances of a phenylalanine residue in the haem pocket had been incorrectly assigned to Phe41 in a previous study, A new assignment, based on additional information from two-dimensional nuclear Overhauser enhancement spectroscopy, was made to Phe152. The assignments made for the Phe41 → Val variant were also used as a basis lo investigate the structure of the complex formed with the aromatic donor molecule, benzhydroxamic acid. [ABSTRACT FROM AUTHOR]

The gene merP, coding for a mercuric-ion-binding periplasmic protein (P protein), was cloned into the expression vector pCA. In an Escherichia coli strain bearing the resulting plasmid, the P protein constitutes about 20% of total soluble protein. P protein was purified using ammonium sulfate precipitation and two chromatography steps. Typical yields were 20–30 mg from 7.5 I bacterial culture. The protein is a monomer with a molecular mass of 7500 Da. The periplasmic signal peptide was processed identically in both the recombinant and the wild-type proteins. CD spectra of both proteins were identical and indicated that the structure is highly ordered, containing approximately 80% α-helix. Purification in the presence of excess cysteine resulted in a form of the protein containing two reduced thiols, in agreement with the published sequence which has two cysteine residues. When cysteine was omitted from the purification buffers, no reduced thiol groups could be detected suggesting that the cysteine residues are oxidized. Both of these forms of the protein were found to bind approximately five Hg2+ ions/protein molecule in an apparently non-specific manner. However, in the presence of external thiol compounds, the protein with reduced thiols bound only one Hg2+ ion/protein molecule with an apparent Kd of 3.7 ± 1.3 μM. Under these conditions, the protein with oxidized thiols did not bind Hg2+. The possible physiological role of this protein in Hg2+ detoxification is discussed. [ABSTRACT FROM AUTHOR]

We have performed three-dimensional NMR studies on a central component of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli denoted as HPr. The protein was uniformly enriched with 15N and 13C to overcome spectral overlap. Complete assignments were obtained for the backbone ¹H, 15N and 13C resonances, using three-dimensional heteronuclear ¹H NOE ¹H-15N multiple-quantum coherence spectroscopy (3D-NOESY-HMQC) and three-dimensional heteronuclear total correlation ¹H-15N multiple-quantum coherence spectroscopy (3DTOCSY-HMQC) experiments on 15N-enriched HPr and an additional three-dimensional tripleresonance ¹HN-15N-13Cα correlation spectroscopy (HNCA) experiment on 13C, 15N-enriched HPr. Many of the sequential backbone ¹H assignments, as derived from two-dimensional NMR studies [Klevit, R. E., Drobny, G. P. & Waygood, E. B. (1986) Biochemistry 25, 7760-7769], were corrected. Almost all discrepancies are in the helical regions, leaving the published antiparallel β-sheet topology almost completely intact. [ABSTRACT FROM AUTHOR]

Escherichia coli glutaredoxin (85 amino acid residues, Mr = 9100), the glutathione-dependent hydrogen donor for ribonucleotide reductase, was purified from an inducible λPL expression system both with a natural isotope content and with uniform l5N labelling. This material was used for obtaining sequence-specific 1H magnetic resonance assignments and the identification of regular secondary structures in the oxidized form of the protein, which contains the redox-active disulfide Cysll-Pro-Tyr-Cysl4. Oxidized glutaredoxin contains a four-stranded β-sheet, with the peripheral strand 32–37 arranged parallel to the strand 2–7, which further combines with the two additional strands 61–64 and 67–69 in an antiparallel fashion. The protein further contains three helices extending approximately from residues 13–28, 45–54 and 72–84. [ABSTRACT FROM AUTHOR]

