51
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Lampinen J, Virta M, Karp M. Use of controlled luciferase expression to monitor chemicals affecting protein synthesis. Appl Environ Microbiol 1995; 61:2981-9. [PMID: 16535100 PMCID: PMC1388554 DOI: 10.1128/aem.61.8.2981-2989.1995] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this article, we present a new bioluminescent test system for the screening of chemical compounds with an inhibitory effect on protein synthesis. The test is based on the measurement of real-time in vivo light production by Escherichia coli strains expressing different luciferase genes. The eukaryotic lucGR gene from Pyrophorus plagiophthalamus was found to be the best of three types of luciferase genes tested. Chemicals with known inhibitory effects on protein synthesis were used as test chemicals together with some general toxicants. The incubation of a test chemical with cells was performed either prior to or after the induction of protein synthesis, and the difference in the results of the two methods distinguishes the possible influence on protein synthesis from direct metabolic inhibition. Using lyophilized bacteria, the test is performed in less than an hour without any bacterial cultivation, which makes the test suitable for rapid and sensitive screening of chemicals or environmental samples. Compared with the standardized 50% inhibitory concentration calculation method of the bioluminescent cytotoxicity test, the more direct approach of calculation developed in this study proved to be more convenient than and as reliable as the standard method.
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52
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Alfano JR, Ham JH, Collmer A. Use of Tn5tac1 to clone a pel gene encoding a highly alkaline, asparagine-rich pectate lyase isozyme from an Erwinia chrysanthemi EC16 mutant with deletions affecting the major pectate lyase isozymes. J Bacteriol 1995; 177:4553-6. [PMID: 7635842 PMCID: PMC177214 DOI: 10.1128/jb.177.15.4553-4556.1995] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Erwinia chrysanthemi mutant CUCPB5047, delta(pelA pelE) delta(pelB pelC)::28bp delta(pelX) delta 4bp pehX::omega Cmr, was constructed, mutated with Tn5tac1, and screened for isopropyl-beta-D-thiogalactopyranoside-dependent pectate lyase (Pel) production. A Kmr SacI fragment from the hyperexpressing Pel+ mutant CUCPB5066 was cloned into Escherichia coli and sequenced. The gene identified, pelL, encodes a novel, asparagine-rich, highly alkaline enzyme that is similar in primary structure to PelX and in enzymological properties to PelE.
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Affiliation(s)
- J R Alfano
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853-4203, USA
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53
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Guzman LM, Belin D, Carson MJ, Beckwith J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 1995; 177:4121-30. [PMID: 7608087 PMCID: PMC177145 DOI: 10.1128/jb.177.14.4121-4130.1995] [Citation(s) in RCA: 4005] [Impact Index Per Article: 138.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We have constructed a series of plasmid vectors (pBAD vectors) containing the PBAD promoter of the araBAD (arabinose) operon and the gene encoding the positive and negative regulator of this promoter, araC. Using the phoA gene and phoA fusions to monitor expression in these vectors, we show that the ratio of induction/repression can be 1,200-fold, compared with 50-fold for PTAC-based vectors. phoA expression can be modulated over a wide range of inducer (arabinose) concentrations and reduced to extremely low levels by the presence of glucose, which represses expression. Also, the kinetics of induction and repression are very rapid and significantly affected by the ara allele in the host strain. Thus, the use of this system which can be efficiently and rapidly turned on and off allows the study of important aspects of bacterial physiology in a very simple manner and without changes of temperature. We have exploited the tight regulation of the PBAD promoter to study the phenotypes of null mutations of essential genes and explored the use of pBAD vectors as an expression system.
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Affiliation(s)
- L M Guzman
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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54
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Lyngstadaas A, Løbner-Olesen A, Boye E. Characterization of three genes in the dam-containing operon of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:546-54. [PMID: 7603433 DOI: 10.1007/bf00290345] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The dam-containing operon in Escherichia coli is located at 74 min on the chromosomal map and contains the genes aroK, aroB, a gene called urf74.3, dam and trpS. We have determined the nucleotide sequence between the dam and trpS genes and show that it encodes two proteins with molecular weights of 24 and 27 kDa. Furthermore, we characterize the three genes urf74.3, 24kDa, 27kDa and the proteins they encode. The predicted amino acid sequences of the 24 and 27 kDa proteins are similar to those of the CbbE and CbbZ proteins, respectively, of the Alcaligenes eutrophus cbb operon, which encodes enzymes involved in the Calvin cycle. In separate experiments, we have shown that the 24 kDa protein has d-ribulose-5-phosphate epimerase activity (similar to CbbE), and we call the gene rpe. Similarly, the 27 kDa protein has 2-phosphoglycolate phosphatase activity (similar to CbbZ), and we name the gene gph. The Urf74.3 protein, with a predicted molecular weight of 46 kDa, migrated as a 70 kDa product under denaturing conditions. Overexpression of Urf74.3 induced cell filamentation, indicating that Urf74.3 directly or indirectly interferes with cell division. We present evidence for translational coupling between aroB and urf74.3 and also between rpe and gph. Proteins encoded in the dam superoperon appear to be largely unrelated: Dam, and perhaps Urf74.3, are involved in cell cycle regulation, AroK, AroB, and TrpS function in aromatic amino acid biosynthesis, whereas Rpe and Gph are involved in carbohydrate metabolism.
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Affiliation(s)
- A Lyngstadaas
- Department of Biophysics, Institute for Cancer Research, Montebello, Oslo, Norway
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55
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Nielsen AK, Gerdes K. Mechanism of post-segregational killing by hok-homologue pnd of plasmid R483: two translational control elements in the pnd mRNA. J Mol Biol 1995; 249:270-82. [PMID: 7783193 DOI: 10.1006/jmbi.1995.0296] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The pnd system of plasmid R483 mediates plasmid stabilization by killing of plasmid-free cells. The pnd mRNA is very stable and can be translated into PndA protein, a cell toxin which kills the cells from within by damaging the cell membrane. Translation of the pnd mRNA is inhibited by the PndB antisense, a small labile RNA of 63 nt. The rapid decay of the PndB antidote leads to onset of PndA synthesis in plasmid-free segregants or after addition of rifampicin. Surprisingly however, the full-length pnd mRNA was found to be translationally inactive whereas a 3'-end truncated version of it was found to be active. We have therefore suggested previously, that the 3'-end of the full-length pnd mRNA encodes a fold-back inhibitory sequence (fbi), which prevents its translation. Here we present an analysis of the metabolism of the pnd mRNAs. A mutational analysis shows that single point mutations in the fbi motif results in more rapid truncation. The fbi mutations could not be complemented by second-site mutations in either of the pndA or pndC Shine-Dalgarno (SD) elements. Surprisingly, mutations in the pndC SD element also lead to a more rapid truncation. The effect of these latter mutations was, however, complemented by mutations in a proposed anti-SD element upstream of the pndC SD. Mutations in the anti-SD element were lethal. These results show, that the pnd mRNA contains two negative control elements, one located in its very 3'-end (fbi), and one located just upstream of the pndC SD region (the anti-SD element). These observations add to the complexity of the induction scheme previously proposed to explain activation of pndA expression in plasmid-free cells: In addition to its negative effect of translation, the fbi structure also maintains a reduced processing rate in the 3'-end of the mRNA. This permits the accumulation of a reservoir of pnd mRNA, which can be activated by 3'-end processing in plasmid-free cells. The anti-SD may prevent translation of the pnd mRNA during transcription, thus preventing detrimental synthesis of toxin.
