1
|
Chengguang H, Sabatini P, Brandi L, Giuliodori AM, Pon CL, Gualerzi CO. Ribosomal selection of mRNAs with degenerate initiation triplets. Nucleic Acids Res 2017; 45:7309-7325. [PMID: 28575317 PMCID: PMC5499595 DOI: 10.1093/nar/gkx472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 05/12/2017] [Indexed: 12/27/2022] Open
Abstract
To assess the influence of degenerate initiation triplets on mRNA recruitment by ribosomes, five mRNAs identical but for their start codon (AUG, GUG, UUG, AUU and AUA) were offered to a limiting amount of ribosomes, alone or in competition with an identical AUGmRNA bearing a mutation conferring different electrophoretic mobility to the product. Translational efficiency and competitiveness of test mRNAs toward this AUGmRNA were determined quantifying the relative amounts of the electrophoretically separated wt and mutated products synthesized in vitro and found to be influenced to different extents by the nature of their initiation triplet and by parameters such as temperature and nutrient availability in the medium. The behaviors of AUAmRNA, UUGmRNA and AUGmRNA were the same between 20 and 40°C whereas the GUG and AUUmRNAs were less active and competed poorly with the AUGmRNA, especially at low temperature. Nutrient limitation and preferential inhibition by ppGpp severely affected activity and competitiveness of all mRNAs bearing non-AUG starts, the UUGmRNA being the least affected. Overall, our data indicate that beyond these effects exclusively due to the degenerate start codons within an optimized translational initiation region, an important role is played by the context in which the rare start codons are present.
Collapse
Affiliation(s)
- He Chengguang
- College of Life Sciences, Engineering Research Centre of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, Jilin, China.,Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Paola Sabatini
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Letizia Brandi
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Anna M Giuliodori
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | - Cynthia L Pon
- Laboratory of Genetics, University of Camerino 62032 Camerino, Italy
| | | |
Collapse
|
2
|
Kapralou S, Fabbretti A, Garulli C, Gualerzi CO, Pon CL, Spurio R. Characterization of Bacillus stearothermophilus infA and of its product IF1. Gene 2008; 428:31-5. [PMID: 18951960 DOI: 10.1016/j.gene.2008.09.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 09/23/2008] [Accepted: 09/24/2008] [Indexed: 11/28/2022]
Abstract
Bacillus stearothermophilus infA encoding translation initiation factor IF1 was cloned and expressed in Escherichia coli and its transcript and protein product characterized. Although the functional properties of B. stearothermophilus and E. coli IF1, compared in several translational tests in the presence of both homologous and heterologous components, are not entirely identical, the two proteins are interchangeable in an in vitro translational system programmed with a natural mRNA. The availability of purified B. stearothermophilus IF1 now allows us to analyze the translation initiation pathway using efficient in vitro tests based entirely on purified components derived from this thermophilic Gram-positive bacterium.
Collapse
Affiliation(s)
- Stavroula Kapralou
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, Camerino (MC), Italy
| | | | | | | | | | | |
Collapse
|
3
|
Kapralou S, Fabbretti A, Garulli C, Spurio R, Gualerzi CO, Dahlberg AE, Pon CL. Translation initiation factor IF1 of Bacillus stearothermophilus and Thermus thermophilus substitute for Escherichia coli IF1 in vivo and in vitro without a direct IF1-IF2 interaction. Mol Microbiol 2008; 70:1368-77. [PMID: 18976282 DOI: 10.1111/j.1365-2958.2008.06466.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Bacterial translation initiation factor IF1 is homologous to archaeal aIF1A and eukaryal eIF1A, which form a complex with their homologous IF2-like factors (aIF5B and eIF5B respectively) during initiation of protein synthesis. A similar IF1-IF2 interaction is assumed to occur in all bacteria and supported by cross-linking data and stabilization of the 30S-IF2 interaction by IF1. Here we compare Escherichia coli IF1 with thermophilic factors from Bacillus stearothermophilus and Thermus thermophilus. All three IF1s are structurally similar and functionally interchangeable in vivo and in vitro. However, the thermophilic factors do not stimulate ribosomal binding of IF2DeltaN, regardless of 30S subunits and IF2 origin. We conclude that an IF1-IF2 interaction is not universally conserved and is not essential for cell survival.