The UDP-N-acetylmuramoyl-L-atanyl-D-glutamate :meso-2.6-diaminopimclate ligase was over-produced and purified from two plasmid-harbouring strains of Escherichia coli. The first strain. E. coli JM83(pHE5), gave a 15-fold over-production relative to parental strain. The enzyme could be partially purified (8.8-fold) by ionexchange chromatography. With the second strain. E. coli JM83(pMLD25), a very strong over-production was obtained, since the enzyme represented about 20% of the cytoplasmic proteins. Purification yielded 77% protein homogeneity. However, the enzymatic activity, which was very unstable, was lost during the purification procedure. Several properties of the enzyme were studied. The enzyme gave maximal activity around pH 8. The isoelectric point was 5.2. The activity was increased by potassium phosphate. Reverse and exchange reactions could be catalysed. The N-terminal sequence of the protein was determined and correlated with the nucteotide sequence of the mute gene. The actual initiation codon was assigned. [ABSTRACT FROM AUTHOR]

The subunit association capacity of 30S and 50S ribosomal subunits from Escherichia coli mutants lacking protein S20 or L11 as well as of 50S subunits depleted of L7/L12 was tested by sucrose gradient centrifugation and by a nitrocellulose filtration method based on the protection from hydrolysis with peptidyl-tRNA hydrolase of ribosome-bound AcPhe-tRNA. It was found that the subunits lacking either S20 or L11 display an altered association capacity, while the 50S subunits lacking L7/L12 have normal association behavior. The association of S20-lacking 30S subunits is quantitatively reduced, especially at low Mg2+ concentrations (5–12 mM), and produces loosely interacting particles which dissociate during sucrose gradient centrifugation. The association of L11-lacking 50S subunits is quantitatively near-normal at all Mg2+ concentrations and produces loosely associating particles only at low Mg2+ concentrations (5–8 mM); the mechanism of their association with 30S subunits, however, or the structure of the resulting 30S–50S couples is altered in such a way as to cause the ejection of an AcPhe-tRNA molecule pre-bound to the 30S subunits in response to poly(U). [ABSTRACT FROM AUTHOR]

The cDNA and the chromosomal gene encoding proteinase K from Tritirachium album Limber have been cloned in Escherichia coli and the entire nucleotide sequences of the coding region, as well as 5'- and 3'-flanking regions have been determined. The deduced primary translation product consisting of 384 amino acid residues (molecular mass = 40231 Da) contains an N-terminal region of 105 amino acids not present in the mature protein. By analogy to the evolutionary-related bacterial subtilisins and other serine proteinases it is inferred that the primary secreted product is a zymogen containing a 15-amino-acid signal sequence and a 90-amino-acid propeptide. The propeptide is presumably removed in the later steps of the secretion process or upon secretion into the medium. The nucleotide-sequence analysis of the gene and its flanking regions has revealed that the proteinase-K gene is composed of two exons and one 63-bp-long intron located in the proregion. Furthermore, a putative promoter sequence and a capping site have been identified, suggesting that the transcription-start site is located 103-bp upstream of the ATG initiation codon. To express the proproteinase-K gene in E. coli, proproteinase-K cDNA was cloned in a plasmid vector under control of the tac promoter. The hybrid plasmid pSPPRO, constructed for this purpose, contained the cDNA coding for proproteinase K [from Ala (-91) to the C-terminal Ala (279)] fused to the N-terminal-signal-peptide sequence of the alkaline-phosphatase gene preceded by the fac promoter. E. coli BMH71-18, harbouring this plasmid, exhibited slight proteolytic activity when tested on skimmed-milk plates, suggesting that some fusion proteins were correctly secreted into the periplasm and processed to the mature proteinase K. [ABSTRACT FROM AUTHOR]

Based on sequence information from tryptic peptides an almost full-size cDNA coding for the human vascular anticoagulant was isolated from a placental cDNA library and sequenced. The coding region was cloned into an Escherichia coli expression vector and the protein expressed at high levels. The recombinant protein was purified and found to be indistinguishable from its natural counterpart in several biological assays. [ABSTRACT FROM AUTHOR]

