1
|
Baur ST, Poehlein A, Renz NJ, Hollitzer SK, Montoya Solano JD, Schiel-Bengelsdorf B, Daniel R, Dürre P. Modulation of sol mRNA expression by the long non-coding RNA Assolrna in Clostridium saccharoperbutylacetonicum affects solvent formation. Front Genet 2022; 13:966643. [PMID: 36035128 PMCID: PMC9402939 DOI: 10.3389/fgene.2022.966643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022] Open
Abstract
Solvents such as butanol are important platform chemicals and are often produced from petrochemical sources. Production of butanol and other compounds from renewable and sustainable resources can be achieved by solventogenic bacteria, such as the hyper-butanol producer Clostridium saccharoperbutylacetonicum. Its sol operon consists of the genes encoding butyraldehyde dehydrogenase, CoA transferase, and acetoacetate decarboxylase (bld, ctfA, ctfB, adc) and the gene products are involved in butanol and acetone formation. It is important to understand its regulation to further optimize the solvent production. In this study, a new long non-coding antisense transcript complementary to the complete sol operon, now called Assolrna, was identified by transcriptomic analysis and the regulatory mechanism of Assolrna was investigated. For this purpose, the promoter-exchange strain C. saccharoperbutylacetonicum ΔPasr::Pasr** was constructed. Additionally, Assolrna was expressed plasmid-based under control of the native Pasr promoter and the lactose-inducible PbgaL promoter in both the wild type and the promoter-exchange strain. Solvent formation was strongly decreased for all strains based on C. saccharoperbutylacetonicum ΔPasr::Pasr** and growth could not be restored by plasmid-based complementation of the exchanged promoter. Interestingly, very little sol mRNA expression was detected in the strain C. saccharoperbutylacetonicum ΔPasr::Pasr** lacking Assolrna expression. Butanol titers were further increased for the overexpression strain C. saccharoperbutylacetonicum [pMTL83151_asr_PbgaL] compared to the wild type. These results suggest that Assolrna has a positive effect on sol operon expression. Therefore, a possible stabilization mechanism of the sol mRNA by Assolrna under physiological concentrations is proposed.
Collapse
Affiliation(s)
- Saskia Tabea Baur
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
- *Correspondence: Saskia Tabea Baur,
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Niklas Jan Renz
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| | | | | | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Ulm, Germany
| |
Collapse
|
2
|
Transcriptional Organization of the Salmonella Typhimurium Phage P22 pid ORFan Locus. Int J Mol Sci 2022; 23:ijms23031253. [PMID: 35163175 PMCID: PMC8835761 DOI: 10.3390/ijms23031253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Many phage genes lack sequence similarity to any other open reading frame (ORF) in current databases. These enigmatic ORFan genes can have a tremendous impact on phage propagation and host interactions but often remain experimentally unexplored. We previously revealed a novel interaction between phage P22 and its Salmonella Typhimurium host, instigated by the ORFan gene pid (for phage P22 encoded instigator of dgo expression) and resulting in derepression of the host dgoRKAT operon. The pid gene is highly expressed in phage carrier cells that harbor a polarly located P22 episome that segregates asymmetrically among daughter cells. Here, we discovered that the pid locus is fitted with a weak promoter, has an exceptionally long 5′ untranslated region that is instructive for a secondary pid mRNA species, and has a 3′ Rho-independent termination loop that is responsible for stability of the pid transcript.
Collapse
|
3
|
Bhaskar Y, Su X, Xu C, Xu J. Predicting Selective RNA Processing and Stabilization Operons in Clostridium spp. Front Microbiol 2021; 12:673349. [PMID: 34177856 PMCID: PMC8219983 DOI: 10.3389/fmicb.2021.673349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/28/2021] [Indexed: 11/29/2022] Open
Abstract
In selective RNA processing and stabilization (SRPS) operons, stem–loops (SLs) located at the 3′-UTR region of selected genes can control the stability of the corresponding transcripts and determine the stoichiometry of the operon. Here, for such operons, we developed a computational approach named SLOFE (stem–loop free energy) that identifies the SRPS operons and predicts their transcript- and protein-level stoichiometry at the whole-genome scale using only the genome sequence via the minimum free energy (ΔG) of specific SLs in the intergenic regions within operons. As validated by the experimental approach of differential RNA-Seq, SLOFE identifies genome-wide SRPS operons in Clostridium cellulolyticum with 80% accuracy and reveals that the SRPS mechanism contributes to diverse cellular activities. Moreover, in the identified SRPS operons, SLOFE predicts the transcript- and protein-level stoichiometry, including those encoding cellulosome complexes, ATP synthases, ABC transporter family proteins, and ribosomal proteins. Its accuracy exceeds those of existing in silico approaches in C. cellulolyticum, Clostridium acetobutylicum, Clostridium thermocellum, and Bacillus subtilis. The ability to identify genome-wide SRPS operons and predict their stoichiometry via DNA sequence in silico should facilitate studying the function and evolution of SRPS operons in bacteria.
