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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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Brandis G, Cao S, Hughes D. Operon Concatenation Is an Ancient Feature That Restricts the Potential to Rearrange Bacterial Chromosomes. Mol Biol Evol 2020; 36:1990-2000. [PMID: 31132113 PMCID: PMC6735719 DOI: 10.1093/molbev/msz129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The last common ancestor of the Gammaproteobacteria carried an important 40-kb chromosome section encoding 51 proteins of the transcriptional and translational machinery. These genes were organized into eight contiguous operons (rrnB-tufB-secE-rpoBC-str-S10-spc-alpha). Over 2 Gy of evolution, in different lineages, some of the operons became separated by multigene insertions. Surprisingly, in many Enterobacteriaceae, much of the ancient organization is conserved, indicating a strong selective force on the operons to remain colinear. Here, we show for one operon pair, tufB-secE in Salmonella, that an interruption of contiguity significantly reduces growth rate. Our data show that the tufB-secE operons are concatenated by an interoperon terminator–promoter overlap that plays a significant role regulating gene expression. Interrupting operon contiguity interferes with this regulation, reducing cellular fitness. Six operons of the ancestral chromosome section remain contiguous in Salmonella (tufB-secE-rpoBC and S10-spc-alpha) and, strikingly, each of these operon pairs is also connected by an interoperon terminator–promoter overlap. Accordingly, we propose that operon concatenation is an ancient feature that restricts the potential to rearrange bacterial chromosomes and can select for the maintenance of a colinear operon organization over billions of years.
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Affiliation(s)
- Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
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Abstract
A feature of bacterial chromosomes is that highly expressed essential genes are usually located close to the origin of replication. Because bacteria have overlapping cycles of replication, genes located close to the origin will often be present in multiple copies, and this is thought to be of selective benefit where high levels of expression support high growth rate. However, the magnitude of this selective effect and whether other forces could be at play are poorly understood. To study this, we translocated a highly expressed essential operon, tufB, to different locations and measured growth fitness. We found that transcriptional regulation buffered the effects of translocation and that even under conditions where growth rate was reduced, genetic changes that increased the expression of tufB were easily and rapidly selected. We conclude, at least for tufB, that forces other than gene dosage may be significant in selecting for chromosomal location. Highly expressed genes are commonly located close to the origin of replication of bacterial chromosomes (OriC). This location skew is thought to reflect selective advantages associated with gene dosage effects during the replication cycle. The expression of constitutively expressed genes can vary up to fivefold based on chromosomal location, but it is not clear what level of variation would occur in naturally regulated operons. We tested the magnitude of the chromosome location effect using EF-Tu (tufA, tufB), an abundant protein whose cellular level correlates with, and limits, the maximum growth rate. We translocated the Salmonella tufB operon to four locations across the chromosome. The distance from OriC had only a small effect on growth rate, consistent with this operon having the natural ability to upregulate expression and compensate for reduced gene dosage. In contrast, when the total EF-Tu concentration was limiting for the growth rate (tufA deleted), we observed a strong gene dosage effect when tufB was located further from OriC. However, only a short period of experimental evolution was required before the bacteria adapted to this EF-Tu starvation situation by acquiring genetic changes that increased expression levels from the translocated tufB gene, restoring growth rates. Our findings demonstrate that, at least for the tufB operon, gene dosage is probably not the dominant force selecting for a chromosomal location close to OriC. We suggest that the colocation of highly expressed genes close to OriC might instead be selected because it enhances their coregulation during various growth states, with gene dosage being a secondary benefit.
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Brandis G, Cao S, Hughes D. Co-evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella. Mol Microbiol 2018; 108:697-710. [PMID: 29603442 DOI: 10.1111/mmi.13959] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2018] [Indexed: 12/14/2022]
Abstract
Bacteria can have multiple copies of a gene at separate locations on the same chromosome. Some of these gene families, including tuf (translation elongation factor EF-Tu) and rrl (ribosomal RNA), encode functions critically important for bacterial fitness. Genes within these families are known to evolve in concert using homologous recombination to transfer genetic information from one gene to another. This mechanism can counteract the detrimental effects of nucleotide sequence divergence over time. Whether such mechanisms can also protect against the potentially lethal effects of mobile genetic element insertion is not well understood. To address this we constructed two different length insertion cassettes to mimic mobile genetic elements and inserted these into various positions of the tuf and rrl genes. We measured rates of recombinational repair that removed the inserted cassette and studied the underlying mechanism. Our results indicate that homologous recombination can protect the tuf and rrl genes from inactivation by mobile genetic elements, but for insertions within shorter gene sequences the efficiency of repair is very low. Intriguingly, we found that physical distance separating genes on the chromosome directly affects the rate of recombinational repair suggesting that relative location will influence the ability of homologous recombination to maintain homogeneity.
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Affiliation(s)
- Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Box 582 Biomedical Center, Uppsala University, Uppsala, Sweden
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5
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Liu Y, Hammer LA, Liu W, Hobbs MM, Zielke RA, Sikora AE, Jerse AE, Egilmez NK, Russell MW. Experimental vaccine induces Th1-driven immune responses and resistance to Neisseria gonorrhoeae infection in a murine model. Mucosal Immunol 2017; 10:1594-1608. [PMID: 28272393 PMCID: PMC5591041 DOI: 10.1038/mi.2017.11] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/23/2017] [Indexed: 02/04/2023]
Abstract
Female mice were immunized intravaginally with gonococcal outer membrane vesicles (OMVs) plus microencapsulated interleukin-12 (IL-12), and challenged using an established model of genital infection with Neisseria gonorrhoeae. Whereas sham-immunized and control animals cleared the infection in 10-13 days, those immunized with OMV plus IL-12 cleared infection with homologous gonococcal strains in 6-9 days. Significant protection was also seen after challenge with antigenically distinct strains of N. gonorrhoeae, and protective anamnestic immunity persisted for at least 6 months after immunization. Serum and vaginal immunoglobulin G (IgG) and IgA antibodies were generated against antigens expressed by homologous and heterologous strains. Iliac lymph node CD4+ T cells secreted interferon-γ (IFNγ), but not IL-4, in response to immunization, and produced IL-17 in response to challenge regardless of immunization. Antigens recognized by immunized mouse serum included several shared between gonococcal strains, including two identified by immunoproteomics approaches as elongation factor-Tu (EF-Tu) and PotF3. Experiments with immunodeficient mice showed that protective immunity depended upon IFNγ and B cells, presumably to generate antibodies. The results demonstrated that immunity to gonococcal infection can be induced by immunization with a nonliving gonococcal antigen, and suggest that efforts to develop a human vaccine should focus on strategies to generate type 1 T helper cell (Th1)-driven immune responses in the genital tract.
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Affiliation(s)
- Yingru Liu
- TherapyX, Inc., Buffalo, NY, USA,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
| | | | - Wensheng Liu
- Department of Pediatrics, Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, NY, USA
| | - Marcia M. Hobbs
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Ann E. Jerse
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Nejat K. Egilmez
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
| | - Michael W. Russell
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
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6
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Brandis G, Bergman JM, Hughes D. Autoregulation of the tufB operon in Salmonella. Mol Microbiol 2016; 100:1004-16. [PMID: 26934594 DOI: 10.1111/mmi.13364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2016] [Indexed: 11/27/2022]
Abstract
In Salmonella enterica and related species, translation elongation factor EF-Tu is encoded by two widely separated but near-identical genes, tufA and tufB. Two thirds of EF-Tu is expressed from tufA with the remaining one third coming from tufB. Inactivation of tufA is partly compensated by a doubling in the amount of EF-TuB but the mechanism of this up-regulation is unknown. By experimental evolution selecting for improved growth rate in a strain with an inactive tufA we selected six different noncoding or synonymous point mutations close to the tufB start codon. Based on these results we constructed a total of 161 different point mutations around the tufB start codon, as well as tufB 3'-truncations, and measured tufB expression using tufB-yfp transcriptional and translational fusions. The expression data support the presence of two competing stem-loop structures that can form in the 5'-end of the tufB mRNA. Formation of the 'closed' structure leads to Rho-dependent transcriptional termination of the tufB mRNA. We propose a model in which translational speed is used as a sensor for EF-Tu concentration and where the expression of tufB is post-transcriptionally regulated. This model describes for the first time how expression of the most abundant Salmonella protein is autoregulated.