The locations of proteins BL1, BL6, BL23 and BL29 from Bacillus stearothermophilus have been determined on the ribosomal surface by immunoelectron microscopy. All four proteins were localized in the same region of the 50S subunit as their homologous counterparts from Escherichia coli, indicating that the ribosomal architecture is the same in both species. This finding is of great importance as it allows structural data obtained on ribosomes from either organism to be incorporated into a unique ribosome model. [ABSTRACT FROM AUTHOR]

Maltooligosaccharides with two to six (α1-4)-linked glucose residues, carrying at their reducing end a 3-azi-1-methoxybutyl group in either α or in β glycosidic linkage, were synthesized. These maltooligosaccharide analogues inhibit maltose uptake via the maltose-binding-protein-dependent transport system in Escherichia coli. The concentration of half-maximal inhibition of maltose transport, at 15 nM concentration, decreases with increasing chain length of the analogue, levelling off at 40 µM after a chain length of four glucose residues in the α series and at 350 µM after a chain length of three glucose residues in the β series. The inhibition of maltose transport occurs at the level of the periplasmic maltose-binding protein. 3-Azi-1-methoxybutyl α-D-[⊃H]maltotrioside was bound by the maltose-binding protein with a Kd of 0.18 mM. Irradiation at 350 nm of purified maltose-binding protein in the presence of 4 µM of this substrate labeled the protein covalently; labeling was prevented by 1 mM maltose. Using a crude preparation of periplasmic proteins two proteins were labeled, the maltose-binding protein and α-amylase. Thus, 3-azi-1-methoxybutyl α-D-maltooligosaccharides are potent photoaffinity labels for proteins with maltooligosaccharides-binding sites. [ABSTRACT FROM AUTHOR]

An in vitro transcription-translation system was developed using cell-free extracts from the symbiotic nitrogen-fixing bacterium Rhizobium meliloti strain 41. Conditions for preparation of the 30 000 x g supernatant extract and for measurement of protein-synthesizing activity were determined and compared to the activity of an Eschericha coli cell-free system. Genes expressed in the free-living or in the symbiotic state were studied. The product of a recA-like gene (41-kDA protein) was synthesized both in R. meliloti and E. coli extracts, although less efficiently in the heterologous system. In agreement with earlier results obtained in E. coli minicells, three proteins (44, 28.5 and 23 kDa) were synthesized from a cloned 3.3 x 10⊃-base DNA region carrying genes for nodulation (nod). However, differences in the transcription-translation of nod and host specificity (hsn) genes were observed when protein expression was compared in R. meliloti and E. coli cell-free extracts, and the possible explanations of these findings are discussed. [ABSTRACT FROM AUTHOR]

The mutant strain of Escherichia coli, TP28, synthesises ribosomes by an abnormal pathway and accumulates large quantities of 47S ribonucleoprotein particles. The protein complement of mutant 70S ribosomes is normal but 47S particles contain only traces of proteins L28 and L33 and have a significantly reduced content of four other proteins. The mutation reduces the rates of synthesis of L28 and L33 by about half but other widespread alterations ensue. In particular, ribosomal protein synthesis in the mutant strain becomes less well balanced than in its parent: some proteins, particularly those from promoter-proximal genes, are oversynthesized and their excess then degraded. [ABSTRACT FROM AUTHOR]

The fidelity of Qβ RNA translation by intact Escherichia coli cells has been studied. After infection, host protein synthesis was eliminated by adding rifampicin and the radioactive, phage-specified, proteins separated by one or two-dimensional gel electrophoresis. Labeled histidine and tryptophan were incorporated into the phage coat protein, whose message does not specify these amino acids, at a frequency of 0.09–0.13 per molecule. Errors leading to a change in the pI of the coat protein occurred at a rate of 0.05 per molecule, while the coat protein UGA stop codon was misread 6.5% of the time. These error talcs arc similar to data in some recent publications but much higher than the canonical 3–4 × 10-4. They further provide are reference point in vivo to which the translation of the same message by E. coli extracts can be compared. [ABSTRACT FROM AUTHOR]