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Affiliation(s)
- A K Nielsen
- Department of Molecular Biology, Odense University, Denmark
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56
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Bernander R, Akerlund T, Nordström K. Inhibition and restart of initiation of chromosome replication: effects on exponentially growing Escherichia coli cells. J Bacteriol 1995; 177:1670-82. [PMID: 7896687 PMCID: PMC176792 DOI: 10.1128/jb.177.7.1670-1682.1995] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Escherichia coli strains in which initiation of chromosome replication could be specifically blocked while other cellular processes continued uninhibited were constructed. Inhibition of replication resulted in a reduced growth rate and in inhibition of cell division after a time period roughly corresponding to the sum of the lengths of the C and D periods. The division inhibition was not mediated by the SOS regulon. The cells became elongated, and a majority contained a centrally located nucleoid with a fully replicated chromosome. The replication block was reversible, and restart of chromosome replication allowed cell division and rapid growth to resume after a time delay. After the resumption, the septum positions were nonrandomly distributed along the length axis of the cells, and a majority of the divisions resulted in at least one newborn cell of normal size and DNA content. With a transient temperature shift, a single synchronous round of chromosome replication and cell division could be induced in the population, making the constructed system useful for studies of cell cycle-specific events. The coordination between chromosome replication, nucleoid segregation, and cell division in E. coli is discussed.
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Affiliation(s)
- R Bernander
- Department of Microbiology, Uppsala University, Sweden
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57
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Kronemeyer W, Peekhaus N, Krämer R, Sahm H, Eggeling L. Structure of the gluABCD cluster encoding the glutamate uptake system of Corynebacterium glutamicum. J Bacteriol 1995; 177:1152-8. [PMID: 7868586 PMCID: PMC176718 DOI: 10.1128/jb.177.5.1152-1158.1995] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To assess the mechanism and function of the glutamate uptake system of gram-positive Corynebacterium glutamicum, a mutant deficient in glutamate uptake was isolated and was then used to isolate a DNA fragment restoring this deficiency. In a low-copy-number vector, this fragment resulted in an increased glutamate uptake rate of 4.9 nmol/min/mg (wild type, 1.5 nmol/min/mg). In addition, carbon source-dependent regulation of the glutamate uptake system was determined with the fragment, showing that the entire structures required for expression and control reside on the fragment isolated. Sequencing of 3,977 bp revealed the presence of a four-gene cluster (gluABCD) with deduced polypeptide sequences characteristic of a nucleotide-binding protein (GluA), a periplasmic binding protein (GluB), and integral membrane proteins (GluC and GluD), identifying the glutamate transporter as a binding protein-dependent system (ABC transporter). This identification was confirmed by the kinetic characteristics obtained for cells grown in the presence of globomycin, which exhibited an increased Km of 1,400 microM (without globomycin, the Km was 1.5 microM) but a nearly unaltered maximum velocity. By applying gene-directed mutagenesis, a strain with the entire cluster deleted was constructed. With this mutant, the glutamate uptake rate was reduced from 1.4 to less than 0.1 nmol/min/mg, which is proof that this system is the only relevant one for glutamate uptake. With this strain, the glutamate excretion rate was unaffected (18 nmol/min/mg), showing that no component of gluABCD is involved in export but rather that a specific machinery functions for the latter purpose.
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Affiliation(s)
- W Kronemeyer
- Institut für Biotechnologie 1, Forschungszentrum Jülich GmbH, Germany
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58
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Vester B, Douthwaite S. Domain V of 23S rRNA contains all the structural elements necessary for recognition by the ErmE methyltransferase. J Bacteriol 1994; 176:6999-7004. [PMID: 7961464 PMCID: PMC197073 DOI: 10.1128/jb.176.22.6999-7004.1994] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The ErmE methyltransferase from the erythromycin-producing actinomycete Saccharopolyspora erythraea dimethylates the N-6 position of adenine 2058 in domain V of 23S rRNA. This modification confers resistance to erythromycin and to other macrolide, lincosamide, and streptogramin B antibiotics. We investigated what structural elements in 23S rRNA are required for specific recognition by the ErmE methyltransferase. The ermE gene was cloned into R1 plasmid derivatives, providing a means of inducible expression in Escherichia coli. Expression of the methyltransferase in vivo confers resistance to erythromycin and clindamycin. The degree of resistance corresponds to the level of ermE expression. In turn, ermE expression also correlates with the proportion of 23S rRNA molecules that are dimethylated at adenine 2058. The methyltransferase was isolated in an active, concentrated form from E. coli, and the enzyme efficiently modifies 23S rRNA in vitro. Removal of most of the 23S rRNA structure, so that only domain V (nucleotides 2000 to 2624) remains, does not affect the efficiency of modification by the methyltransferase. In addition, modification still occurs after the rRNA tertiary structure has been disrupted by removal of magnesium ions. We conclude that the main features that are specifically recognized by the ErmE methyltransferase are displayed within the primary and secondary structures of 23S rRNA domain V.
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Affiliation(s)
- B Vester
- Department of Molecular Biology, Odense University, Denmark
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59
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Lebedeva MI, Rogozhkina EV, Tsyba NA, Mashko SV. A new T7 RNA polymerase-driven expression system induced via thermoamplification of a recombinant plasmid carrying a T7 promoter-Escherichia coli lac operator. Gene 1994; 142:61-6. [PMID: 8181758 DOI: 10.1016/0378-1119(94)90355-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A new temperature-regulated T7 RNA polymerase-driven transcription system has been developed. This system is based on a hybrid regulatory region: the phage T7 late promoter (PT7) linked to the Escherichia coli lac operator (Olac) [Giordano et al., Gene 84 (1989) 209-219], which was located in an earlier obtained [Mashko et al., Gene 97 (1991) 259-266] temperature-controlled amplifiable plasmid, carrying cat under the control of PT7-Olac and, in addition, lambda major early promoter-operator regions and gene cIts857. Plasmids of the pT7-Olac-cat-tsr series were stably maintained at a low-copy-number when grown at low temperature (28 degrees C). In E. coli BL21(DE3), carrying the Plac-controllable T7 RNA polymerase-encoding gene, efficient repression of cat transcription was observed, that was provided by the LacI repressor and, probably, the thermolabile repressor CIts857. At low and moderate temperatures (28/37 degrees C), this 'cooperative' repression was so tight that cat expression was not observed in the cells carrying PT7-Olac on the plasmids, even after IPTG-inducible T7 RNA polymerase biosynthesis. As a result of the thermo-amplification of the recombinant plasmids and temperature-inactivation of CIts857, expression of the T7 RNA polymerase-encoding gene was derepressed due to the titration of LacI by the increasing copies of Olac which in turn, led to the highly efficient T7 RNA polymerase-driven accumulation of CAT in the cells.