Collapse
Affiliation(s)
- Stavroula Kapralou
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
| | | | | | | | | | | | | |
Collapse
|
4
|
Brandi L, Fabbretti A, Milon P, Carotti M, Pon CL, Gualerzi CO. Methods for identifying compounds that specifically target translation. Methods Enzymol 2007; 431:229-67. [PMID: 17923238 DOI: 10.1016/s0076-6879(07)31012-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This chapter presents methods and protocols suitable for the identification and characterization of inhibitors of the prokaryotic and/or eukaryotic translational apparatus as a whole or targeting specific, underexploited targets of the bacterial protein synthetic machinery such as translation initiation and aminoacylation. Some of the methods described have been used successfully for the high-throughput screening of libraries of natural or synthetic compounds and make use of model "universal" mRNAs that can be translated with similar efficiency by cellfree extracts of bacterial, yeast, and HeLa cells. Other methods presented here are suitable for secondary screening tests aimed at identifying a specific target of an antibiotic within the translational pathway of prokaryotic cells.
Collapse
|
5
|
Milon P, Konevega AL, Peske F, Fabbretti A, Gualerzi CO, Rodnina MV. Transient kinetics, fluorescence, and FRET in studies of initiation of translation in bacteria. Methods Enzymol 2007; 430:1-30. [PMID: 17913632 DOI: 10.1016/s0076-6879(07)30001-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Initiation of mRNA translation in prokaryotes requires the small ribosomal subunit (30S), initiator fMet-tRNA(fMet), three initiation factors, IF1, IF2, and IF3, and the large ribosomal subunit (50S). During initiation, the 30S subunit, in a complex with IF3, binds mRNA, IF1, IF2.GTP, and fMet-tRNA(fMet) to form a 30S initiation complex which then recruits the 50S subunit to yield a 70S initiation complex, while the initiation factors are released. Here we describe a transient kinetic approach to study the timing of elemental steps of 30S initiation complex formation, 50S subunit joining, and the dissociation of the initiation factors from the 70S initiation complex. Labeling of ribosomal subunits, fMet-tRNA(fMet), mRNA, and initiation factors with fluorescent reporter groups allows for the direct observation of the formation or dissociation of complexes by monitoring changes in the fluorescence of single dyes or fluorescence resonance energy transfer (FRET) between two fluorophores. Subunit joining was monitored by light scattering or by FRET between dyes attached to the ribosomal subunits. The kinetics of chemical steps, that is, GTP hydrolysis by IF2 and peptide bond formation following the binding of aminoacyl-tRNA to the 70S initiation complex, were measured by the quench-flow technique. The methods described here are based on results obtained with initiation components from Escherichia coli but can be adopted for mechanistic studies of initiation in other prokaryotic or eukaryotic systems.