The proteins KdpD and KdpE are regulatory factors critically involved in the osmotic regulation of the kdpABC operon that is responsible for a high-affinity transport system in Escherichia coli. In this study, we obtained biochemical evidence supporting the view that the KdpD protein is a sensory protein kinase that exhibits autophosphorylation and KdpE-phospho-transfer characteristics. During the course of such studies we established a procedure for purifying the KdpE protein in large quantities. We also developed a procedure for preparing cytoplasmic membrane enriched with the KdpD protein that exhibits in vitro ability with regard to phosphorylation of KdpE protein. [ABSTRACT FROM AUTHOR]

Escherichia coli strains have been isolated in which 3, 39 or 805 5′-end codons of lacZ, the gene for the cytoplasmic enzyme β-galactosidase are fused to codon 9 of lacY, the gene for lactose permease. Lactose-permease-deficient cells, carrying the lacZ-Y fusions on F′ lac pro episomes, are phenotypically positive on eosin/methylene blue/lactose or on melibiose plates, demonstrating that the β-D-galactosidase-lactose-permease chimaeras transport lactose and melibiose in vivo. The apparent affinity for β-D-galactopypanosyl 1-thio-β-D-galactopyranoside (GalSGal) in cells is similar to that of the wild-type gene product. The maximum velocity of active GalSGal transport is reduced in all three fusion strains. Both lactose and p-nitrophenyl α-galactopyranoside inhibit GalSGal uptake. As demonstrated by immunoblot experiments the chimaeras cross-react with polyclonal antibodies directed against native lactose permease and they are present in the cell envelope fraction of homogenates. Their apparent molecular weights upon electrophoresis in NaDodSO4/polyacrylamide gels correspond to those expected from t heir respective primary sequences, taking into account the migration properties of wild-type lactose permease. It is proposed that substitution of eight N-terminal lactose permease residues by N-terminal β-galactosidase residues neither prevents membrane incorporation of permease nor completely impairs the ability In transport ,galactosides actively. Alternative interpretations of the experimental results are discussed. [ABSTRACT FROM AUTHOR]

The ompA gene from Enterobacter aerogenes was subcloned into a low-copy-number plasmid vector and the resultant plasmid, pTU7En, used to study its expression in Escherichia coli K12. Ahhough the gene was strongly expressed and large amounts of OmpA protein were present in the outer membrane its product was not functionally identical to the E. coli polypeptide. In particular, the E. aerogenes OmpA protein was unable to confer sensitivity to OmpA-specific phages of E. coli. When the primary structure of the protein was deduced from the nucleotide sequence of its gone it was found that three domains differed extensively from the corresponding regions of the E. coli protein. As two of these are known to be exposed on the cell surface we inferred that these alterations are responsible for differences in the biological activity of the two proteins. [ABSTRACT FROM AUTHOR]

From an Escherichia coli purine auxotroph a mutant defective in phosphoribosylpyrophosphate (PRib-PP) synthetase has been isolated and partially characterized. In contrast to the parental strain, the mutant was able to grow on nucleosides as purine source, whereas growth on purine bases was reduced. Kinetic analysis of the mutant PRib-PP synthetase revealed an apparent Km for ATP and ribose 5-phosphate of 1.0 mM and 240 µ;M respectively, compared to 60 µ;M and 45 µM respectively for the wild-type enzyme, ADP, which inhibits the wild-type enzyme at a concentration of 0.5 mM ribose 5-phosphate, stimulated the mutant enzyme. The activity of PRib-PP synthetase in crude extract was higher in the mutant than in the parent. When starved for purines an accumulation of PRib-PP was observed in the parent strain, while the pool decreased in the mutant. During pyrimidine starvation derepression of PRib-PP synthetase activity was observed in both strains, although to a lesser extent in the mutant. Our data suggest that the mutant harbors a mutation in the structural gene for PRib-PP synthetase. The mutation responsible for the altered PRib-PP synthetase was located in the purBhemA region at 26 min on the recalibrated linkage map. [ABSTRACT FROM AUTHOR]