Collapse
Affiliation(s)
- Yogendra Bhaskar
- Single-Cell Center and CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoquan Su
- Single-Cell Center and CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chenggang Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Jian Xu
- Single-Cell Center and CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Gale GAR, Wang B, McCormick AJ. Evaluation and Comparison of the Efficiency of Transcription Terminators in Different Cyanobacterial Species. Front Microbiol 2021; 11:624011. [PMID: 33519785 PMCID: PMC7843447 DOI: 10.3389/fmicb.2020.624011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria utilize sunlight to convert carbon dioxide into a wide variety of secondary metabolites and show great potential for green biotechnology applications. Although cyanobacterial synthetic biology is less mature than for other heterotrophic model organisms, there are now a range of molecular tools available to modulate and control gene expression. One area of gene regulation that still lags behind other model organisms is the modulation of gene transcription, particularly transcription termination. A vast number of intrinsic transcription terminators are now available in heterotrophs, but only a small number have been investigated in cyanobacteria. As artificial gene expression systems become larger and more complex, with short stretches of DNA harboring strong promoters and multiple gene expression cassettes, the need to stop transcription efficiently and insulate downstream regions from unwanted interference is becoming more important. In this study, we adapted a dual reporter tool for use with the CyanoGate MoClo Assembly system that can quantify and compare the efficiency of terminator sequences within and between different species. We characterized 34 intrinsic terminators in Escherichia coli, Synechocystis sp. PCC 6803, and Synechococcus elongatus UTEX 2973 and observed significant differences in termination efficiencies. However, we also identified five terminators with termination efficiencies of >96% in all three species, indicating that some terminators can behave consistently in both heterotrophic species and cyanobacteria.
Collapse
Affiliation(s)
- Grant A. R. Gale
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alistair J. McCormick
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
5
|
Akoopie A, Müller UF. Lower temperature optimum of a smaller, fragmented triphosphorylation ribozyme. Phys Chem Chem Phys 2018; 18:20118-25. [PMID: 27053323 DOI: 10.1039/c6cp00672h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA world hypothesis describes a stage in the early evolution of life in which catalytic RNAs mediated the replication of RNA world organisms. One challenge to this hypothesis is that most existing ribozymes are much longer than what may be expected to originate from prebiotically plausible methods, or from the polymerization by currently existing polymerase ribozymes. We previously developed a 96-nucleotide long ribozyme, which generates a chemically activated 5'-phosphate (a 5'-triphosphate) from a prebiotically plausible molecule, trimetaphosphate, and an RNA 5'-hydroxyl group. Analogous ribozymes may have been important in the RNA world to access an energy source for the earliest life forms. Here we reduce the length of this ribozyme by fragmenting the ribozyme into multiple RNA strands, and by successively removing its longest double strand. The resulting ribozyme is composed of RNA fragments with none longer than 34 nucleotides. The temperature optimum was ∼20 °C, compared to ∼40 °C for the parent ribozyme. This shift in temperature dependence may be a more general phenomenon for fragmented ribozymes, and may have helped RNA world organisms to emerge at low temperature.
Collapse
Affiliation(s)
- Arvin Akoopie
- Department of Chemistry & Biochemistry, University of California, San Diego, USA.
| | - Ulrich F Müller
- Department of Chemistry & Biochemistry, University of California, San Diego, USA.