Collapse
MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Fluorescence Resonance Energy Transfer
- GTP Phosphohydrolases/metabolism
- Models, Molecular
- Prokaryotic Initiation Factors/chemistry
- Prokaryotic Initiation Factors/genetics
- Prokaryotic Initiation Factors/metabolism
- Protein Biosynthesis
- Protein Structure, Quaternary
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- Ribosome Subunits, Small, Bacterial/chemistry
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
Collapse
Affiliation(s)
- Pohl Milon
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, Camerino, Italy
| | | | | | | | | | | |
Collapse
|
6
|
Falconi M, Higgins NP, Spurio R, Pon CL, Gualerzi CO. Expression of the gene encoding the major bacterial nucleoid protein H-NS is subject to transcriptional auto-repression. Mol Microbiol 2006; 10:273-282. [PMID: 28776853 DOI: 10.1111/j.1365-2958.1993.tb01953.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Expression of a promoterless cat gene fused to a DNA fragment of approximately 400 bp, beginning at -313 of Escherichia coli hns, was significantly repressed in E. coli and Salmonella typhimurium strains with wild-type hns but not in mutants carrying hns alleles. CAT expression from fusions containing a shorter (110 bp) segment of hns was essentially unaffected in the same genetic backgrounds. The stage of growth was found to influence the extent of repression which was maximum (approximately 75%) in mid-log cultures and negligible in cells entering the stationary phase. The level of repression in early-log phase was lower than in mid-log phase cultures, probably because of the presence of high levels of Fis protein, which counteracts the H-NS inhibition by stimulating hns transcription. The effects observed in vivo were mirrored by similar results obtained in vitro upon addition of purified H-NS and Fis protein to transcriptional systems programmed with the same hns caf fusions. Electrophoretic gel shift assays, DNase I footprinting and cyclic permutation get analyses revealed that H-NS binds preferentially to the upstream region of its own gene recognizing two rather extended segments of DNA on both sides of a bend centred around -150. When these sites are filled by H-NS, an additional site between approximately -20 and -65, which partly overlaps the promoter, is also occupied. Binding of H-NS to this site is probably the ultimate cause of transcriptional auto-repression.
Collapse
Affiliation(s)
- Maurizio Falconi
- Department of Biology, University of Camerino, 62032 Camerino (MC), Italy.Department of Biochemistry, University of Alabama, Birmingham, Alabama, USA
| | - N Patrick Higgins
- Department of Biology, University of Camerino, 62032 Camerino (MC), Italy.Department of Biochemistry, University of Alabama, Birmingham, Alabama, USA
| | - Roberto Spurio
- Department of Biology, University of Camerino, 62032 Camerino (MC), Italy.Department of Biochemistry, University of Alabama, Birmingham, Alabama, USA
| | - Cynthia L Pon
- Department of Biology, University of Camerino, 62032 Camerino (MC), Italy.Department of Biochemistry, University of Alabama, Birmingham, Alabama, USA
| | - Claudio O Gualerzi
- Department of Biology, University of Camerino, 62032 Camerino (MC), Italy.Department of Biochemistry, University of Alabama, Birmingham, Alabama, USA
| |
Collapse
|
7
|
Giuliodori AM, Brandi A, Gualerzi CO, Pon CL. Preferential translation of cold-shock mRNAs during cold adaptation. RNA (NEW YORK, N.Y.) 2004; 10:265-76. [PMID: 14730025 PMCID: PMC1370538 DOI: 10.1261/rna.5164904] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 11/03/2003] [Indexed: 05/23/2023]
Abstract
Upon temperature downshift below the lower threshold of balanced growth (approximately 20 degrees C), the Escherichia coli translational apparatus undergoes modifications allowing the selective translation of the transcripts of cold shock-induced genes, while bulk protein synthesis is drastically reduced. Here we were able to reproduce this translational bias in E. coli cell-free extracts prepared at various times during cold adaptation which were found to display different capacities to translate different types of mRNAs as a function of temperature. Several causes were found to contribute to the cold-shock translational bias: Cold-shock mRNAs contain cis-elements, making them intrinsically more prone to being translated in the cold, and they are selective targets for trans-acting factors present in increased amounts in the translational apparatus of cold-shocked cells. CspA was found to be among these trans-acting factors. In addition to inducing a higher level of CspA, cold shock was found to cause a strong (two- to threefold) stoichiometric imbalance of the ratio between initiation factors (IF1, IF2, IF3) and ribosomes without altering the stoichiometric ratio between the factors themselves. The most important sources of cold-shock translational bias is IF3, which strongly and selectively favors translation of cold-shock mRNAs in the cold. IF1 and the RNA chaperone CspA, which stimulate translation preferentially in the cold without mRNA selectivity, can also contribute to the translational bias. Finally, in contrast to a previous claim, translation of cold-shock cspA mRNA in the cold was found to be as sensitive as that of a non-cold-shock mRNA to both chloramphenicol and kanamycin inhibition.