Escherichia coli ribosomal protein S1 and its mutant, shorter, form m1-S1 were cleaved at internal methionyl residues to yield, respectively, six and five fragments of M1 ranging from 1000 to 24000. Methods are described to isolate the fragments in pure form. Four of the fragments (designated F2a, F2b, F3 and F4) contain between 86 and 215 amino acids and are therefore as large as other ribosomal proteins. Fragment F2a, derived from the N-terminal region, has previously been shown to contain the major ribosome binding domain of S1 [S. Giorginis and A. R. Subramanian (1980) J. Mot Biol. 1411 393 -408]. Here we show that the RNA binding domain of S1 is essentially contained in F3 derived from the middle region of S1 and carrying the nonreactive - SH group. The reactive a SF! group of SI, whose activity is modified by ligand binding, was localized in F2b, a fragment with little RNA binding capacity. The characteristic RNA binding domain and a weak ribosome binding domain of S1 have previously been localized in the large trypsin-resistent core SI-Fl [T. Suryanarayana and A. It Subramanian(1979) J. Mol. Biol. 127, 41-54]. Together these data indicate that two of the key functional domains of SI are located in two regions of the molecule separated by an open, exposed segment. The present study also revealed that the nonreactive - SM group of S1 becomes reactive in m1-S1 by the loss of the remote C-terminal region in the latter. [ABSTRACT FROM AUTHOR]

A method is described for the isolation of highly purified proteins from the 50-S subunit of Escherichia coli ribosomes. All the proteins from the large subunit could be isolated with the exception of L14, L26, L31 and L34. The isolated proteins are functionally active in reconstituted particles. The method consists of successive NH4Cl/EtOH and LiCl washing steps, which split off distinct groups of proteins from the ribosome. The protein groups are further separated by a combination of gel filtration (Sephadex G-100) and ion-exchange chromatography (carboxymethylcellulose) in the presence of 6 M urea, at neutral pH and 4°C. The purity of the proteins was analyzed by two-dimensional gel electrophoresis. In addition, ten protein complexes were isolated and identified. [ABSTRACT FROM AUTHOR]

Penicillin-binding proteins in Pseudomonas aeruginosa were compared with those of Escherichia coli. These in P. aeruginosa were found exclusively in the cytoplasmic membrane fraction (fraction soluble in sodium N-lauroyl sarcosinate). Sodium dodecyl sulfate/acrylamide gel electrophoresis of the proteins bound to [14C]penicillin G resulted in the separation of six major bands and several minor bands. The proteins in these bands are referred to as proteins 1A, 1B, 2, 3, 4 and 5 in order of increasing electrophoretical mobility. The electrophoretic mobilities and other properties of penicillin-binding proteins in P. aeruginosa and E. coli were compared and correlated. Fundamentally they seem to be very similar in the two bacteria, but proteins 1A and 1B in P. aeruginosa seem to correspond respectively to proteins 1B and 1A in E. coli, and protein 6 seems to be missing or present in only small amount in P. aeruginosa. In addition, the affinities of currently developed/Mactam antibiotics to each protein of P. aeruginosa and E. coli were examined in relation to the morphological changes of the cells induced by these antibiotics and their antibacterial potencies. Mecillinam showed high affinity to only protein 2 in both P. aeruginosa and E. coli. At a minimal inhibitory concentration, it converted cells of both P. aeruginosa and E. coli from rods to spherical cells, although its minimal inhibitory concentration was much higher for P. aeruginosa than for E. coli. [ABSTRACT FROM AUTHOR]