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Affiliation(s)
- M I Lebedeva
- Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
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60
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Rasmussen SW. Sequence of a 28.6 kb region of yeast chromosome XI includes the FBA1 and TOA2 genes, an open reading frame (ORF) similar to a translationally controlled tumour protein, one ORF containing motifs also found in plant storage proteins and 13 ORFs with weak or no homology to known proteins. Yeast 1994; 10 Suppl A:S63-8. [PMID: 8091862 DOI: 10.1002/yea.320100008] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The complete DNA sequence of cosmid clone pUKG148 comprising 28,600 base pairs was determined from an ordered set of subclones. The sequence contains 22 open reading frames longer than 100 amino acids of which five are entirely covered by other, longer reading frames. YKL054 exhibits 25% homology at the amino acid level to a number of plant storage proteins of the glutenin type, YKL056 is 40% homologous to a translationally controlled mammalian tumour protein, YKL058 (TOA2) is identical to the small subunit of transcription factor TFIIA from yeast and YKL060 is identical to the FBA1 gene also from yeast, already sequenced but not mapped to chromosome XI. The remaining 13 open reading frames show weak or no homology to known genes.
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Affiliation(s)
- S W Rasmussen
- Department of Physiology, Carlsberg Laboratory, Copenhagen, Denmark
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61
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Dam M, Gerdes K. Partitioning of plasmid R1. Ten direct repeats flanking the parA promoter constitute a centromere-like partition site parC, that expresses incompatibility. J Mol Biol 1994; 236:1289-98. [PMID: 8126720 DOI: 10.1016/0022-2836(94)90058-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The parA partitioning system of plasmid R1 consists of three different components: the cis-acting centromere-like parC site, and the two trans-acting proteins ParM and ParR. These three components are contained within a region of 1.6 kb. The parC site is located upstream of the two genes, parM and parR, which are expressed as an operon from the parA promoter. The parC site contains an array of ten 11 base-pair direct repeats, organized in two sets of five repeats flanking the parA core promoter sequences. Deletions and point mutations were introduced in the parA locus, resulting in partially stable and unstable plasmids. An analysis of these parA- plasmids showed that ParM and ParR are transacting. The 160 bp minimal parC region contained sufficient in cis information for efficient trans-complementation. Both proteins were required for maximal stabilization of a parC+ mini-R1 plasmid, although ParR alone, donated either in cis or in trans, yielded partial stabilization. Plasmids that overexpressed ParR caused destabilization of a co-resident parA+ plasmid, whereas overexpression of ParM had no such effect. The parC site exerted incompatibility (incA) at high but not at low copy number. Likewise, the entire parA system exerted incompatibility in a copy number-dependent fashion, and stronger than the incompatibility expressed by parC alone.
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Affiliation(s)
- M Dam
- Department of Molecular Biology, Odense University, Denmark
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62
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Williams MD, Ouyang TX, Flickinger MC. Starvation-induced expression of SspA and SspB: the effects of a null mutation in sspA on Escherichia coli protein synthesis and survival during growth and prolonged starvation. Mol Microbiol 1994; 11:1029-43. [PMID: 8022275 DOI: 10.1111/j.1365-2958.1994.tb00381.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Maxicell labelling and two-dimensional gel electrophoresis (2-D PAGE) have identified the proteins encoded by sspA and sspB (SspA, SspB) as proteins D27.1 and A25.8, respectively, in the Escherichia coli gene-protein database. SspA expression increases with decreasing growth rate and is induced by glucose, nitrogen, phosphate or amino acid starvation. The promoter, Pssp, is similar to gearbox promoters. Inactivation of SspA (sspA::neo) blocks sspB expression. [35S]-methionine-labelled proteins synthesized during growth and during stationary phase are different in delta sspA strains compared to sspA+ strains. This difference is enhanced during extended stationary phase (24-72 h). Long-term (10 d) viability of arginine-starved isogenic strains shows that sspA+ cultures remain viable significantly longer than delta sspA mutants. 2-D PAGE of proteins expressed during exponential growth shows that expression of at least 11 proteins is altered in delta sspA strains. A functional relA gene is required for sspA to affect protein synthesis.
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Affiliation(s)
- M D Williams
- Department of Biochemistry, University of Minnesota, Saint Paul 55108-6106
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63
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Suzuki T, Murai T, Fukuda I, Tobe T, Yoshikawa M, Sasakawa C. Identification and characterization of a chromosomal virulence gene, vacJ, required for intercellular spreading of Shigella flexneri. Mol Microbiol 1994; 11:31-41. [PMID: 8145644 DOI: 10.1111/j.1365-2958.1994.tb00287.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Intercellular spreading of shigellae is a prerequisite for shigellosis, although the molecular mechanisms underlying the phenomenon are still largely obscure. To elucidate some of these mechanisms, we performed random Tn10 insertion mutagenesis in Shigella flexneri YSH6000T and found a chromosomal locus in the NotI-J segment responsible for bacterial spreading. The locus affected in the mutant, designated vacJ, was neither involved in the invasion of epithelial cells nor in intracellular movement, but was required for intercellular spread. The vacJ mutant was capable of forming bacterium-containing membranous protrusions within the infected cell, but had diminished ability to move from the protrusions into the cytoplasm of the adjacent epithelial cells. Cloning and sequencing of the vacJ region indicated that the vacJ gene encoded a 28.0 kDa protein possessing a signal peptide at the N-terminus, which contained the motif characteristic of lipoproteins. The analysis of the vacJ product indicated that VacJ was exposed on the bacterial surface. The vacJ gene was distributed among shigellae and enteroinvasive Escherichia coli, and the constructed vacJ mutants failed to spread intercellularly, indicating that vacJ is a chromosomal gene essential for the pathogenicity of shigellae.
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Affiliation(s)
- T Suzuki
- Department of Bacteriology, University of Tokyo, Japan
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64
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Wülfing C, Plückthun A. A versatile and highly repressible Escherichia coli expression system based on invertible promoters: expression of a gene encoding a toxic product. Gene 1993; 136:199-203. [PMID: 8294003 DOI: 10.1016/0378-1119(93)90464-e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A very flexible and tightly regulatable expression system has been constructed. It uses the principle of invertible promoters [Podhajska et al., Gene 40 (1985) 163-168]. Here, we describe the construction of a plasmid that provides the integrase, which causes promoter inversion in a tightly regulated fashion, as well as modified plasmids carrying the invertible module. The way the integrase is provided on a separate plasmid closely mimicks expression of the integrase from a lambda lysogen. Thus, the flexibility of the original system is considerably extended by making it strain-independent without compromising the tight regulation. We present the expression of a single-chain T-cell receptor fragment as an example of application, in order to illustrate the properties of this expression system.
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Affiliation(s)
- C Wülfing
- Protein Engineering Group, Max-Planck-Institut für Biochemie, Martinsried, Germany
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65
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Borel F, Härtlein M, Leberman R. In vivo overexpression and purification of Escherichia coli tRNA(ser). FEBS Lett 1993; 324:162-6. [PMID: 7685296 DOI: 10.1016/0014-5793(93)81385-d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
DNA fragments corresponding to the sequences of Escherichia coli tRNA(2ser) and amber suppressor tRNA(ser), were synthesized from overlapping oligonucleotides. These were interposed between a strong promotor and a synthetic transcriptional terminator to ensure the production of a transcript of the correct size. The genes of promotor, fragment and terminator were cloned into a conditional runaway replication plasmid. At temperatures below 37 degrees C this vector has a low copy number but, following a temperature shift to 42 degrees C, the copy number is no longer regulated. Using these constructs an overexpression of tRNA(ser) of about 20 times the level of the wild-type pool could be obtained (corresponding e.g. to 200 times the expression tRNA(2ser)). From these systems 10 mg quantities of tRNA(ser)s could be isolated with a serine acceptance of 1,100 pmol/A280 unit.