Collapse
Affiliation(s)
- Anna Maria Giuliodori
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy
| | | | | | | |
Collapse
|
8
|
Petrelli D, Garofalo C, Lammi M, Spurio R, Pon CL, Gualerzi CO, La Teana A. Mapping the active sites of bacterial translation initiation factor IF3. J Mol Biol 2003; 331:541-56. [PMID: 12899827 DOI: 10.1016/s0022-2836(03)00731-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
IF3C is the C-terminal domain of Escherichia coli translation initiation factor 3 (IF3) and is responsible for all functions of this translation initiation factor but for its ribosomal recycling. To map the number and nature of the active sites of IF3 and to identify the essential Arg residue(s) chemically modified with 2,3-butanedione, the eight arginine residues of IF3C were substituted by Lys, His, Ser and Leu, generating 32 variants that were tested in vitro for all known IF3 activities. The IF3-30S subunit interaction was inhibited strongly by substitutions of Arg99, Arg112, Arg116, Arg147 and Arg168, the positive charges being important at positions 116 and 147. The 70S ribosome dissociation was affected by mutations of Arg112, Arg147 and, to a lesser extent, of Arg99 and Arg116. Pseudo-initiation complex dissociation was impaired by substitution of Arg99 and Arg112 (whose positive charges are important) and, to a lesser extent, of Arg116, Arg129, Arg133 and Arg147, while the dissociation of non-canonical 30S initiation complexes was preserved at wild-type levels in all 32 mutants. Stimulation of mRNA translation was reduced by mutations of Arg116, Arg129 and, to a lesser extent, of Arg99, Arg112 and Arg131 whereas inhibition of non-canonical mRNA translation was affected by substitutions of Arg99, Arg112, Arg168 and, to a lesser extent, Arg116, Arg129 and Arg131. Finally, repositioning the mRNA on the 30S subunit was affected weakly by mutations of Arg133, Arg131, Arg168, Arg147 and Arg129. Overall, the results define two active surfaces in IF3C, and indicate that the different functions of IF3 rely on different molecular mechanisms involving separate active sites.
Collapse
Affiliation(s)
- Dezemona Petrelli
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino, Italy
| | | | | | | | | | | | | |
Collapse
|
9
|
Gualerzi CO, Giuliodori AM, Pon CL. Transcriptional and post-transcriptional control of cold-shock genes. J Mol Biol 2003; 331:527-39. [PMID: 12899826 DOI: 10.1016/s0022-2836(03)00732-0] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mesophile like Escherichia coli responds to abrupt temperature downshifts (e.g. from 37 degrees C to 10 degrees C) with an adaptive response that allows cell survival and eventually resumption of growth under the new unfavorable environmental conditions. During this response, bulk transcription and translation slow or come to an almost complete stop, while a set of about 26 cold-shock genes is preferentially and transiently expressed. At least some of the proteins encoded by these genes are essential for survival in the cold, but none plays an exclusive role in cold adaptation, not even the "major cold-shock protein" CspA and none is induced de novo. The majority of these proteins binds nucleic acids and are involved in fundamental functions (DNA packaging, transcription, RNA degradation, translation, ribosome assembly, etc.). Although cold-induced activation of specific promoters has been implicated in upregulating some cold-shock genes, post-transcriptional mechanisms play a major role in cold adaptation; cold stress-induced changes of the RNA degradosome determine a drastic stabilization of the cold-shock transcripts and cold shock-induced modifications of the translational apparatus determine their preferential translation in the cold. This preferential translation at low temperature is due to cis elements present in the 5' untranslated region of at least some cold-shock mRNAs and to trans-acting factors whose levels are increased substantially by cold stress. Protein CspA and the three translation initiation factors (IF3 in particular), whose stoichiometry relative to the ribosomes is more than doubled during the acclimation period, are among the trans elements found to selectively stimulate cold-shock mRNA translation in the cold.