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Affiliation(s)
- Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Box 582, SE, 75123, Uppsala, Sweden
| | - Jessica M Bergman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Box 582, SE, 75123, Uppsala, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Box 582, SE, 75123, Uppsala, Sweden
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Leeds JA. Antibacterials Developed to Target a Single Organism: Mechanisms and Frequencies of Reduced Susceptibility to the Novel Anti-Clostridium difficile Compounds Fidaxomicin and LFF571. Cold Spring Harb Perspect Med 2016; 6:a025445. [PMID: 26834162 PMCID: PMC4743069 DOI: 10.1101/cshperspect.a025445] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clostridium difficile is the most common cause of antibacterial-associated diarrhea. Clear clinical presentation and rapid diagnostics enable targeted therapy for C. difficile infection (CDI) to start quickly. CDI treatment includes metronidazole and vancomycin (VAN). Despite decades of use for CDI, no clinically meaningful resistance to either agent has emerged. Fidaxomicin (FDX), an RNA polymerase inhibitor, is also approved to treat CDI. Mutants with reduced susceptibility to FDX have been selected in vitro by single and multistep methods. Strains with elevated FDX minimum inhibitory concentrations (MICs) were also identified from FDX-treated patients in clinical trials. LFF571 is an exploratory agent that inhibits EF-Tu. In a proof-of-concept study, LFF571 was safe and effective for treating CDI. Spontaneous mutants with reduced susceptibility to LFF571 were selected in vitro in a single step, but not via serial passage. Although there are several agents in development for treatment of CDI, this review summarizes the frequencies and mechanisms of C. difficile mutants displaying reduced susceptibility to FDX or LFF71.
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Affiliation(s)
- Jennifer A Leeds
- Infectious Disease Area, Novartis Institutes for BioMedical Research, Emeryville, California 94608
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Wu C, Du C, Gubbens J, Choi YH, van Wezel GP. Metabolomics-Driven Discovery of a Prenylated Isatin Antibiotic Produced by Streptomyces Species MBT28. JOURNAL OF NATURAL PRODUCTS 2015; 78:2355-2363. [PMID: 26438963 DOI: 10.1021/acs.jnatprod.5b00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Actinomycetes are a major source of antimicrobials, anticancer compounds, and other medically important products, and their genomes harbor extensive biosynthetic potential. Major challenges in the screening of these microorganisms are to activate the expression of cryptic biosynthetic gene clusters and the development of technologies for efficient dereplication of known molecules. Here we report the identification of a previously unidentified isatin-type antibiotic produced by Streptomyces sp. MBT28, following a strategy based on NMR-based metabolomics combined with the introduction of streptomycin resistance in the producer strain. NMR-guided isolation by tracking the target proton signal resulted in the characterization of 7-prenylisatin (1) with antimicrobial activity against Bacillus subtilis. The metabolite-guided genome mining of Streptomyces sp. MBT28 combined with proteomics identified a gene cluster with an indole prenyltransferase that catalyzes the conversion of tryptophan into 7-prenylisatin. This study underlines the applicability of NMR-based metabolomics in facilitating the discovery of novel antibiotics.
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Affiliation(s)
| | | | - Jacob Gubbens
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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9
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Abstract
My journey into a research career began in fermentation biochemistry in an applied science department during the difficult post-World War II time in Japan. Subsequently, my desire to do research in basic science developed. I was fortunate to be a postdoctoral fellow in the United States during the early days of molecular biology. From 1957 to 1960, I worked with three pioneers of molecular biology, Sol Spiegelman, James Watson, and Seymour Benzer. These experiences helped me develop into a basic research scientist. My initial research projects at Osaka University, and subsequently at the University of Wisconsin, Madison, were on the mode of action of colicins as well as on mRNA and ribosomes. Following success in the reconstitution of ribosomal subunits, my efforts focused more on ribosomes, initially on the aspects of structure, function, and in vitro assembly, such as the construction of the 30S subunit assembly map. After this, my laboratory studied the regulation of the synthesis of ribosomes and ribosomal components in Escherichia coli. Our achievements included the discovery of translational feedback regulation of ribosomal protein synthesis and the identification of several repressor ribosomal proteins used in this regulation. In 1984, I moved to the University of California, Irvine, and initiated research on rRNA transcription by RNA polymerase I in the yeast Saccharomyces cerevisiae. The use of yeast genetics combined with biochemistry allowed us to identify genes uniquely involved in rRNA synthesis and to elucidate the mechanism of initiation of transcription. This essay is a reflection on my life as a research scientist.
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Affiliation(s)
- Masayasu Nomura
- Department of Biological Chemistry, University of California, Irvine, California 92697-1700
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10
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Ventura M, Canchaya C, Meylan V, Klaenhammer TR, Zink R. Analysis, characterization, and loci of the tuf genes in lactobacillus and bifidobacterium species and their direct application for species identification. Appl Environ Microbiol 2004; 69:6908-22. [PMID: 14602655 PMCID: PMC262312 DOI: 10.1128/aem.69.11.6908-6922.2003] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed the tuf gene, encoding elongation factor Tu, from 33 strains representing 17 Lactobacillus species and 8 Bifidobacterium species. The tuf sequences were aligned and used to infer phylogenesis among species of lactobacilli and bifidobacteria. We demonstrated that the synonymous substitution affecting this gene renders elongation factor Tu a reliable molecular clock for investigating evolutionary distances of lactobacilli and bifidobacteria. In fact, the phylogeny generated by these tuf sequences is consistent with that derived from 16S rRNA analysis. The investigation of a multiple alignment of tuf sequences revealed regions conserved among strains belonging to the same species but distinct from those of other species. PCR primers complementary to these regions allowed species-specific identification of closely related species, such as Lactobacillus casei group members. These tuf gene-based assays developed in this study provide an alternative to present methods for the identification for lactic acid bacterial species. Since a variable number of tuf genes have been described for bacteria, the presence of multiple genes was examined. Southern analysis revealed one tuf gene in the genomes of lactobacilli and bifidobacteria, but the tuf gene was arranged differently in the genomes of these two taxa. Our results revealed that the tuf gene in bifidobacteria is flanked by the same gene constellation as the str operon, as originally reported for Escherichia coli. In contrast, bioinformatic and transcriptional analyses of the DNA region flanking the tuf gene in four Lactobacillus species indicated the same four-gene unit and suggested a novel tuf operon specific for the genus Lactobacillus.
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Affiliation(s)
- Marco Ventura
- Nestlé Research Center, 1000 Lausanne 26, Switzerland.