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Affiliation(s)
- F Borel
- European Molecular Biology Laboratory, Grenoble Outstation, France
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66
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Reuven NB, Deutscher MP. Substitution of the 3' terminal adenosine residue of transfer RNA in vivo. Proc Natl Acad Sci U S A 1993; 90:4350-3. [PMID: 7685099 PMCID: PMC46508 DOI: 10.1073/pnas.90.10.4350] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We have altered by site-directed mutagenesis the 3' terminal adenosine residue of a tRNA(Tyrsu3+) gene encoded on a single-copy plasmid and examined the consequences of these substitutions on suppressor activity in vivo. Our data show that mutant su3 genes containing 3'-CCC, -CCG, or -CCU termini instead of -CCA can be efficiently transcribed and processed in Escherichia coli to generate functional suppressor tRNAs. However, in contrast to normal tRNA genes, both tRNA nucleotidyltransferase and exoribonuclease activities are required to obtain suppression by the mutant tRNAs, indicating that removal of the incorrect 3' terminal residue and resynthesis of the normal -CCA terminus are occurring in this situation. In addition, a low level of suppressor activity and tRNA repair was found in cells devoid of tRNA nucleotidyltransferase, suggesting that an additional activity able to partially repair the 3' end of tRNA is present in E. coli. The use of mutant strains lacking one or several exoribonucleases revealed that the various RNAses have very different specificities for removal of incorrect 3' residues and that these differ greatly from their action on CCA-ending tRNA. These data show that the 3' terminal adenosine residue is necessary for tRNA function in vivo and that cells can compensate for its alteration by changes in the normal pathway of tRNA metabolism.
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Affiliation(s)
- N B Reuven
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06030-3305
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67
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Hjalt T, Wagner EG. The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control. Nucleic Acids Res 1992; 20:6723-32. [PMID: 1282705 PMCID: PMC334592 DOI: 10.1093/nar/20.24.6723] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Most natural antisense RNAs display a high degree of secondary structure with stem-loops as their most prominent feature. Mutations affecting the inhibitory activity of these RNAs most often map in or close to loop regions in both the antisense and target RNAs. The primary recognition loops often contain 5-7 unpaired nucleotides. Nucleotide changes in the loops affect the binding rate and, hence, the inhibitory effect on the activity of the target RNA. Here we address the question whether loop sizes affect binding rates between antisense and target RNAs, using the replication control system of plasmid R1 as a model system. By creating a series of loop size mutants we show that loop size alterations have strong effects on the binding rates between the two reactant RNAs in vitro, and that most of the mutations analyzed display corresponding effects on antisense RNA control in vivo. Our data suggest that the three-dimensional structures of antisense and target RNA stem-loops are crucial for determining binding rates. The implications of these results for the design of efficient artificial antisense RNA control systems are discussed.
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Affiliation(s)
- T Hjalt
- Department of Microbiology, Uppsala University, Sweden
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68
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Xu GL, Kapfer W, Walter J, Trautner TA. BsuBI--an isospecific restriction and modification system of PstI: characterization of the BsuBI genes and enzymes. Nucleic Acids Res 1992; 20:6517-23. [PMID: 1480472 PMCID: PMC334566 DOI: 10.1093/nar/20.24.6517] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The enzymes of the Bacillus subtilis BsuBI restriction/modification (R/M) system recognize the target sequence 5'CTGCAG. The genes of the BsuBI R/M system have been cloned and sequenced and their products have been characterized following overexpression and purification. The gene of the BsuBI DNA methyltransferase (M.BsuBI) consists of 1503 bp, encoding a protein of 501 amino acids with a calculated M(r) of 57.2 kD. The gene of the restriction endonuclease (R.BsuBI), comprising 948 bp, codes for a protein of 316 amino acids with a predicted M(r) of 36.2 kD. M.BsuBI modifies the adenine (A) residue of the BsuBI target site, thus representing the first A-N6-DNA methyltransferase identified in B. subtilis. Like R.PstI, R.BsuBI cleaves between the A residue and the 3' terminal G of the target site. Both enzymes of the BsuBI R/M system are, therefore, functionally identical with those of the PstI R/M system, encoded by the Gram negative species Providencia stuartii. This functional equivalence coincides with a pronounced similarity of the BsuBI/PstI DNA methyltransferases (41% amino acid identity) and restriction endonucleases (46% amino acid identity). Since the genes are also very similar (58% nucleotide identity), the BsuBI and PstI R/M systems apparently have a common evolutionary origin. In spite of the sequence conservation the gene organization is strikingly different in the two R/M systems. While the genes of the PstI R/M system are separated and transcribed divergently, the genes of the BsuBI R/M system are transcribed in the same direction, with the 3' end of the M gene overlapping the 5' end of the R gene by 17 bp.
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Affiliation(s)
- G L Xu
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
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69
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Dibbens JA, Egan JB. Control of gene expression in the temperate coliphage 186. IX. B is the sole phage function needed to activate transcription of the phage late genes. Mol Microbiol 1992; 6:2629-42. [PMID: 1447972 DOI: 10.1111/j.1365-2958.1992.tb01440.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Using plasmid clones we have determined that the late control function B is the only phage function that is needed to activate a late promoter of coliphage 186, and we predict that it functions as an auxiliary factor to RNA polymerase in the activation of late transcription. We have also shown that a high concentration of B will activate late transcription from a prophage, and we conclude that replicating DNA is not a template requirement for B to function. The original demonstration of a need for the replication gene A in late transcription can be explained by the fact that replication leads to an increase in B gene dosage, with the consequent increase in B concentration leading to the efficient activation of the late promoters.
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Affiliation(s)
- J A Dibbens
- Department of Biochemistry, University of Adelaide, South Australia
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70
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Dibbens JA, Gregory SL, Egan JB. Control of gene expression in the temperate coliphage 186. X. The cI repressor directly represses transcription of the late control gene B. Mol Microbiol 1992; 6:2643-50. [PMID: 1447973 DOI: 10.1111/j.1365-2958.1992.tb01441.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have found that the repressor of 186 lytic transcription, CI, represses transcription of the late control gene B, with no involvement of the B protein itself. In clone studies we showed that CI repressed transcription from the B promoter and that temperature inactivation of CIts led to B derepression. We conclude that CI repressor directly represses transcription of the B gene and, with prophage induction, it is probable that the inactivation of the CI repressor not only derepresses early lytic transcription, but also derepresses B gene transcription, leading to the activation of transcription from the late promoters.