Collapse
Affiliation(s)
- Claudio O Gualerzi
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC), Italy.
| | | | | |
Collapse
|
10
|
Forster AC, Weissbach H, Blacklow SC. A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid. Anal Biochem 2001; 297:60-70. [PMID: 11567528 DOI: 10.1006/abio.2001.5329] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The study of the early events in translation would be greatly facilitated by reconstitution with easily purified components. Here, Escherichia coli oligopeptide synthesis has been reconstituted using five purified recombinant His-tagged E. coli initiation and elongation factors. Highly purified ribosomes are required to yield products with strong dependencies on the translation factors. Based on HPLC separation of radiolabeled translation products from an mRNA encoding a tetrapeptide, approximately 80% of peptide products are full length, and the remaining 20% are the dipeptide and tripeptide products resulting from pausing or premature termination. Oligopeptide synthesis is enhanced when a commonly used epsilon (enhancer of protein synthesis initiation) sequence is included in the mRNA. The system incorporates a selectable, large, unnatural amino acid and may ultimately form the basis of a pure translation display technology for the directed evolution of peptidomimetic ligands and drug candidates. The recombinant clones can be exploited to prepare initiation factors and initiation complexes for structural studies, to study initiation and elongation in ribosomal peptide synthesis, and to screen for eubacterial-specific drugs.
Collapse
Affiliation(s)
- A C Forster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, Massachusetts 02115, USA.
| | | | | |
Collapse
|
11
|
Petrelli D, LaTeana A, Garofalo C, Spurio R, Pon CL, Gualerzi CO. Translation initiation factor IF3: two domains, five functions, one mechanism? EMBO J 2001; 20:4560-9. [PMID: 11500382 PMCID: PMC125572 DOI: 10.1093/emboj/20.16.4560] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Initiation factor IF3 contains two domains separated by a flexible linker. While the isolated N-domain displayed neither affinity for ribosomes nor a detectable function, the isolated C-domain, added in amounts compensating for its reduced affinity for 30S subunits, performed all activities of intact IF3, namely: (i) dissociation of 70S ribosomes; (ii) shift of 30S-bound mRNA from 'stand-by' to 'P-decoding' site; (iii) dissociation of 30S-poly(U)-NacPhe-tRNA pseudo- initiation complexes; (iv) dissociation of fMet-tRNA from initiation complexes containing mRNA with the non-canonical initiation triplet AUU (AUUmRNA); (v) stimulation of mRNA translation regardless of its start codon and inhibition of AUUmRNA translation at high IF3C/ribosome ratios. These results indicate that while IF3 performs all its functions through a C-domain-30S interaction, the N-domain function is to provide additional binding energy so that its fluctuating interaction with the 30S subunit can modulate the thermodynamic stability of the 30S-IF3 complex and IF3 recycling. The localization of IF3C far away from the decoding site and anticodon stem-loop of P-site-bound tRNA indicates that the IF3 fidelity function does not entail its direct contact with these structures.