Purified non-histone proteins from mouse mammary cells bind specifically to homologous DNA or chromatin. Complexes of non-histone protein with DNA or chromatin, isolated on agarose columns, were transcribed with both Escherichia coli RNA polymerase and RNA polymerase B from calf thymus. The fact that complexing of DNA with non-histone proteins increases transcription by E. coli RNA polymerase but not by RNA polymerase B suggests different mechanisms of transcription by these two enzymes. Similar experiments with mouse and Drosophila chromatin indicate that non-histone proteins specifically stimulate the transcription of mouse chromatin by RNA polymerase B. Non-histone proteins stimulate the transcription of mouse mammary tumor virus sequences in chromatin by RNA polymerase B but not by E. coli RNA polymerase. We conclude that those non-histone proteins bound specifically to chromatin are able to activate the transcription of specific genes by eukaryotic RNA polymerase. [ABSTRACT FROM AUTHOR]

A membrane-bound fraction of polysomes of Escherichia coli has been isolated after lysis of cells without the use of lysozyme. Protein-synthesis studies in vitro show that membrane-bound and free polysomes are different in the following respects. 1. Membrane-bound polysomes synthesize proteins which are exported from the cell. The products include proteins of the outer membrane and secreted periplasmic protein, the maltose-binding protein. 2. The major product synthesized by free polysomes is elongation factor Tu, a soluble cytoplasmic protein. 3. The activity of membrane-bound polysomes in vitro is more resistant to puromycin than is the activity of free polysomes. In addition, the mRNA associated with membrane-bound polysomes is more stable than the bulk of cellular mRNA as revealed by studies with rifampicin. [ABSTRACT FROM AUTHOR]

Phosphofructokinase has been purified from Escherichia coli strain K-12 grown in a glucose-limited chemostat, both aerobically and anaerobically. The enzymes migrated together in polyacrylamide gel electrophoresis, had the same subunit size in denaturing (dodecylsulfate) gels Mr approx. 34000) and the same kinetic characteristics as described earlier for E. coli phosphofructokinase [e.g. Blangy et al. (1968) J. Mol. Biol. 31, 13–35]: a sigmoid curve of velocity vs. fructose 6-phosphate concentration, activation by ADP, and inhibition by phosphoenolpyruvate. Findings [e.g. Doelle (1975) Eur. J. Biochem. 50, 335–342] of quite different enzymes in aerobic and anaerobic cells were not confirmed. [ABSTRACT FROM AUTHOR]

Plasma membranes from Streptomyces albus had 5.2 mol of sulfhydryl groups and 6 mol of disulfide bridges/50 kg protein whereas Escherichia coli membranes had 3.4 mol sulfhydryl groups and 4 tool disulfide bridges/50 kg protein. About 66% of the sulfhydryl groups of S. albus membranes and 22% of those of E. coli membranes were readily accessible to titration with 5.5′-dithiobis(2-dinitrobenzoic acid). o-[(3 Hydroxymercuri-2-methoxypropyl)-carbamyl]-phenoxyacetic acid (mersalyc acid) and p-chloromercuribenzoate were effective in solubilizing membrane proteins from the two bacteria. Other sulfhydryl group reagents, such as N-ethylmaleimide, iodoacetamide and iodoacetic acid, were less effective. Dithiothreitol affected the dodecylsulphate gel electrophoresis patterns of S. albus membranes and soluble fractions. This effect resulted from the reduction of pre-existing disulfide intramolecular bridges and some interchain disulfide formed during solubilization and/or storage. Dithiothreitol also affected the dodecylsulphate gel electrophoresis patterns of E. co//membranes and their soluble fractions. These results suggest that sulfhydryl groups and disulfide bridges play a role in the structural organization of these prokaryotic membranes. [ABSTRACT FROM AUTHOR]