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Affiliation(s)
- J A Dibbens
- Department of Biochemistry, University of Adelaide, South Australia
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71
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RNase PH is essential for tRNA processing and viability in RNase-deficient Escherichia coli cells. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41954-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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72
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Diederich L, Rasmussen LJ, Messer W. New cloning vectors for integration in the lambda attachment site attB of the Escherichia coli chromosome. Plasmid 1992; 28:14-24. [PMID: 1387714 DOI: 10.1016/0147-619x(92)90032-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A set of plasmid cloning vectors has been constructed, allowing the integration of any DNA fragment into the bacteriophage lambda attachment site attB of the Escherichia coli chromosome. The system is based upon two components: (i) a number of cloning vectors containing the lambda attachment site attP and (ii) a helper plasmid, bearing the lambda int gene, transcribed from the lambda PR promoter under the control of the temperature-sensitive repressor cI857. The DNA fragment of interest is cloned into the multicloning site of one of the attP-harboring plasmids. Subsequently, the origin of the plasmid, located on a cloning cassette, is cut out and the DNA becomes newly ligated, resulting in a circular DNA molecule without replication ability. The strain of choice, containing the int gene carrying helper plasmid, is transformed with this DNA molecule and incubated at 42 degrees C to induce int gene expression. Additionally, the temperature shift leads to the loss of the helper plasmid after a few cell generations, because the replication ability of its replicon is blocked at 42 degrees C. These vectors have been successfully used for integration of several promoter-lacZ fusions into the chromosome. The ratio between integration due to homologous recombination and Int protein-mediated integration has been determined.
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Affiliation(s)
- L Diederich
- Max-Planck-Institut für molekulare Genetik, Berlin, Germany
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73
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Nordström K, Uhlin BE. Runaway–Replication Plasmids as Tools to Produce Large Quantities of Proteins from Cloned Genes in Bacteria. Nat Biotechnol 1992; 10:661-6. [PMID: 1368887 DOI: 10.1038/nbt0692-661] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we review the properties and uses of runaway-replication vectors, a class of versatile plasmids discovered and developed in Escherichia coli. They are based on the IncFII plasmid, R1, in which an antisense RNA (CopA RNA) negatively controls the formation of a protein that is rate-limiting for replication. The copy number of the plasmid is determined by the balance between the rates of formation of CopA RNA and RepA mRNA. A small increase in the rate of formation of the latter drastically reduces the rate of formation of CopA RNA due to convergent transcription, which may lead to a total loss of copy number control (runaway replication), resulting in massive DNA amplification, and plasmid copy numbers up to 1000 per genome. Since this amplification occurs in the presence of protein synthesis, the protein that is encoded by a cloned gene can also be amplified, and may constitute 10-50% of the total protein.
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Affiliation(s)
- K Nordström
- Department of Microbiology, Uppsala University, Sweden
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74
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Kleibl K, Margison GP, Skorvaga M, Brozmanová J, Masek F. A recA-ada hybrid gene inducible by DNA damage. Mutat Res 1992; 282:39-42. [PMID: 1374156 DOI: 10.1016/0165-7992(92)90071-o] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A damage-inducible expression vector was constructed in which the original recA structural gene was replaced by the protein-coding region of the ada gene. The O6-alkylguanine-DNA alkyltransferase encoded by the ada gene can be measured by a rapid and highly sensitive assay. The introduction of this construct into an appropriate host cell provides an effective bacterial assay for genotoxins.
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Affiliation(s)
- K Kleibl
- Department of Molecular Genetics, Slovak Academy of Sciences, Bratislava, Czechoslovakia
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75
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Strudsholm K, Nielsen J, Emborg C. Product formation during batch fermentation with recombinant Escherichia coli containing a runaway plasmid. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/bf01254234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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76
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Christensen LS, Boye M. Establishment of a genomic bank of bovine herpesvirus 1 using a novel positive selection plasmid vector. J Virol Methods 1992; 36:277-82. [PMID: 1313826 DOI: 10.1016/0166-0934(92)90058-l] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A small positive selection cloning vector, designated pSiig1, suitable for the construction of genomic banks in E. coli is described and used for the establishment of a bank of the bovine herpesvirus 1 genome. Hybrid transformants are directly selected on agar plates containing ampicillin. The vector is based on the replicon of R1 and has a lambda PR promotor inserted upstream of the replication control genes. The vector has an uncontrolled (runaway) replication and is lethal to the host cell unless the PR promotor is brought under trans-acting control of the lambda cI repressor or runaway replication is blocked by an insertion between the PR promotor and the replicon. The vector contains a unique Bg/II site between PR and the replicon which is suitable for insertion of genomic DNA.
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Affiliation(s)
- L S Christensen
- State Veterinary Institute for Virus Research, Lindholm, Kalvehave, Denmark
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77
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Hussey C. Recombinant plasmids. SAFETY IN INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLOGY 1992. [PMCID: PMC7155667 DOI: 10.1016/b978-0-7506-1105-3.50010-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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78
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Heitzer A, Mason CA, Hamer G. Heat shock gene expression in continuous cultures of Escherichia coli. J Biotechnol 1992; 22:153-69. [PMID: 1367813 DOI: 10.1016/0168-1656(92)90139-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Temperature inducible systems for the controlled expression of recombinant genes are finding increasing industrial applications. These involve either short or long term exposure of the process culture to superoptimum temperatures. It is well known that bacteria respond to a sudden increase in their environmental temperature with an immediate transient increase in the synthesis rates of specific heat shock proteins. The use of continuous flow processes for the production of recombinant proteins would allow higher productivity and smaller scale bioreactors. However, the induction patterns of heat shock proteins in continuous culture after defined heat shocks are not well defined despite a large amount of information which is now available concerning heat shock protein induction in batch cultures. An overview of this information is presented to enable a better understanding of the response in continuous cultures. The latter was investigated by monitoring the transient expression of a representative heat shock gene, htpG, in E. coli in continuous culture. The relative magnitude of the response was found to be both temperature and exposure time dependent, but growth rate independent. Changing medium composition resulted in both different steady and transient state expression levels.
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Affiliation(s)
- A Heitzer
- Institute of Aquatic Sciences and Water Pollution Control, Swiss Federal Institute of Technology Zürich, Dübendorf
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79
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Kapfer W, Walter J, Trautner TA. Cloning, characterization and evolution of the BsuFI restriction endonuclease gene of Bacillus subtilis and purification of the enzyme. Nucleic Acids Res 1991; 19:6457-63. [PMID: 1721700 PMCID: PMC329197 DOI: 10.1093/nar/19.23.6457] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The restriction endonuclease (R.BsuFI) of Bacillus subtilis recognizes the target DNA sequence 5' CCGG. The R.BsuFI gene was found in close proximity to the cognate M.BsuFI gene, which had previously been characterized (1). Cloning of the R.BsuFI gene in E.coli was only possible with the M.BsuFI Mtase gene present on a compatible plasmid. The cloned R.BsuFI gene was expressed in E. coli and restriction activity was observed in vivo and in vitro. The R.BsuFI gene consists of 1185 bp, coding for a protein of 395 amino acids with a calculated molecular weight of 45.6 kD. The R.BsuFI enzyme was purified to homogeneity following overexpression. It presumably works as a dimer and cleaves the 5' CCGG target sequence between the two cytosines to produce sticky ends with 5' CG overhangs, like the isoschizomers R.MspI and R.HpaII. The relatedness between R.BsuFI and R.MspI is reflected by significant similarities of the amino acid sequences of both enzymes. This is the first case where such similarities have been observed between isoschizomeric restriction endonucleases which belong to 5mC specific R/M systems. This observation suggests that R.BsuFI and R.MspI genes derive from a common ancestor. In spite of such functional and evolutionary relatedness, the R/M systems differ in the arrangement of their R and M genes. In the BsuFI system transcription of the two genes is convergent, whereas divergent transcription occurs in the MspI system.