Collapse
Affiliation(s)
- Dezemona Petrelli
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, I-62032 Camerino (MC) and Institute of Biochemistry, University of Ancona, I-60131 Ancona, Italy Corresponding author e-mail
| | - Anna LaTeana
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, I-62032 Camerino (MC) and Institute of Biochemistry, University of Ancona, I-60131 Ancona, Italy Corresponding author e-mail
| | - Cristiana Garofalo
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, I-62032 Camerino (MC) and Institute of Biochemistry, University of Ancona, I-60131 Ancona, Italy Corresponding author e-mail
| | - Roberto Spurio
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, I-62032 Camerino (MC) and Institute of Biochemistry, University of Ancona, I-60131 Ancona, Italy Corresponding author e-mail
| | - Cynthia L. Pon
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, I-62032 Camerino (MC) and Institute of Biochemistry, University of Ancona, I-60131 Ancona, Italy Corresponding author e-mail
| | - Claudio O. Gualerzi
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, I-62032 Camerino (MC) and Institute of Biochemistry, University of Ancona, I-60131 Ancona, Italy Corresponding author e-mail
| |
Collapse
|
12
|
Dahlquist KD, Puglisi JD. Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. J Mol Biol 2000; 299:1-15. [PMID: 10860719 DOI: 10.1006/jmbi.2000.3672] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Initiation Factor 1 (IF1) is required for the initiation of translation in Escherichia coli. However, the precise function of IF1 remains unknown. Current evidence suggests that IF1 is an RNA-binding protein that sits in the A site of the decoding region of 16 S rRNA. IF1 binding to 30 S subunits changes the reactivity of nucleotides in the A site to chemical probes. The N1 position of A1408 is enhanced, while the N1 positions of A1492 and A1493 are protected from reactivity with dimethyl sulfate (DMS). The N1-N2 positions of G530 are also protected from reactivity with kethoxal. Quantitative footprinting experiments show that the dissociation constant for IF1 binding to the 30 S subunit is 0.9 microM and that IF1 also alters the reactivity of a subset of Class III sites that are protected by tRNA, 50 S subunits, or aminoglycoside antibiotics. IF1 enhances the reactivity of the N1 position of A1413, A908, and A909 to DMS and the N1-N2 positions of G1487 to kethoxal. To characterize this RNA-protein interaction, several ribosomal mutants in the decoding region RNA were created, and IF1 binding to wild-type and mutant 30 S subunits was monitored by chemical modification and primer extension with allele-specific primers. The mutations C1407U, A1408G, A1492G, or A1493G disrupt IF1 binding to 30 S subunits, whereas the mutations G530A, U1406A, U1406G, G1491U, U1495A, U1495C, or U1495G had little effect on IF1 binding. Disruption of IF1 binding correlates with the deleterious phenotypic effects of certain mutations. IF1 binding to the A site of the 30 S subunit may modulate subunit association and the fidelity of tRNA selection in the P site through conformational changes in the 16 S rRNA.
Collapse
MESH Headings
- Aldehydes/metabolism
- Alleles
- Aminoglycosides
- Anti-Bacterial Agents/metabolism
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites
- Butanones
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Eukaryotic Initiation Factor-1/metabolism
- Models, Biological
- Models, Molecular
- Mutation/genetics
- Nucleic Acid Conformation
- Phenotype
- Prokaryotic Initiation Factor-1
- Protein Binding
- RNA/genetics
- RNA/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Sulfuric Acid Esters/metabolism
- Thermodynamics
Collapse
Affiliation(s)
- K D Dahlquist
- Department of Structural Biology, Stanford University, School of Medicine, CA 94305-5126, USA
| | | |
Collapse
|
13
|
Spurio R, Falconi M, Brandi A, Pon CL, Gualerzi CO. The oligomeric structure of nucleoid protein H-NS is necessary for recognition of intrinsically curved DNA and for DNA bending. EMBO J 1997; 16:1795-805. [PMID: 9130723 PMCID: PMC1169782 DOI: 10.1093/emboj/16.7.1795] [Citation(s) in RCA: 158] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Escherichia coli hns, encoding the abundant nucleoid protein H-NS, was subjected to site-directed mutagenesis either to delete Pro115 or to replace it with alanine. Unlike the wild-type protein, hyperproduction of the mutant proteins did not inhibit macromolecular syntheses, was not toxic to cells and caused a less drastic compaction of the nucleoid. Gel shift and ligase-mediated circularization tests demonstrated that the mutant proteins retained almost normal affinity for non-curved DNA, but lost the wild-type capacity to recognize preferentially curved DNA and to actively bend non-curved DNA, a property of wild-type H-NS demonstrated here for the first time. DNase I foot-printing and in vitro transcription experiments showed that the mutant proteins also failed to recognize the intrinsically bent site of the hns promoter required for H-NS transcription autorepression and to inhibit transcription from the same promoter. The failure of the Pro115 mutant proteins to recognize curved DNA and to bend DNA despite their near normal affinity for non-curved DNA can be attributed to a defect in protein-protein interaction resulting in a reduced capacity to form oligomers observed in vitro and by a new in vivo test based on functional replacement by H-NS of the oligomerization domain (C-domain) of bacteriophage lambda cI repressor.