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11
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Schnell R, Abdulkarim F, Kálmán M, Isaksson LA. Functional EF-Tu with large C-terminal extensions in an E coli strain with a precise deletion of both chromosomal tuf genes. FEBS Lett 2003; 538:139-44. [PMID: 12633867 DOI: 10.1016/s0014-5793(03)00159-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An Escherichia coli strain was constructed in which both chromosomal genes encoding elongation factor (EF)-Tu (tufA and tufB) have been inactivated with precise coding sequence replacements. A tufA gene in an expression vector is supplied as the sole EF-Tu source. By using plasmid replacement, based on plasmid incompatibility, mutant EF-Tu variants with a large C'-terminal extension up to 270 amino acids were studied and proved to be functional in a strain lacking the chromosomal tufA and tufB genes.
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Affiliation(s)
- Robert Schnell
- Department of Microbiology, Stockholm University, S-106 91 Stockholm, Sweden
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12
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Krásný L, Vacík T, Fucík V, Jonák J. Cloning and characterization of the str operon and elongation factor Tu expression in Bacillus stearothermophilus. J Bacteriol 2000; 182:6114-22. [PMID: 11029432 PMCID: PMC94746 DOI: 10.1128/jb.182.21.6114-6122.2000] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete primary structure of the str operon of Bacillus stearothermophilus was determined. It was established that the operon is a five-gene transcriptional unit: 5'-ybxF (unknown function; homology to eukaryotic ribosomal protein L30)-rpsL (S12)-rpsG (S7)-fus (elongation factor G [EF-G])-tuf (elongation factor Tu [EF-Tu])-3'. The main operon promoter (strp) was mapped upstream of ybxF, and its strength was compared with the strength of the tuf-specific promoter (tufp) located in the fus-tuf intergenic region. The strength of the tufp region to initiate transcription is about 20-fold higher than that of the strp region, as determined in chloramphenicol acetyltransferase assays. Deletion mapping experiments revealed that the different strengths of the promoters are the consequence of a combined effect of oppositely acting cis elements, identified upstream of strp (an inhibitory region) and tufp (a stimulatory A/T-rich block). Our results suggest that the oppositely adjusted core promoters significantly contribute to the differential expression of the str operon genes, as monitored by the expression of EF-Tu and EF-G.
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Affiliation(s)
- L Krásný
- Department of Protein Biosynthesis, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 166 37 Prague 6, Czech Republic
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13
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Krásný L, Mesters JR, Tieleman LN, Kraal B, Fucík V, Hilgenfeld R, Jonák J. Structure and expression of elongation factor Tu from Bacillus stearothermophilus. J Mol Biol 1998; 283:371-81. [PMID: 9769211 DOI: 10.1006/jmbi.1998.2102] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The tuf gene coding for elongation factor Tu (EF-Tu) of Bacillus stearothermophilus was cloned and sequenced. This gene maps in the same context as the tufA gene of Escherichia coli str operon. Northern-blot analysis and primer extension experiments revealed that the transcription of the tuf gene is driven from two promoter regions. One of these is responsible for producing a 4.9-kb transcript containing all the genes of B. stearothermophilus str operon and the other, identified adjacent to the stop codon of the fus gene and designated tufp, for producing a 1.3-kb transcript of the tuf gene only. In contrast to the situation in E. coli, the ratio between the transcription products was found to be about 10:1 in favour of the tuf gene transcript. This high transcription activity from the tufp promoter might be accounted for by the presence of an extremely A+T-rich block consisting of 29 nucleotides which immediately precedes the consensus -35 region of the promoter. A very similar tuf gene transcription strategy and the same tufp promoter organization with the identical A/T block were found in Bacillus subtilis. The tuf gene specifies a protein of 395 amino acid residues with a molecular mass of 43,290 Da, including the N-terminal methionine. A computer-generated three-dimensional homology model shows that all the structural elements essential for binding guanine nucleotides and aminoacyl-tRNA are conserved. The presence of serine at position 376 and a low affinity for kirromycin determined by zone-interference gel electrophoresis (Kd approximately 8 microM) and by polyacrylamide gel electrophoresis under non-denaturing conditions are in agreement with the reported resistance of this EF-Tu to the antibiotic. The replacement of the highly conserved Leu211 by Met was identified as a possible cause of pulvomycin resistance.
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Affiliation(s)
- L Krásný
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo n.2, Praha 6, 166 37, Czech Republic
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Tieleman LN, van Wezel GP, Bibb MJ, Kraal B. Growth phase-dependent transcription of the Streptomyces ramocissimus tuf1 gene occurs from two promoters. J Bacteriol 1997; 179:3619-24. [PMID: 9171408 PMCID: PMC179156 DOI: 10.1128/jb.179.11.3619-3624.1997] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The str operon of Streptomyces ramocissimus contains the genes for ribosomal proteins S12 (rpsL) and S7 (rpsG) and for the polypeptide chain elongation factors G (EF-G) (fus) and Tu (EF-Tu) (tuf). This kirromycin producer contains three tuf or tuf-like genes; tuf1 encodes the regular EF-Tu and is located immediately downstream of fus. In vivo and in vitro transcription analysis revealed a transcription start site directly upstream of S. ramocissimus tuf1, in addition to the operon promoter rpsLp. Transcription from these promoters appeared to be growth phase dependent, diminishing drastically upon entry into stationary phase and at the onset of production of the EF-Tu-targeted antibiotic kirromycin. In surface-grown cultures, a second round of tuf1 transcription, coinciding with aerial mycelium formation and kirromycin production, was observed. The tuf1-specific promoter (tuf1p) was located in the intercistronic region between fus and tuf1 by high-resolution S1 mapping, in vitro transcription, and in vivo promoter probing. During logarithmic growth, the tuf1p and rpsLp transcripts are present at comparable levels. In contrast to Escherichia coli, which has two almost identical tuf genes, the gram-positive S. ramocissimus contains only tuf1 for its regular EF-Tu. High levels of EF-Tu may therefore be achieved by the compensatory activity of tuf1p.
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Affiliation(s)
- L N Tieleman
- Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, The Netherlands
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15
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Tremousaygue D, Bardet C, Dabos P, Regad F, Pelese F, Nazer R, Gander E, Lescure B. Genome DNA sequencing around the EF-1 alpha multigene locus of Arabidopsis thaliana indicates a high gene density and a shuffling of noncoding regions. Genome Res 1997; 7:198-209. [PMID: 9074924 DOI: 10.1101/gr.7.3.198] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In Arabidopsis thaliana, EF-1 alpha proteins are encoded by a multigene family of four members. Three of them are clustered at the same locus, which was positioned 24 cM from the top of chromosome 1. A region of DNA spanning 63 kb around these locus was sequenced and analyzed. One main characteristic of the locus is the mosaic organization of both genes and intergenic regions. Fourteen genes were identified, among which only four were already described, and other unidentified are most likely present. Functionally diverse genes are found at close intervals. Exon and intron distribution is highly variable at this locus, one gene being split into at least 20 introns. Several duplications were found within the sequenced segment both in coding and noncoding regions, including two gene families. Moreover, a sequence corresponding to the 5' noncoding region of the EF-1 alpha genes and harboring a 5' intervening sequence is duplicated and found upstream of several genes, suggesting that noncoding regions can be shuffled during evolution.
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Affiliation(s)
- D Tremousaygue
- Laboratoire de Biologie Moleculaire des relations Plantes-Microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France.