A high-molecular-weight, acidic protein whose amount per ribosomal particle depends on the growth cycle is shown to be associated with Escherichia coli ribosomes. The protein is associated with ribosomes from cells harvested at different phases of the growth cycle, hut a large increase in its amount is seen with ribosomes from post-exponential phase cells. The protein is only slightly washed off the ribosomes by 1 M NH4Cl. When ribosomes are dissociated it remains entirely with the 30-S subunits. We have purified the protein to homogeneity. It has a molecular weight of 70000 and its amino acid composition showed some resemblance to that of ribosomal protein S1. However, the two proteins are shown to be different. These results, together with the earlier-shown variation in the acetylation of L12 during the growth cycle, indicate that certain proteins of (or associated with) E. coli ribosomes may carry specific biochemical roles connected with cellular adaption toward the stationary phase. [ABSTRACT FROM AUTHOR]

The binding of 10 isomeric α-amino-heptanoic acids, of two isomeric α-amino-octanoic acids, of isoleucinol and valinol, and of various α-hydroxy acids to isoleucyl-tRNA synthetase from Escherichia coli MRE 600 has been investigated by an ultracentrifuge method. It was found that the enzyme requires a primary amino group together with a not-too-small side chain as prerequisites for ligand recognition. Though the enzyme is absolutely specific for the L isomers, it is fairly tolerant against replacement of the carboxyl group of the natural substrate by more or less hydrophobic substituents. These findings can be explained in terms of Ogston's three-point-attachment model, if it is additionally assumed that there is no further space available in the binding region normally occupied by the α-hydrogen atom to accept other substituents which are as bulky as the carboxyl moiety. Similarly, the architecture of the binding region of the aliphatic side chain is discussed. Our measurements show that the free energy of binding strongly depends on the size and the structure of the remainder of the molecule. None of the isoleucine analogues employed is bound as tightly as the natural substrate itself, but there is a clear preference for side chains branched at the/3-carbon atom. The functioning of the side-chain recognition site is best understood by imagining a two-finger glove, of which one finger is tailored to a methyl and the other to an ethyl group. Both these fingers, together with the binding region for the glycine moiety and a steric barrier against a fourth substituent bulkier than hydrogen, are responsible for a high steric specificity towards the one side chain over its Cβ epimer. [ABSTRACT FROM AUTHOR]

A cleavable bifunctional reagent, dimethyl 3,3′-dithiobispropionimidate, has been used to crosslink proteins that occupy neighboring positions in the 30-S ribosomal subunit of Escherichia coli. The crosslinked proteins were identified, fully or partly, by their positions in two two-dimensional gel electrophoretic systems, one diagonal and the other quasi-diagonal, in which the complexes were cleaved after the first-dimensional run. It was found to be necessary to block the protein sulfhydryl groups in order to prevent artifactual disulfide crosslinking after extraction of the protein from the ribosome. Eleven crosslinked complexes were detected. Four were fully identified: the triplet S4-S5-S8, and the pairs s2-S3, S4-S5, and S5-S8. In five others one component was identified unambiguously. No additional complexes were seen when the longer homologous butyro and capro reagents were used. [ABSTRACT FROM AUTHOR]

16-S RNA and five pure ribosomal proteins (S3, S4, S6, S7 and S8) from Escherichia coli 30-S subunits were studied by circular dichroism in regard to the reconstitution of biologically active subunits. A small structural variation upon heating could be measured for RNA. It cannot be interpreted in terms of stacking or disruption of hydrogen bonds. However, most proteins underwent important structural modifications when heated to 42 °C in reconstitution solvent. This effect was not dependent on the presence of magnesium salt. The relative amounts of secondary structure of native and heat-denatured ribosomal proteins were calculated by using three reference curves obtained from standard proteins, the exact secondary structure of which has been determined by X-ray crystallography. In contrast with earlier results, about 18 %, β-structure was detected in native proteins. This discrepancy can most probably be attributed to the calculation method used. Results are discussed in relation to reconstitution of ribosomes. [ABSTRACT FROM AUTHOR]