Collapse
Affiliation(s)
- R Spurio
- Laboratory of Genetics, Department of Biology, University of Camerino, Italy
| | | | | | | | | |
Collapse
|
14
|
[17] Synthesis and expression of synthetic genes: Applications to structure-function studies of receptors. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s1043-9471(05)80047-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
15
|
Spurio R, Paci M, Pawlik RT, La Teana A, DiGiacco BV, Pon CL, Gualerzi CO. Site-directed mutagenesis and NMR spectroscopic approaches to the elucidation of the structure-function relationships in translation initiation factors IF1 and IF3. Biochimie 1991; 73:1001-6. [PMID: 1742345 DOI: 10.1016/0300-9084(91)90141-m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- R Spurio
- Max-Planck-Institut für Molekulare Genetik, Abt Wittmann, Berlin-Dahlem, Germany
| | | | | | | | | | | | | |
Collapse
|
16
|
Grohmann L, Graack HR, Kitakawa M. Molecular cloning of the nuclear gene for mitochondrial ribosomal protein YmL31 from Saccharomyces cerevisiae. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 183:155-60. [PMID: 2666132 DOI: 10.1111/j.1432-1033.1989.tb14907.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The nuclear gene for mitochondrial ribosomal protein YmL31 (MRP-L31) of Saccharomyces cerevisiae was cloned using synthetic oligonucleotide mixtures which correspond to the N-terminal amino acid sequence of the mature YmL31. The gene MRP-L31 codes for a basic protein with a calculated molecular mass of 15.5 kDa and resides on chromosome XI. A comparison of the amino acid sequence deduced from the nucleotide sequence of the MRP-L31 gene and the N-terminal sequence of the isolated protein revealed the existence of a leader peptide sequence of 12 amino acid residues. No significant similarity to known ribosomal protein sequences of other organisms was found.
Collapse
Affiliation(s)
- L Grohmann
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin, Federal Republic of Germany
| | | | | |
Collapse
|
17
|
Canonaco MA, Gualerzi CO, Pon CL. Alternative occupancy of a dual ribosomal binding site by mRNA affected by translation initiation factors. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 182:501-6. [PMID: 2666129 DOI: 10.1111/j.1432-1033.1989.tb14856.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The interaction between Escherichia coli 30S ribosomal subunits and mRNAs, and the effect of the initiation factors on this process, have been studied using MS2 RNA, polyribonucleotides and model mRNAs encoded by synthetic genes. The interactions were analyzed by gel filtration, by sucrose gradient centrifugation and by competition for ribosome binding between the various mRNAs and a Shine-Dalgarno deoxyoctanucleotide. It was found that the initiation factors do not significantly affect the Shine-Dalgarno interaction nor the apparent Ka values of the 30S-subunit-mRNA binary complexes, but influence the positioning of the mRNAs on the 30S subunit with respect to the Shine-Dalgarno octanucleotide. The results suggest that, in the absence of initiation factors, the mRNA occupies a ribosomal "stand-by" site which is close to or includes the region where the Shine-Dalgarno interaction takes place; in the presence of the factors, the mRNA is shifted away from the stand-by site, towards another ribosomal site with similar affinity for the mRNA. This shift does not require the presence of fMet-tRNA and, depending upon the type of mRNA, is mediated by IF-2 and/or IF-3.