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16
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Syvänen AC, Amiri H, Jamal A, Andersson SG, Kurland CG. A chimeric disposition of the elongation factor genes in Rickettsia prowazekii. J Bacteriol 1996; 178:6192-9. [PMID: 8892818 PMCID: PMC178489 DOI: 10.1128/jb.178.21.6192-6199.1996] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
An exceptional disposition of the elongation factor genes is observed in Rickettsia prowazekii, in which there is only one tuf gene, which is distant from the lone fus gene. In contrast, the closely related bacterium Agrobacterium tumefaciens has the normal bacterial arrangement of two tuf genes, of which one is tightly linked to the fus gene. Analysis of the flanking sequences of the single tuf gene in R. prowazekii shows that it is preceded by two of the four tRNA genes located in the 5' region of the Escherichia coli tufB gene and that it is followed by rpsJ as well as associated ribosomal protein genes, which in E. coli are located downstream of the tufA gene. The fus gene is located within the str operon and is followed by one tRNA gene as well as by the genes secE and nusG, which are located in the 3' region of tufB in E. coli. This atypical disposition of genes suggests that intrachromosomal recombination between duplicated tuf genes has contributed to the evolution of the unique genomic architecture of R. prowazekii.
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Affiliation(s)
- A C Syvänen
- Department of Molecular Biology, Biomedical Center, Uppsala University, Sweden
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17
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Laalami S, Grentzmann G, Bremaud L, Cenatiempo Y. Messenger RNA translation in prokaryotes: GTPase centers associated with translational factors. Biochimie 1996; 78:577-89. [PMID: 8955901 DOI: 10.1016/s0300-9084(96)80004-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
During the decoding of messenger RNA, each step of the translational cycle requires the intervention of protein factors and the hydrolysis of one or more GTP molecule(s). Of the prokaryotic translational factors, IF2, EF-Tu, SELB, EF-G and RF3 are GTP-binding proteins. In this review we summarize the latest findings on the structures and the roles of these GTPases in the translational process.
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Affiliation(s)
- S Laalami
- Institut de Biologie Moléculaire et d'Ingénierie Génétique, URA-CNRS 1172, Université de Poitiers, France
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18
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Bremaud L, Fremaux C, Laalami S, Cenatiempo Y. Genetic and molecular analysis of the tRNA-tufB operon of the myxobacterium Stigmatella aurantiaca. Nucleic Acids Res 1995; 23:1737-43. [PMID: 7784178 PMCID: PMC306930 DOI: 10.1093/nar/23.10.1737] [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: 01/27/2023] Open
Abstract
The tufB gene, encoding elongation factor Tu (EF-Tu), from the myxobacterium Stigmatella aurantiaca was cloned and sequenced. It is preceded by four tRNA genes, the first ever described in myxobacteria. The tRNA synthesized from these genes and the general organization of the locus seem identical to that of Escherichia coli, but differences of potential importance were found in the tRNA sequences and in the intergenic regions. The primary structure of EF-Tu was deduced from the tufB DNA sequence. The factor is composed of 396 amino acids, with a predicted molecular mass of 43.4 kDa, which was confirmed by expression of tufB in maxicells. Sequence comparisons between S.aurantiaca EF-Tu and other bacterial homologues from E.coli, Salmonella typhimurium and Thermus thermophilus displayed extensive homologies (75.9%). Among the variable positions, two Cys residues probably involved in the temperature sensitivity of E.coli and S.typhimurium EF-Tu are replaced in T.thermophilus and S.aurantiaca EF-Tu. Since two or even three tuf genes have been described in other bacterial species, the presence of multiple tuf genes was sought for. Southern and Northern analysis are consistent with two tuf genes in the genome of S.aurantiaca. Primer extension experiments indicate that the four tRNA genes and tufB are organized in a single operon.
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Affiliation(s)
- L Bremaud
- Institut de Biologie Moléculaire et d'Ingénierie Génétique-CNRS URA 1172, Université de Poitiers, France
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19
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Ichi-ishi A, Inoue H. Cloning, nucleotide sequence, and expression of tef-1, the gene encoding translation elongation factor 1 alpha (EF-1 alpha) of Neurospora crassa. IDENGAKU ZASSHI 1995; 70:273-87. [PMID: 7605676 DOI: 10.1266/jjg.70.273] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The tef-1 gene encoding translation elongation factor 1 alpha was cloned from the ascomycete fungus Neurospora crassa. The sequences of genomic DNA and cDNA clones showed that the tef-1 gene contained one ORF of 1380 bp length that is interrupted by three short introns. The deduced polypeptide contained 460 amino acid residues, and the sequence had a high similarity with those of EF-1 alpha polypeptides from other species. The level of tef-1 mRNA was low in conidia but high in growing cells. When mycelia were transferred to poor nutrient media, the level of tef-1 gene mRNA decreased remarkably. The pattern of tef-1 expression was similar to the expression of genes for ribosomal proteins. The tef-1 gene was mapped between arg-3 and leu-4 loci on linkage group I by restriction fragment length polymorphism mapping. Southern blot analysis showed that Neurospora genomic DNA contained only one copy of the tef-1 gene in a genome.
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Affiliation(s)
- A Ichi-ishi
- Department of Regulation Biology, Faculty of Science, Saitama University, Urawa, Japan
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20
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ICHI-ISHI A, INOUE H. Cloning, nucleotide sequence, and expression of tef-1, the gene encoding translation elongation factor 1α (EF-1α) of Neurospora crassa. Genes Genet Syst 1995. [DOI: 10.1266/ggs.70.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Characterization of the regulatory elements in the promoter of the human elongation factor-1 alpha gene. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43956-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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Steiner S, Philippsen P. Sequence and promoter analysis of the highly expressed TEF gene of the filamentous fungus Ashbya gossypii. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:263-71. [PMID: 8107673 DOI: 10.1007/bf00280415] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ashbya gossypii carries only a single gene (TEF) coding for the abundant translation elongation factor 1 alpha. Cloning and sequencing of this gene and deletion analysis of the promoter region revealed an extremely high degree of similarity with the well studied TEF genes of the yeast Saccharomyces cerevisiae including promoter upstream activation sequence (UAS) elements. The open reading frames in both species are 458 codons long and show 88.6% identity at the DNA level and 93.7% identity at the protein level. A short DNA segment in the promoter, between nucleotides -268 and -213 upstream of the ATG start codon, is essential for high-level expression of the A. gossypii TEF gene. It carries two sequences, GCCCATACAT and ATCCATACAT, with high homology to the UASrpg sequence of S. cerevisiae, which is an essential promoter element in genes coding for highly expressed components of the translational apparatus. UASrpg sequences are binding sites for the S. cerevisiae protein TUF, also called RAP1 or GRF1. In gel retardation with A. gossypii protein extracts we demonstrated specific protein binding to the short TEF promoter segment carrying the UASrpg homologous sequences.
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Affiliation(s)
- S Steiner
- Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Germany
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23
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Hou Y, Lin YP, Sharer JD, March PE. In vivo selection of conditional-lethal mutations in the gene encoding elongation factor G of Escherichia coli. J Bacteriol 1994; 176:123-9. [PMID: 8282687 PMCID: PMC205022 DOI: 10.1128/jb.176.1.123-129.1994] [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: 01/29/2023] Open
Abstract
The ribosome translocation step that occurs during protein synthesis is a highly conserved, essential activity of all cells. The precise movement of one codon that occurs following peptide bond formation is regulated by elongation factor G (EF-G) in eubacteria or elongation factor 2 (EF-2) in eukaryotes. To begin to understand molecular interactions that regulate this process, a genetic selection was developed with the aim of obtaining conditional-lethal alleles of the gene (fusA) that encodes EF-G in Escherichia coli. The genetic selection depends on the observation that resistant strains arose spontaneously in the presence of sublethal concentrations of the antibiotic kanamycin. Replica plating was performed to obtain mutant isolates from this collection that were restrictive for growth at 42 degrees C. Two tightly temperature-sensitive strains were characterized in detail and shown to harbor single-site missense mutations within fusA. The fusA100 mutant encoded a glycine-to-aspartic acid change at codon 502. The fusA101 allele encoded a glutamine-to-proline alteration at position 495. Induction kinetics of beta-galactosidase activity suggested that both mutations resulted in slower elongation rates in vivo. These missense mutations were very near a small group of conserved amino acid residues (positions 483 to 493) that occur in EF-G and EF-2 but not EF-Tu. It is concluded that these sequences encode a specific domain that is essential for efficient translocase function.