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Affiliation(s)
- W Kapfer
- Max-Planck-Institut für Molekulare Genetik, Berlin, FRG
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80
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Nielsen AK, Thorsted P, Thisted T, Wagner EG, Gerdes K. The rifampicin-inducible genes srnB from F and pnd from R483 are regulated by antisense RNAs and mediate plasmid maintenance by killing of plasmid-free segregants. Mol Microbiol 1991; 5:1961-73. [PMID: 1722558 DOI: 10.1111/j.1365-2958.1991.tb00818.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The gene systems srnB of plasmid F and pnd of plasmid R483 were discovered because of their induction by rifampicin. Induction caused membrane damage, RNase I influx, degradation of stable RNA and, consequently, cell killing. We show here that the srnB and pnd systems mediate efficient stabilization of a mini-R1 test-plasmid. We also show that the killer genes srnB' and pndA are regulated by antisense RNAs, and that the srnC- and pndB-encoded antisense RNAs, denoted SrnC- and PndB-RNAs, are unstable molecules of approximately 60 nucleotides. The srnB and pndA mRNAs were found to be very stable. The differential decay rates of the inhibitory antisense RNAs and the killer-gene-encoding mRNAs explain the induction of these gene systems by rifampicin. Furthermore, the observed plasmid-stabilization phenotype associated with the srnB and pnd systems is a consequence of this differential RNA decay: the newborn plasmid-free cells inherit the stable mRNAs, which, after decay of the unstable antisense RNAs, are translated into killer proteins, thus leading to selective killing of the plasmid-free segregants. Thus our observations lead us to conclude that the F srnB and R483 pnd systems are phenotypically indistinguishable from the R1 hok/sok system, despite a 50% dissimilarity at the level of DNA sequence.
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Affiliation(s)
- A K Nielsen
- Department of Molecular Biology, Odense University, Denmark
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81
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Poulsen LK, Refn A, Molin S, Andersson P. The gef gene from Escherichia coli is regulated at the level of translation. Mol Microbiol 1991; 5:1639-48. [PMID: 1943701 DOI: 10.1111/j.1365-2958.1991.tb01911.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We describe post-transcriptional regulation of the chromosomal gene, gef, from Escherichia coli. The gef gene is a member of a gene family consisting of the chromosomal gef and relF genes from Escherichia coli and the hok, flmA, srnB, and pndA genes, which are situated on conjugative plasmids. All the genes encode small, toxic proteins of approximately 50 amino acids which are functionally and structurally homologous. Furthermore, the gene family shares post-transcriptional regulation of expression, albeit by different mechanisms. We demonstrate here that translation of gef is coupled to an upstream open reading frame which, in turn, is regulated by a transacting factor, probably an antisense RNA.
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Affiliation(s)
- L K Poulsen
- Genetic Engineering Group, Technical University of Denmark, Lyngby
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82
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Modeling fermentations with recombinant microorganisms: Formulation of a structured model. Biotechnol Bioeng 1991; 37:802-8. [DOI: 10.1002/bit.260370903] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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83
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Petersen SK, Foged NT, Bording A, Nielsen JP, Riemann HK, Frandsen PL. Recombinant derivatives of Pasteurella multocida toxin: candidates for a vaccine against progressive atrophic rhinitis. Infect Immun 1991; 59:1387-93. [PMID: 1706320 PMCID: PMC257854 DOI: 10.1128/iai.59.4.1387-1393.1991] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Potential vaccine components for protection against atrophic rhinitis in pigs were developed. This was achieved by deletion mutagenesis of the gene encoding the Pasteurella multocida toxin. Four purified toxin derivatives lacking different and widely separated regions in the amino acid sequence were characterized by a lack of toxic activity. One such component was shown to induce efficient protection of vaccinated female mice and their offspring against challenge with purified P. multocida toxin.
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Affiliation(s)
- S K Petersen
- Genetic Engineering Group, Technical University of Denmark, Lyngby
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84
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Bernander R, Dasgupta S, Nordström K. The E. coli cell cycle and the plasmid R1 replication cycle in the absence of the DnaA protein. Cell 1991; 64:1145-53. [PMID: 1848482 DOI: 10.1016/0092-8674(91)90269-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In E. coli strain EC::71CW chromosome replication is under the control of the R1 miniplasmid pOU71. A dnaA850::Tn10 derivative of EC::71CW was viable, which confirmed that R1 can replicate in the absence of the DnaA protein. The frequency of initiation of replication was, however, lowered and cell division was severely disturbed due to underreplication of the chromosome. Both replication and cell division could be restored to normal by increasing the production of RepA, the rate-limiting protein for initiation of replication from the integrated R1 origin. Therefore, the RepA protein seems to compensate for the absence of DnaA in the initiation of replication and assembly of replisomes. The role of the DnaA protein in the initiation of DNA replication, and as an overall regulator of the chromosome replication and cell division cycles of E. coli, is discussed in view of these results.
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Affiliation(s)
- R Bernander
- Department of Microbiology, Uppsala University, Sweden
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85
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Ralphs NT, Garrett S, Morse R, Cookson JB, Andrew PW, Boulnois GJ. A DNA primer/probe system for the rapid and sensitive detection of Mycobacterium tuberculosis-complex pathogens. THE JOURNAL OF APPLIED BACTERIOLOGY 1991; 70:221-6. [PMID: 1903132 DOI: 10.1111/j.1365-2672.1991.tb02928.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A 1.5 kb EcoRI-BamHI restriction fragment from Mycobacterium tuberculosis was found to hybridize specifically with genomic DNA from M. tuberculosis-complex organisms. Primers were designed from the terminal sequences of this fragment and used to amplify uniquely M. tuberculosis-group DNA in a polymerase chain reaction. It is suggested that a combination of these primers and probe will prove a useful tool for the early diagnosis of tuberculous infections.
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Affiliation(s)
- N T Ralphs
- Department of Microbiology, University of Leicester, UK
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86
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Korat B, Mottl H, Keck W. Penicillin-binding protein 4 of Escherichia coli: molecular cloning of the dacB gene, controlled overexpression, and alterations in murein composition. Mol Microbiol 1991; 5:675-84. [PMID: 2046551 DOI: 10.1111/j.1365-2958.1991.tb00739.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The penicillin-binding protein 4 (PBP4), from Escherichia coli, a DD-carboxypeptidase/DD-endopeptidase, was purified in an enzymatically active form to homogeneity by affinity chromatography on 6-aminopenicillanic acid/Sepharose and heparin/Sepharose. Polyclonal antibodies raised against the pure protein were used to identify and isolate PBP4 overproducing clones from an E. coli expression library, which was established on the basis of a temperature-inducible runaway replication plasmid. Three positive clones were isolated, one of which carried the intact structural gene dacB that codes for PBP4, on a 1.9kb SmaI-EcoRI fragment, whereas the other two carried truncated forms of this gene. The direction of transcription was determined. The PBP4 overproducing strain, when grown in rich medium, tolerated 160-fold overexpression. After disrupting cells by sonication, the majority (80%) of the overproduced PBP4 was detected in the 100,000 X g supernatant. Southern blotting analysis using the cloned dacB gene as a probe revealed that, in contrast to that described by Takeda et al. (1981), the plasmid pLC18-38 of the Clarke-Carbon collection does not code for PBP4. The overall composition of murein, synthesized in vitro or in vivo by the PBP4 overproducing strain, as determined by high-performance liquid chromatography analysis, suggests that PBP4 is not involved in transpeptidation but exclusively catalyses a DD-carboxypeptidase and DD-endopeptidase reaction.