Collapse
Affiliation(s)
- M A Canonaco
- Max-Planck-Institut für Molekulare Genetik, Berlin
| | | | | |
Collapse
|
18
|
Calogero RA, Pon CL, Canonaco MA, Gualerzi CO. Selection of the mRNA translation initiation region by Escherichia coli ribosomes. Proc Natl Acad Sci U S A 1988; 85:6427-31. [PMID: 3045816 PMCID: PMC281985 DOI: 10.1073/pnas.85.17.6427] [Citation(s) in RCA: 133] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Two genes specifying model mRNAs of minimal size and coding capacity, with or without the Shine-Dalgarno (SD) sequence, were assembled, cloned, and transcribed in high yields. These mRNAs, as well as synthetic polynucleotides, phage MS2 RNA, and a deoxyoctanucleotide complementary to the 3' end of 16S rRNA were used to study the mechanism of translation initiation in vitro. Escherichia coli 30S ribosomal subunits interact with all these nucleic acids, albeit with different affinities; the affinity for the mRNA with the SD sequence (Ka approximately 2 x 10(7) M-1) is more than an order of magnitude higher than that for the mRNA lacking this sequence. The initiation factors are equally required, regardless of the presence of the SD sequence, for 30S and 70S initiation complex formation and for mRNA translation, but the initiation factors do not affect the SD interaction or the binding of the mRNAs to the ribosomes. The SD interaction is also mechanistically irrelevant for 30S initiation complex formation and is not essential for translation in vitro or for the selection of the mRNA reading frame. It is suggested that the function of the SD interaction is to ensure a high concentration of the initiation triplet near the ribosomal peptidyl-tRNA binding site, whereas the selection of the translational start is achieved kinetically, under the influence of the initiation factors, during decoding of the initiator tRNA.
Collapse
Affiliation(s)
- R A Calogero
- Max-Planck-Institut für Molekulare Genetik, Abt. Wittmann, Berlin, Germany
| | | | | | | |
Collapse
|
19
|
Paci M, Pon CL, Gualerzi CO. Structure-function relationship in Escherichia coli translational initiation factors. Characterization of IF1 by high-resolution 1H-NMR spectroscopy. FEBS Lett 1988; 236:303-8. [PMID: 3044826 DOI: 10.1016/0014-5793(88)80042-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Escherichia coli translational initiation factor IF1 was studied by 1H-NMR spectroscopy at 400 MHz. IF1 displays a very well resolved spectrum in both aromatic and aliphatic regions. Other spectral characteristics include relatively narrow resonance lines and lack of relevant cross-relaxation phenomena. The resonances of the aromatic residues, in particular of the two His and two Tyr, were assigned by selective chemical modifications and spectroscopic techniques to individual residues in the protein sequence. The relative mobility of various residues of IF1 has been evaluated on the basis of the spin-lattice relaxation times which are rather short and homogeneous. Overall the factor appears to have a complex secondary and tertiary structure and to be a flexible protein whose residues have a high degree of internal mobility.
Collapse
Affiliation(s)
- M Paci
- Department of Chemical Science and Technology, University of Rome, Italy
| | | | | |
Collapse
|
20
|
|
21
|
Pon CL, Calogero RA, Gualerzi CO. Identification, cloning, nucleotide sequence and chromosomal map location of hns, the structural gene for Escherichia coli DNA-binding protein H-NS. MOLECULAR & GENERAL GENETICS : MGG 1988; 212:199-202. [PMID: 2841565 DOI: 10.1007/bf00334684] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Beginning with a synthetic oligonucleotide probe derived from its amino acid sequence, we have identified, cloned and sequenced the hns gene encoding H-NS, an abundant Escherichia coli 15 kDa DNA-binding protein with a possible histone-like function. The amino acid sequence of the protein deduced from the nucleotide sequence is in full agreement with that determined for H-NS. By comparison of the restriction map of the cloned gene and of its neighboring regions with the physical map of E. coli K12 as well as by hybridization of the hns gene with restriction fragments derived from the total chromosome, we have located the hns gene oriented counterclockwise at 6.1 min on the E. coli chromosome, just before an IS30 insertion element.
Collapse
Affiliation(s)
- C L Pon
- Max-Planck-Institut für Molekulare Genetik, Abt. Wittmann, Berlin
| | | | | |
Collapse
|