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Affiliation(s)
- Y Hou
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway 08854
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24
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Tubulekas I, Hughes D. Growth and translation elongation rate are sensitive to the concentration of EF-Tu. Mol Microbiol 1993; 8:761-70. [PMID: 8332067 DOI: 10.1111/j.1365-2958.1993.tb01619.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have used quantitative immunoblotting to estimate the amount of EF-Tu in a variety of S. typhimurium strains with wild-type, mutant, insertionally inactivated or plasmid-borne tuf genes. In the same strains we have measured translation elongation rate, exponential growth rate and the level of nonsense codon readthrough. In the wild-type strain, at moderate to fast growth rates, our data show that EF-Tu makes up 8-9% of total cell protein. Strains with either of the tuf genes insertionally inactivated have 65% of the wild-type EF-Tu level, irrespective of which tuf gene remains active, or whether that gene is wild-type or a kirromycin-resistant mutant. Strains with only one active tuf gene have reduced growth and translation elongation rates. From the magnitude of the reduction in elongation rate relative to the level of EF-Tu we calculate that in glucose minimal medium the in vivo saturation level of wild-type ribosomes by ternary complexes is only 63%. Strains with a ribosome mutation causing a poor interaction with ternary complex are non-viable on minimal medium when the level of EF-Tu is reduced.
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Affiliation(s)
- I Tubulekas
- Department of Molecular Biology, Uppsala University, Sweden
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25
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McTavish H, LaQuier F, Arciero D, Logan M, Mundfrom G, Fuchs JA, Hooper AB. Multiple copies of genes coding for electron transport proteins in the bacterium Nitrosomonas europaea. J Bacteriol 1993; 175:2445-7. [PMID: 8385668 PMCID: PMC204534 DOI: 10.1128/jb.175.8.2445-2447.1993] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The genome of Nitrosomonas europaea contains at least three copies each of the genes coding for hydroxylamine oxidoreductase (HAO) and cytochrome c554. A copy of an HAO gene is always located within 2.7 kb of a copy of a cytochrome c554 gene. Cytochrome P-460, a protein that shares very unusual spectral features with HAO, was found to be encoded by a gene separate from the HAO genes.
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Affiliation(s)
- H McTavish
- Department of Genetics and Cell Biology, University of Minnesota, St. Paul 55108
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26
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Zeidler W, Kreutzer R, Sprinzl M. Participation of the overproduced elongation factor Tu from Thermus thermophilus in protein biosynthesis of Escherichia coli. FEBS Lett 1993; 319:185-8. [PMID: 8454054 DOI: 10.1016/0014-5793(93)80064-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The influence of the overproduced elongation factor Tu (EF-Tu) from Thermus thermophilus on the protein biosynthesis in Escherichia coli was investigated both in vivo and in vitro. A kirromycin-resistant E. coli strain became sensitive to this antibiotic upon the expression of the tuf A-gene of T. thermophilus present on a plasmid. In in vitro translation with components of the kirromycin-resistant E. coli strain the poly(Phe) synthesis stopped when minute amounts of the EF-Tu from T. thermophilus were added. Both results indicate the sensitivity of the T. thermophilus EF-Tu to kirromycin and its participation in the polypeptide synthesis of E. coli.
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Affiliation(s)
- W Zeidler
- Laboratorium für Biochemie, Universität Bayreuth, Germany
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27
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Johanson U, Hughes D. Comparison of the complete sequence of the str operon in Salmonella typhimurium and Escherichia coli. Gene 1992; 120:93-8. [PMID: 1398129 DOI: 10.1016/0378-1119(92)90014-g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The nucleotide (nt) sequences of the str operon in Escherichia coli K-12 and Salmonella typhimurium LT2 were completed and compared at the nt and amino acid (aa) level. The order of conservation at the nt and aa level is rpsL greater than tufA greater than rpsG greater than f usA. A striking difference is that the rpsG-encoded ribosomal protein, S7, in E. coli K-12 is 23 aa longer than in S. typhimurium. The very low (0.18) codon adaptation index of this part of the E. coli K-12-encoding gene and the unusual stop codon (UGA) suggest that this is a relatively recent extension. A trend towards a higher G+C content in fusA (gene encoding elongation factor (EF)-G) and tufA (gene encoding EF-Tu) in S. typhimurium is noted. In fusA, nt substitutions at all three positions in a codon occur at a much higher frequency than expected from the number of nt substitutions in the gene, assuming they are random and independent events. An analysis of substitutions in this and other genes suggests that the triple substitutions in fusA, and some other genes, are the result of the sequential accumulation of individual mutations, probably driven by selection pressure for particular codons or aa.
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Affiliation(s)
- U Johanson
- Department of Molecular Biology, Uppsala University, Sweden
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28
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Satoh M, Tanaka T, Kushiro A, Hakoshima T, Tomita K. Molecular cloning, nucleotide sequence and expression of the tufB gene encoding elongation factor Tu from Thermus thermophilus HB8. FEBS Lett 1991; 288:98-100. [PMID: 1908798 DOI: 10.1016/0014-5793(91)81011-v] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The tufB gene encoding elongation factor Tu (EF-Tu) of Thermus thermophilus HB8 was cloned and expressed. Compared with the known tufA gene of T. thermophilus, nucleotide differences were found at 10 positions out of 1221 nucleotides, and amino acid substitutions were found at 4 positions out of 406 amino acids. The tufB product was 70.9% homologous to the corresponding sequence of the tufB product of E. coli. The G+C content of the third base of the codon in the tufB gene was 84.8% and G was especially preferred in this position.
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Affiliation(s)
- M Satoh
- Faculty of Pharmaceutical Sciences, Osaka University, Japan
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29
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Tiboni O, Cantoni R, Creti R, Cammarano P, Sanangelantoni AM. Phylogenetic depth of Thermotoga maritima inferred from analysis of the fus gene: amino acid sequence of elongation factor G and organization of the Thermotoga str operon. J Mol Evol 1991; 33:142-51. [PMID: 1920450 DOI: 10.1007/bf02193628] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The gene (fus) coding for elongation factor G (EF-G) of the extremely thermophilic eubacterium Thermotoga maritima was identified and sequenced. The EF-G coding sequence (2046 bp) was found to lie in an operon-like structure between the ribosomal protein S7 gene (rpsG) and the elongation factor Tu (EF-Tu) gene (tuf). The rpsG, fus, and tuf genes follow each other immediately in that order, which corresponds to the order of the homologous genes in the str operon of Escherichia coli. The derived amino acid sequence of the EF-G protein (682 residues) was aligned with the homologous sequences of other eubacteria, eukaryotes (hamster), and archaebacteria (Methanococcus vannielii). Unrooted phylogenetic dendrograms, obtained both from the amino acid and the nucleotide sequence alignments, using a variety of methods, lend further support to the notion that the (present) root of the (eu)bacterial tree lies between Thermotoga and the other bacterial lineages.