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Affiliation(s)
- B Korat
- Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Germany
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87
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Nordström K, Bernander R, Dasgupta S. Analysis of the bacterial cell cycle using strains in which chromosome replication is controlled by plasmid R1. Res Microbiol 1991; 142:181-8. [PMID: 1656493 DOI: 10.1016/0923-2508(91)90028-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As an alternative approach in the study of the Escherichia coli cell cycle, we have constructed strains in which chromosome replication is under the control of various plasmid R1 derivatives, IntR1 strains. The physiological properties of such strains are described. In intR1 strains, chromosome replication can be manipulated independently of cell-cycle-related control mechanisms, and the effects on cell division can be analysed. Using this approach, we have found that the timing of replication during the cell cycle is random in intR1 strains, that overreplication of the chromosome is lethal, and that chromosome replication does not trigger cell division. Current investigations include the study of the E. coli cell cycle in the absence of the DnaA protein, the effect on cell division of a specific inhibition of the initiation of chromosome replication, and the molecular basis of uni- and bidirectional replication.
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Affiliation(s)
- K Nordström
- Department of Microbiology, Uppsala University, Sweden
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88
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Favre D, Cryz SJ, Viret JF. Cloning of the recA gene of Bordetella pertussis and characterization of its product. Biochimie 1991; 73:235-44. [PMID: 1832021 DOI: 10.1016/0300-9084(91)90208-i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A recA gene of Bordetella pertussis was identified in a plasmid library by complementation of a recA mutation in E coli and subcloned as a 2.1-kb Sph I DNA fragment. Southern hybridization experiments showed no similarity to the E coli recA gene, but very strong similarity to other Bordetella species. E coli recA mutant cells containing the B pertussis recA gene at high gene dosage were resistant to DNA-damaging agents such as methyl methane sulfonate or 4-nitroquinoline-N-oxide, displayed induction of SOS functions, and were able to promote DNA recombination, but not induction of phage lambda. The latter phenotype distinguishes the B pertussis recA gene product from the corresponding proteins from most other Gram-negative organisms. Amino acid sequence comparisons revealed a high degree of structural conservation between prokaryotic RecA proteins.
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Affiliation(s)
- D Favre
- Swiss Serum and Vaccine Institute, Berne, Switzerland
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89
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Søgaard-Andersen L, Martinussen J, Møllegaard NE, Douthwaite SR, Valentin-Hansen P. The CytR repressor antagonizes cyclic AMP-cyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12. J Bacteriol 1990; 172:5706-13. [PMID: 2170326 PMCID: PMC526886 DOI: 10.1128/jb.172.10.5706-5713.1990] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We have investigated the regulation of the Escherichia coli deoCp2 promoter by the CytR repressor and the cyclic AMP (cAMP) receptor protein (CRP) complexed to cAMP. Promoter regions controlled by these two proteins characteristically contain tandem cAMP-CRP binding sites. Here we show that (i) CytR selectively regulated cAMP-CRP-dependent initiations, although transcription started from the same site in deoCp2 in the absence or presence of cAMP-CRP; (ii) deletion of the uppermost cAMP-CRP target (CRP-2) resulted in loss of CytR regulation, but had only a minor effect on positive control by the cAMP-CRP complex; (iii) introduction of point mutations in either CRP target resulted in loss of CytR regulation; and (iv) regulation by CytR of deletion mutants lacking CRP-2 could be specifically reestablished by increasing the intracellular concentration of CytR. These findings indicate that both CRP targets are required for efficient CytR repression of deoCp2. Models for the action of CytR are discussed in light of these findings.
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90
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Skovgaard O. Nucleotide sequence of a Proteus mirabilis DNA fragment homologous to the 60K-rnpA-rpmH-dnaA-dnaN-recF-gyrB region of Escherichia coli. Gene 1990; 93:27-34. [PMID: 2172087 DOI: 10.1016/0378-1119(90)90131-a] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A 6.5-kb DNA fragment from Proteus mirabilis hybridized to the Escherichia coli dnaA gene. This DNA fragment was cloned and the nucleotide (nt) sequence determined. The fragment is homologous to a region of the E. coli chromosome containing a part of the gene encoding a 60-kDa membrane-associated protein (60K), the rnpA-rpmH-dnaA-dnaN-recF genes, and the N-terminal part of the gyrB gene. The degree of homology is variable: the amino-acid (aa) sequence of a part of the 60K protein and a part of the DnaA protein is only minimally conserved, whereas the C-terminal 148 aa of DnaA are identical in the two species. The conservation of the nt sequence between the rnpA gene and the gene encoding the 60K protein suggests that this region encodes a hitherto unrecognized protein. The ORF for this protein partially overlaps the 3' end of the rnpA structural gene, and the degree of conservation suggests that this gene is important for these bacteria.
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Affiliation(s)
- O Skovgaard
- Institute of Life Sciences and Chemistry, Roskilde University Centre, Denmark
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91
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LaMarca C, Lenhoff AM, Dhurjati P. Partitioning of host and recombinant cells in aqueous two-phase polymer systems. Biotechnol Bioeng 1990; 36:484-92. [DOI: 10.1002/bit.260360508] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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92
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Brun YV, Breton R, Lanouette P, Lapointe J. Precise mapping and comparison of two evolutionarily related regions of the Escherichia coli K-12 chromosome. Evolution of valU and lysT from an ancestral tRNA operon. J Mol Biol 1990; 214:825-43. [PMID: 2201776 DOI: 10.1016/0022-2836(90)90339-n] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two tRNA operons have been found near the gltX gene encoding the glutamyl-tRNA synthetase of Escherichia coli K-12. The alaW operon previously undetected from genetic data and containing two identical tRNA(GGCAla) genes is 800 base-pairs downstream from the gltX terminator and is transcribed from the same strand. The valU operon containing genes for three identical tRNA(UACVal) and one tRNA(UUULys) (the wild-type allele of supN), is adjacent to gltX and is transcribed from the opposite strand. Five open reading frames were also found in this region encoding putative polypeptides of 62, 105, 130, 167 and 294 amino acid residues. ORF294 is a new member of the lysR family of bacterial transcriptional activators. The possibility that this is the xapR gene is discussed. Comparison of the physical and linkage maps of the E. coli chromosome in the 52 minute region has permitted precise mapping of most of the 18 genes in this region with the order nupC-glk- less than (alaW beta-ala W alpha)-1 kb- less than gltX-0.3 kb-(valU alpha-valU beta-valU gamma-lysV = supN) greater than xapR-xapA- less than lig-1 kb-cysK greater than -0.4 kb-ptsH greater than -0.05 kb-pstI greater than -0.05 kb-crr greater than -cysM-cysA in the clockwise order (greater than and less than indicate the direction of transcription; kb, 10(3) bases). The last two genes of valU (52 min) and lysT (16.5 min) are arranged in a similar fashion and a highly conserved region has been found in both operons. This suggests that the valU and lysT operons probably arose by a duplication of an ancestral tRNA operon. This is the first example of what may be two different tRNA operons from the same organism evolving from an ancestral tRNA gene. Comparison of the 16 and 52 minute regions of the E. coli K-12 chromosome suggests that these two regions could share a common ancestor.