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Affiliation(s)
- O Tiboni
- Dipartimento di Genetica e Microbiologia A. Buzzati-Traverso, Universita di Pavia, Italy
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30
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Abstract
Each of the two genes encoding EF-Tu in Salmonella typhimurium has been inactivated using a mini-Mu MudJ insertion. Eleven independently isolated insertions are described, six in tufA and five in tufB. Transduction analysis shows that the inserted MudJ is 100% linked to the appropriate tuf gene. A mutant strain with electrophoretically distinguishable EF-TuA and EF-TuB was used to show, on two-dimensional gels, that the MudJ insertions result in the loss of the appropriate EF-Tu protein. Southern blotting, using cloned Escherichia coli tuf sequences as probes, shows that each MudJ insertion results in the physical breakage of the appropriate tuf gene. The degree of growth-rate impairment associated with each tuf inactivation is independent of which tuf gene is inactivated. The viability of S. typhimurium strains with either tuf gene inactive contrasts strongly with data suggesting that in the closely related bacterium E. coli, an active tufA gene is essential for growth. Finally the strains described here facilitate the analysis of phenotypes associated with individual mutant or wild-type Tus both in vivo and in vitro.
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Affiliation(s)
- D Hughes
- Department of Molecular Biology, Biomedical Center, Uppsala, Sweden
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31
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Bosch L, Nilsson L, Vijgenboom E, Verbeek H. FIS-dependent trans-activation of tRNA and rRNA operons of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1050:293-301. [PMID: 2145039 DOI: 10.1016/0167-4781(90)90184-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two mechanisms controlling stable RNA synthesis have been described: growth rate-dependent control and stringent response. Although the mechanism underlying growth rate-dependent control is still a matter of dispute, this control is commonly assumed to operate through repression of transcription initiation of stable RNA operons. The same is true for the stringent response. Here we show that the cell utilizes an additional control system operating through activation of the thrU(tufB) operon. This operon, the tyrT and the rrnB operon share a common trans-activating protein that binds to cis-acting DNA regions upstream of the promoters of the two tRNA operons and of the P1 promoter of the rrnB operon. Conceivably, more stable RNA operons may be regulated by trans-activation. Both in vivo and in vitro experiments show that the Escherichia coli protein FIS (Factor for Inversion Stimulation) is involved in the trans-activation. This protein is known to stimulate the inversion of various DNA segments by binding to cis-acting recombinational enhancers and functions as a host factor for the bacteriophages Mu and Lambda.
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Affiliation(s)
- L Bosch
- Department of Biochemistry, Leiden University, Gorlaeus Laboratories, The Netherlands
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32
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Zengel JM, Lindahl L. Mapping of two promoters for elongation factor Tu within the structural gene for elongation factor G. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1050:317-22. [PMID: 2207161 DOI: 10.1016/0167-4781(90)90188-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The str operon of Escherichia coli contains the genes for ribosomal proteins S7 and S12 as well as elongation factors G and Tu (EF-G, EF-Tu). We have previously reported that there is a secondary promoter for expression of EF-Tu mapping within the upstream fus gene encoding EF-G (Zengel, J.M. and Lindahl, L. (1982) Mol. Gen. Genet. 185, 487-492) and have identified several potential promoter sequences within fus (Zengel, J.M., Archer, R.H. and Lindahl, L. (1984) Nucleic Acids Res. 12, 2181-2192). We have now further characterized this promoter activity. Measurements of transcription rates from various regions of the str operon in cells carrying the fus gene and the beginning of the tufA gene on a high copy number plasmid confirmed that transcription was initiated within a 600 bp EcoRI fragment in the distal portion of the fus gene. Furthermore, T1 nuclease mapping studies identified two 5' ends within this region, one about 400 bases upstream of tufA, the other about 270 bases upstream, suggesting that there are two tufA promoters within the fus gene. Both of these promoters are active in the intact chromosomal str operon.
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Affiliation(s)
- J M Zengel
- Department of Biology, University of Rochester, NY 14627
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33
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Tapio S, Isaksson LA. Antisuppression by mutations in elongation factor Tu. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 188:339-46. [PMID: 2180701 DOI: 10.1111/j.1432-1033.1990.tb15409.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two slow-growing kirromycin-resistant Escherichia coli mutants with altered EF-Tu (Ap and Aa) were studied in vivo in strains with an inactive tufB gene. Mutant form Aa was isolated as an antisuppressor of the tyrT(Su3) nonsense suppressor, as described here. Ap, the tufA gene product of strain D2216 (from A. Parmeggiani), has previously been shown to give an increased GTPase activity. The slow cellular growth rates of both EF-Tu mutants are correlated with decreased translational elongation rates. Ap and Aa significantly decrease suppression levels of both nonsense and missense suppressor tRNAs [tyrT(Su3), trpT(Su9), glyT(SuAGA/G)], but have only little or no effect on misreading by wild-type tRNAs. A particular missense suppressor, lysT(SuAAA/G), which acts by virtue of partial mischarging as the result of an alteration in the amino acid stem, is not significantly affected by the EF-Tu mutations. The combination of tufA(Aa) and a rpsD12 ribosomal mutation is lethal at room temperature and the double-mutant strain has an elevated temperature optimum (42 degrees C) for growth rate, translation rate and nonsense suppression. Our data indicate an alterated interaction between Aa and the ribosome, consistent with our in vitro results.
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Affiliation(s)
- S Tapio
- Department of Microbiology, University of Uppsala, Sweden
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34
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Tiboni O, Sanangelantoni A, Cammarano P, Cimino L, Di Pasquale G, Sora S. Expression in Escherichia coli of the tuf Gene from the Extremely Thermophilic Eubacterium Thermotoga maritima: Purification of the Thermotoga Elongation Factor Tu by Thermal Denaturation of the Mesophile Host Cell Proteins. Syst Appl Microbiol 1989. [DOI: 10.1016/s0723-2020(89)80002-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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35
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Goldstein BP, Zaffaroni G, Tiboni O, Amiri B, Denaro M. Determination of the number oftufgenes inChlamydia trachomatisandNeisseria gonorrhoeae. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03491.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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36
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Ichikawa S, Ryoji M, Siegfried Z, Kaji A. Localization of the ribosome-releasing factor gene in the Escherichia coli chromosome. J Bacteriol 1989; 171:3689-95. [PMID: 2661533 PMCID: PMC210112 DOI: 10.1128/jb.171.7.3689-3695.1989] [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: 01/02/2023] Open
Abstract
The ribosome-releasing factor (RRF) gene was localized at a position between 2 and 6 min on the Escherichia coli chromosome by measuring the gene-dosage-dependent production of RRF in various E. coli F' merozygotes. This position was confirmed and refined by using a nucleotide probe corresponding to a 16-amino-acid sequence in RRF. It was found that the RRF gene was contained in pLC 6-32 of the Clark-Carbon Gene Bank. Restriction enzyme mapping of E. coli genomic DNA with the above probe led us to conclude that the RRF gene is situated in the 4-min region, somewhere downstream (clockwise) of the elongation factor Ts gene, tsf. A pLC 6-32-derived DNA fragment which carries the RRF gene was found to contain a partial sequence of tsf. The exact location of the translational initiation site of the RRF gene was determined to be 1.1 kilobases downstream from the translational termination site of tsf. The RRF gene is designated frr.
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Affiliation(s)
- S Ichikawa
- Department of Microbiology, School of Medicine, University of Pennsylvania, Philadelphia 19104
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37
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Pokalsky AR, Hiatt WR, Ridge N, Rasmussen R, Houck CM, Shewmaker CK. Structure and expression of elongation factor 1 alpha in tomato. Nucleic Acids Res 1989; 17:4661-73. [PMID: 2748335 PMCID: PMC318023 DOI: 10.1093/nar/17.12.4661] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A full-length cDNA clone, LeEF-1, has been isolated from tomato for the alpha subunit of elongation factor 1 (EF-1 alpha), a polypeptide which plays a central role in protein synthesis. The 448 amino acid protein encoded by this cDNA appears highly homologous to other EF-1 alpha s having a high degree of similarity (75-78%) to EF1 alpha previously described from both lower eukaryotes and animals. Southern analysis indicated that EF-1 alpha belongs to a small multigene family of 4-8 members in tomato. The pattern of expression of EF-1 alpha mRNA in various tomato tissues was analyzed by Northern analysis, in vitro translation and in situ hybridization. EF-1 alpha mRNA is an abundant species and higher levels of mRNA were found in developing tissues such as young leaves and green fruit compared to the mRNA levels observed in older tissues. The increased levels of EF-1 alpha mRNA therefore appear to correlate with higher levels of protein synthesis in developing tissues.
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Uetsuki T, Naito A, Nagata S, Kaziro Y. Isolation and Characterization of the Human Chromosomal Gene for Polypeptide Chain Elongation Factor-1α. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)83619-5] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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39
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Sela S, Yogev D, Razin S, Bercovier H. Duplication of the tuf gene: a new insight into the phylogeny of eubacteria. J Bacteriol 1989; 171:581-4. [PMID: 2492503 PMCID: PMC209627 DOI: 10.1128/jb.171.1.581-584.1989] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The conservation and duplication of the tuf gene encoding the elongation factor EF-Tu were used to define phylogenetic relationships among eubacteria. When the tufA gene of Escherichia coli was used as a probe in hybridization experiments, duplicate tuf genes were found in gram-negative bacteria from three major phyla: purple bacteria, bacteroides, and cyanobacteria. Only a single copy of tuf was found in gram-positive bacteria, including mycobacteria and mycoplasmas. Gram-positive clostridia were found to carry two copies of tuf.
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Affiliation(s)
- S Sela
- Department of Clinical Microbiology, Hebrew University--Hadassah Medical School, Jerusalem, Israel
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40
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Van Delft JH, Verbeek HM, De Jong PJ, Schmidt DS, Talens A, Bosch L. Control of the tRNA-tufB operon in Escherichia coli. 1. rRNA gene dosage effects and growth-rate-dependent regulation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 175:355-62. [PMID: 2456926 DOI: 10.1111/j.1432-1033.1988.tb14204.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
'Ribosome feedback' effects on the expression of the genes specifying tRNA and EF-Tu in E. coli have been studied at increased rrnB doses (rRNA gene doses). We confirm previous observations that the introduction into the cell of a multicopy plasmid carrying the rrnB operon reduces the cellular content of most tRNAs, including those encoded by the tRNA-tufB operon, but leaves the 5S rRNA content unaffected. Increase of the dosage of intact, but not of deleted rRNA genes, causes a slight drop in total EF-Tu that can be fully accounted for by a decrease in EF-TuB level. The drop in EF-TuB content (approx. 25%) is much smaller than that in tRNA content (approx. 80%). The synthesis rate of total EF-Tu is hardly affected, indicating that the turnover of EF-Tu has not changed. The ratio of tRNA over tuf RNA synthesis rates remains the same after elevation of rrnB dosage. Considering the large decrease in tRNA content this means that both RNA synthesis rates decrease to approximately the same extent. The relatively small drop in EF-Tu synthesis must be due, therefore, to an enhancement of the number of EF-Tu molecules synthesized per mRNA molecule. Apparently a post-transcriptional mechanism, regulating EF-Tu synthesis, becomes operative under these conditions. Growth-rate-dependent regulation of the tRNA-tufB operon has been studied using lysogens carrying tRNA':lacZ and tRNA-tufB':lacZ operon fusions and a tufB':lacZ' gene fusion. These experiments show that the cellular contents of tRNA, tufB RNA and EF-TuB vary in direct proportion to the growth rate. This indicates that growth rate control of tRNA-tufB operon transcription resembles that of stable RNA operons and not of r-protein operons, and that the read-through of the terminator at the end of the tRNA gene cluster remains unaltered.
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Affiliation(s)
- J H Van Delft
- Department of Biochemistry, University of Leiden, The Netherlands
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41
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Tapio S, Isaksson LA. Antagonistic effects of mutant elongation factor Tu and ribosomal protein S12 on control of translational accuracy, suppression and cellular growth. Biochimie 1988; 70:273-81. [PMID: 3134951 DOI: 10.1016/0300-9084(88)90071-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Kirromycin-resistant mutant forms of elongation factor Tu, which are coded by tufA (Ar) or tufB (Bo) and are associated with an increased rate of translational error formation, have been analysed. In vivo, Ar was found to increase misreading as well as suppression of non-sense codons irrespective of Bo in a strain with wild type ribosomes. It is therefore not necessary to evoke both tufA (Ar) and tufB (Bo) mutations together in order to increase translational error as suggested earlier [1]. When combined with a hyperaccurate ribosomal rpsL (S12) mutation, Ar counteracts the restrictive effects on translational error formation caused by the altered protein S12, thus restoring the levels of missense error in vitro and non-sense error and suppression in vivo to near wild type values. As judged from in vitro experiments this results principally from a lowered selectivity of the Ar ternary complex at the initial discrimination step on the ribosome during translation. In vivo, this compensatory effect on the rpsL mutation on non-sense error formation and suppression is seen irrespective of the nature of tRNA or codon context. Furthermore, the tufA mutation enhances the cellular growth rate of the rpsL mutant, whereas it decreases growth of strains with normal ribosomes. Inactivation of one of the two genes coding for EF-Tu (tufB), while leaving the other gene (tufA) intact, can by itself, increase non-sense error formation and suppression.
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Affiliation(s)
- S Tapio
- Department of Microbiology, Uppsala University, Sweden
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42
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Kushiro M, Shimizu M, Tomita K. Molecular cloning and sequence determination of the tuf gene coding for the elongation factor Tu of Thermus thermophilus HB8. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 170:93-8. [PMID: 2826164 DOI: 10.1111/j.1432-1033.1987.tb13671.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The tuf gene, which encodes the elongation factor Tu (EF-Tu) of Thermus thermophilus HB8, and its flanking regions were cloned and sequenced. The gene encoding EF-G was found upstream of the 5' end of the tuf gene. The tuf gene of T. thermophilus HB8 had a very high G + C content and 84.5% of the third base in codon usage was either G or C. The deduced primary structure of the EF-Tu was composed of 405 amino acid residues with a Mr = 44658. A comparison of the amino acid sequence of EF-Tu from T. thermophilus HB8 with those of Escherichia coli and Saccharomyces cerevisiae mitochondria showed a very high sequence homology (65-70%). Two Cys residues out of the three found in E. coli EF-Tu had been replaced with Val in T. thermophilus HB8 EF-Tu. An extra amino acid sequence of ten residues, consisting predominantly of basic amino acids (Met-182-Gly-191), which does not occur in EF-Tu of E. coli, was found in T. thermophilus HB8.