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Affiliation(s)
- Y V Brun
- Département de Biochimie, Faculté des Sciences et de Génie, Université Laval, Québec, Canada
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93
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Putzer H, Brakhage AA, Grunberg-Manago M. Independent genes for two threonyl-tRNA synthetases in Bacillus subtilis. J Bacteriol 1990; 172:4593-602. [PMID: 2115870 PMCID: PMC213293 DOI: 10.1128/jb.172.8.4593-4602.1990] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
With the exception of Escherichia coli lysyl-tRNA synthetase, the genes coding for the different aminoacyl-tRNA synthetases in procaryotes are always unique. Here we report on the occurrence and cloning of two genes (thrSv and thrS2), both encoding functional threonyl-tRNA synthetase in Bacillus subtilis. The two proteins share only 51.5% identical residues, which makes them almost as distinct from each other as each is from E. coli threonyl-tRNA synthetase (42 and 47%). Both proteins complement an E. coli thrS mutant and effectively charge E. coli threonyl tRNA in vitro. Their genes have been mapped to 250 degrees (thrSv) and 344 degrees (thrS2) on the B. subtilis chromosome. The regulatory regions of both genes are quite complex and show structural similarities. During vegetative growth, only the thrSv gene is expressed.
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Affiliation(s)
- H Putzer
- Institut de Biologie Physico-Chimique, Paris, France
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94
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Scofield MA, Lewis WS, Schuster SM. Nucleotide sequence of Escherichia coli asnB and deduced amino acid sequence of asparagine synthetase B. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38244-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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95
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Holland IB, Blight MA, Kenny B. The mechanism of secretion of hemolysin and other polypeptides from gram-negative bacteria. J Bioenerg Biomembr 1990; 22:473-91. [PMID: 2202728 DOI: 10.1007/bf00763178] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the secretion of polypeptides from Gram-negative bacteria, the outer membrane constitutes a specific barrier which has to be circumvented. In the majority of systems, secretion is a two-step process, with initial export to the periplasm involving an N-terminal signal sequence. Transport across the outer membrane then involves a variable number of ancillary polypeptides including both periplasmic and outer membrane. While such ancillary proteins are probably specific for each secreted protein, the mechanism of movement across the outer membrane is unknown. In contrast to these systems, secretion of the E. coli hemolysin (HlyA) has several distinctive features. These include a novel targeting signal located within the last 50 or so C-terminal amino acids, the absence of any periplasmic intermediates in transfer, and a specific membrane-bound translocator, HlyB, with important mammalian homologues such as P-glycoprotein (Mdr) and the cystic fibrosis protein. In this review we discuss the nature of the HlyA targeting signal, the structure and function of HlyB, and the probability that HlyA is secreted directly to the medium through a trans-envelope complex composed of HlyB and HlyD.
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Affiliation(s)
- I B Holland
- Department of Genetics, University of Leicester, UK
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96
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Bentley WE, Kompala DS. Optimal induction of protein synthesis in recombinant bacterial cultures. Ann N Y Acad Sci 1990; 589:121-38. [PMID: 2192654 DOI: 10.1111/j.1749-6632.1990.tb24239.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- W E Bentley
- Department of Chemical Engineering, University of Colorado, Boulder 80309-0424
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97
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Betenbaugh MJ, Dhurjati P. Effects of promoter induction and copy number amplification on cloned gene expression and growth of recombinant cell cultures. Ann N Y Acad Sci 1990; 589:111-20. [PMID: 2192653 DOI: 10.1111/j.1749-6632.1990.tb24238.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- M J Betenbaugh
- Department of Chemical Engineering, University of Delaware, Newark 19716
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98
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Abstract
An essential part of the chromosome replication origin of E. coli K-12 and B/r was replaced by the plasmid pOU71. The average initiation mass of replication for pOU71 decreases with increasing temperature. The constructed strains were grown exponentially at different temperatures, and cell sizes and DNA content were measured by flow cytometry. The average DNA content increased with increasing temperature, but the cell size distribution was largely unaffected. Furthermore, cells in which DNA replication had not yet initiated (cells in the B period) became less abundant with increasing temperature. The increased DNA content could not be explained by an increase in the length of the C period. It is concluded that chromosome replication does not trigger cell division in E. coli, but that the chromosome replication and cell division cycles of E. coli run in parallel independently of each other.
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Affiliation(s)
- R Bernander
- Department of Microbiology, University of Uppsala, Sweden
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99
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Riegman N, Kusters R, Van Veggel H, Bergmans H, Van Bergen en Henegouwen P, Hacker J, Van Die I. F1C fimbriae of a uropathogenic Escherichia coli strain: genetic and functional organization of the foc gene cluster and identification of minor subunits. J Bacteriol 1990; 172:1114-20. [PMID: 1967600 PMCID: PMC208544 DOI: 10.1128/jb.172.2.1114-1120.1990] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genetic organization of the foc gene cluster has been studied; six genes involved in the biogenesis of F1C fimbriae were identified. focA encodes the major fimbrial subunit, focC encodes a product that is indispensable for fimbria formation, focG and focH encode minor fimbrial subunits, and focI encodes a protein which shows similarities to the subunit protein FocA. Apart from the FocA major subunits, purified F1C fimbriae contain at least two minor subunits, FocG and FocH. Minor proteins of similar size were observed in purified S fimbriae. Remarkably, some mutations in the foc gene cluster result in an altered fimbrial morphology, i.e., rigid stubs or long, curly fimbriae.
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Affiliation(s)
- N Riegman
- Department of Molecular Cell Biology, University of Utrecht, The Netherlands
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100
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Masters M, March JB, Oliver IR, Collins JF. A possible role for the pcnB gene product of Escherichia coli in modulating RNA: RNA interactions. MOLECULAR & GENERAL GENETICS : MGG 1990; 220:341-4. [PMID: 1691435 DOI: 10.1007/bf00260507] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The sequence of the PcnB protein of Escherichia coli, a protein required for copy number maintenance of ColE1-related plasmids, was compared with the PIR sequence database. Strong local similarities to the sequence of the E. coli protein tRNA nucleotidyltransferase were found. Since a substrate of the latter protein, tRNA, structurally resembles the RNAs that control ColE1 copy number we believe that we may have identified a region in PcnB that interacts with these RNAs. Consistent with this idea is our observation that PcnB is required for the replication of R1, a plasmid whose replication is also regulated by a small RNA.
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Affiliation(s)
- M Masters
- Department of Molecular Biology, University of Edinburgh, UK
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