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Affiliation(s)
- M Kushiro
- Facility of Pharmaceutical Sciences, Osaka University, Japan
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43
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Van Delft JH, Schmidt DS, Bosch L. The tRNA-tufB operon transcription termination and processing upstream from tufB. J Mol Biol 1987; 197:647-57. [PMID: 2448475 DOI: 10.1016/0022-2836(87)90471-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Two genes, tufA and tufB, located at 73 and 88 minutes of the Escherichia coli linkage map, code for the polypeptide chain elongation factor EF-Tu. tufB is transcribed with four upstream tRNA genes, thrU, tyrU, glyT and thrT, into a cotranscript of approximately 1800 nucleotides. Here we show that in vivo processing yields a 1320 nucleotide transcript of tufB. S1 nuclease fine mapping reveals that the processing site is located in the intergenic region at about 72 to 74 nucleotides upstream from the initiation codon of the tufB cistron. A deletion in the cloned tRNA-tufB operon, encompassing the 3' half of thrU, the complete tyrU, glyT, thrT genes and ten nucleotides of the intergenic region, causes a threefold increase of the rate of plasmid tufB transcription, a fourfold increase of plasmid-borne tufB RNA and a twofold increase of plasmid-borne EF-TuB. We conclude that the deletion has eliminated a transcription termination site probably located after the thrT gene. Termination at this site uncouples tRNA synthesis from tufB transcription.
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Affiliation(s)
- J H Van Delft
- Department of Biochemistry, University of Leiden, The Netherlands
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44
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Abstract
The level of nonsense suppression in Salmonella typhimurium carrying error-enhancing mutations in either or both of the genes coding for the elongation factor EF-Tu has been measured. Suppression of both UGA and UAG is observed. There is no significant suppression of any of six UAA sites tested. Nonsense suppression does not require that both genes for EF-Tu be mutant. Strains carrying one mutant and one wild-type tuf gene suppress nonsense mutations. The level of suppression increases approximately additively when both tuf genes are mutant. It is suggested that these mutant forms of EF-Tu act independently of each other to suppress nonsense mutations. Suppression is not observed at all UGA and UAG sites, but instead shows a strong site specificity.
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Affiliation(s)
- D Hughes
- Institute of Molecular Biology, Biomedical Center, Uppsala, Sweden
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45
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Montandon PE, Knuchel-Aegerter C, Stutz E. Euglena gracilis chloroplast DNA: the untranslated leader of tufA-ORF206 gene contains an intron. Nucleic Acids Res 1987; 15:7809-22. [PMID: 3118328 PMCID: PMC306309 DOI: 10.1093/nar/15.19.7809] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Structural features of a dicistronic 1.95 kb mRNA coding for the chloroplast specific elongation factor Tu and ORF206 are described. The unspliced pre-mRNA is composed of 2562 nucleotides and undergoes four splicing events which remove a total of 606 nucleotides. The first intron splits the untranslated leader, two introns dissect the tufA coding region and the forth intron is within ORF206, which codes for a putative protein that is to 34% homologous with the putative protein of chloroplast ORF184 of tobacco. Introns neither belong to group I nor II, and 5' and 3' intron boundaries do not follow consensus sequences. Potential ribosome binding sites are located 58 and 32 positions upstream of the tufA and ORF206 start codon, respectively.
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Affiliation(s)
- P E Montandon
- Laboratoire de Biochimie, Université de Neuchâtel, Switzerland
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46
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Vijgenboom E, Bosch L. Transfer of plasmid-borne tuf mutations to the chromosome as a genetic tool for studying the functioning of EF-TuA and EF-TuB in the E. coli cell. Biochimie 1987; 69:1021-30. [PMID: 2964874 DOI: 10.1016/0300-9084(87)90002-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The elongation factor EF-Tu of E. coli is a multifunctional protein that lends itself extremely well to studies concerning structure-function relationships. It is encoded by two genes: tufA and tufB. Mutant species of EF-Tu have been obtained by various genetic manipulations, including site- and segment-directed mutagenesis of tuf genes on a vector. The presence of multiple tuf genes in the cell, both chromosomal and plasmid-borne, hampers the characterization of the mutant EF-Tu. We describe a procedure for transferring plasmid-borne tuf gene mutations to the chromosome. Any mutation engineered by genetic manipulation of tuf genes on a vector can be transferred both to the tufA and the tufB position on the chromosome. The procedure facilitated the functional characterization of some of our recently obtained tuf mutations. Of particular relevance is, that it enabled us for the first time to obtain a mutant tufB on the chromosome, encoding an EF-TuB resistant to kirromycin. It thus became possible to study the consequences for growth of tufA inactivation by insertion of bacteriophage Mu. The preliminary evidence obtained suggests that an EF-TuA, active in polypeptide synthesis, is essential for growth whereas such an EF-TuB is dispensable.
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Affiliation(s)
- E Vijgenboom
- Department of Biochemistry, Leiden University, The Netherlands
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47
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Hwang YW, Miller DL. A mutation that alters the nucleotide specificity of elongation factor Tu, a GTP regulatory protein. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45170-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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48
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Tiboni O, Di Pasquale G. Organization of genes for ribosomal proteins S7 and S12, elongation factors EF-Tu and EF-G in the cyanobacterium Spirulina platensis. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 908:113-22. [PMID: 3101737 DOI: 10.1016/0167-4781(87)90050-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The gene encoding ribosomal proteins S12 and probably S7 as well as protein synthesis elongation factors Tu (EF-Tu) and G (EF-G) of Spirulina platensis have been identified and cloned. Gene expression was determined for ribosomal protein S12 by genetic complementation of the appropriate Escherichia coli mutant, whereas for the EF-Tu gene it was determined by production of the protein in E. coli minicells. On the basis of these experiments we suggest the following gene order in the S. platensis chromosome: S12, S7, EF-G, EF-Tu.
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49
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Mickel FS, Spremulli LL. Organization of the genes for protein synthesis elongation factors Tu and G in the cyanobacterium Anacystis nidulans. J Bacteriol 1986; 166:78-82. [PMID: 3082860 PMCID: PMC214559 DOI: 10.1128/jb.166.1.78-82.1986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The genes for protein synthesis elongation factors Tu and G were cloned from the cyanobacterium Anacystis nidulans. The locations of these genes were mapped within the cloned DNA fragment by hybridization with Escherichia coli probes. The organization of the cloned fragment and the DNA flanking it in the A. nidulans chromosome was also determined. The elongation factor Tu and G genes are adjacent to one another and in the same 5'-to-3' orientation. In contrast to other gram-negative bacteria, A. nidulans contains only one gene for elongation factor Tu.
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50
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Jacobs WR, Barrett JF, Clark-Curtiss JE, Curtiss R. In vivo repackaging of recombinant cosmid molecules for analyses of Salmonella typhimurium, Streptococcus mutans, and mycobacterial genomic libraries. Infect Immun 1986; 52:101-9. [PMID: 2937735 PMCID: PMC262204 DOI: 10.1128/iai.52.1.101-109.1986] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of Escherichia coli K-12 were constructed that permitted the amplification of in vitro-packaged recombinant cosmid-transducing particles by in vivo repackaging of recombinant cosmid molecules. Thermal induction of these thermoinducible, excision-defective lysogens containing recombinant cosmid molecules yielded high titers of packaged recombinant cosmids and low levels of PFU. These strains were used to amplify packaged recombinant cosmid libraries of Mycobacterium leprae, Mycobacterium vaccae, Salmonella typhimurium, and Streptococcus mutans DNA. Contiguous and noncontiguous libraries were compared for the successful identification of cloned genes. Construction of noncontiguous libraries allowed the dissociation of desired genes from genes that were deleterious to the survival of a cosmid recombinant and permitted selection for unlinked traits that resulted in a selected phenotype. In vivo repackaging of recombinant cosmids permitted amplification of the original in vitro-packaged collection of transducing particles, storage of cosmid libraries as phage lysates, facilitation of complementation screening, expression analysis of repackaged recombinant cosmids after UV-irradiated cells were infected, in situ enzyme or immunological screening, and facilitation of recovery of recombinant cosmid molecules containing transposon inserts.
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