| |
Collapse
|
6
|
Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli. Mol Cell 2014; 55:199-213. [PMID: 24910100 PMCID: PMC4104026 DOI: 10.1016/j.molcel.2014.05.006] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/21/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022]
Abstract
In bacteria, Hfq is a core RNA chaperone that catalyzes the interaction of mRNAs with regulatory small RNAs (sRNAs). To determine in vivo RNA sequence requirements for Hfq interactions, and to study riboregulation in a bacterial pathogen, Hfq was UV crosslinked to RNAs in enterohemorrhagic Escherichia coli (EHEC). Hfq bound repeated trinucleotide motifs of A-R-N (A-A/G-any nucleotide) often associated with the Shine-Dalgarno translation initiation sequence in mRNAs. These motifs overlapped or were adjacent to the mRNA sequences bound by sRNAs. In consequence, sRNA-mRNA duplex formation will displace Hfq, promoting recycling. Fifty-five sRNAs were identified within bacteriophage-derived regions of the EHEC genome, including some of the most abundant Hfq-interacting sRNAs. One of these (AgvB) antagonized the function of the core genome regulatory sRNA, GcvB, by mimicking its mRNA substrate sequence. This bacteriophage-encoded “anti-sRNA” provided EHEC with a growth advantage specifically in bovine rectal mucus recovered from its primary colonization site in cattle. Transcriptome-wide map of Hfq binding reveals targeting rules Many sRNAs identified in pathogenicity islands Pathogenicity-associated anti-sRNAs antagonize sRNAs encoded in core genome Anti-sRNAs alter cell metabolism as part of niche colonization
Collapse
|
7
|
Martínez-Trujillo M, Sánchez-Trujillo A, Ceja V, Ávila-Moreno F, Bermúdez-Cruz RM, Court D, Montañez C. Sequences required for transcription termination at the intrinsic lambdatI terminator. Can J Microbiol 2010; 56:168-77. [PMID: 20237579 PMCID: PMC7366390 DOI: 10.1139/w09-123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The lambdatI terminator is located approximately 280 bp beyond the lambdaint gene, and it has a typical structure of an intrinsic terminator. To identify sequences required for lambdatI transcription termination a set of deletion mutants were generated, either from the 5' or the 3' end onto the lambdatI region. The termination efficiency was determined by measuring galactokinase (galK) levels by Northern blot assays and by in vitro transcription termination. The importance of the uridines and the stability of the stem structure in the termination were demonstrated. The nontranscribed DNA beyond the 3' end also affects termination. Additionally, sequences upstream have a small effect on transcription termination. The in vivo RNA termination sites at lambdatI were determined by S1 mapping and were located at 8 different positions. Processing of transcripts from the 3' end confirmed the importance of the hairpin stem in protection against exonuclease.
Collapse
Affiliation(s)
- Miguel Martínez-Trujillo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Apartado postal 14-740, C.P. 07360 México, D.F., México
| | - Alejandra Sánchez-Trujillo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Apartado postal 14-740, C.P. 07360 México, D.F., México
| | - Víctor Ceja
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Apartado postal 14-740, C.P. 07360 México, D.F., México
| | - Federico Ávila-Moreno
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Apartado postal 14-740, C.P. 07360 México, D.F., México
| | - Rosa María Bermúdez-Cruz
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Apartado postal 14-740, C.P. 07360 México, D.F., México
| | - Donald Court
- Gene Regulation and Chromosome Biology, National Cancer Institute-Frederick, Frederick, MD 21702-1201, USA
| | - Cecilia Montañez
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N, Apartado postal 14-740, C.P. 07360 México, D.F., México
| |
Collapse
|
8
|
Figueroa-Bossi N, Valentini M, Malleret L, Bossi L. Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. Genes Dev 2009; 23:2004-15. [PMID: 19638370 PMCID: PMC2751969 DOI: 10.1101/gad.541609] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 07/09/2009] [Indexed: 11/25/2022]
Abstract
A relevant, yet little recognized feature of antisense regulation is the possibility of switching roles between regulatory and regulated RNAs. Here we show that induction of a Salmonella gene relies on the conversion of a small RNA from effector to regulatory target. The chiP gene (formerly ybfM), identified and characterized in the present study, encodes a conserved enterobacterial chitoporin required for uptake of chitin-derived oligosaccharides. In the absence of inducer, chiP is kept silent by the action of a constitutively made small RNA, ChiX (formerly SroB, RybC), which pairs with a sequence at the 5' end of chiP mRNA. Silencing is relieved in the presence of chitooligosaccharides due to the accumulation of an RNA that pairs with ChiX and promotes its degradation. Anti-ChiX RNA originates from an intercistronic region of the chb operon, which comprises genes for chitooligosaccharide metabolism and whose transcription is activated in the presence of these sugars. We present evidence suggesting that the chb RNA destabilizes ChiX sRNA by invading the stem of its transcription terminator hairpin. Overall, our findings blur the distinction between effector and target in sRNA regulation, raising the possibility that some of the currently defined targets could actually be inhibitors of sRNA function.
Collapse
Affiliation(s)
- Nara Figueroa-Bossi
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette 91198, France
| | - Martina Valentini
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette 91198, France
| | - Laurette Malleret
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette 91198, France
| | - Lionello Bossi
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette 91198, France
| |
Collapse
|
9
|
Petrillo M, Silvestro G, Di Nocera PP, Boccia A, Paolella G. Stem-loop structures in prokaryotic genomes. BMC Genomics 2006; 7:170. [PMID: 16820051 PMCID: PMC1590033 DOI: 10.1186/1471-2164-7-170] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 07/04/2006] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Prediction of secondary structures in the expressed sequences of bacterial genomes allows to investigate spontaneous folding of the corresponding RNA. This is particularly relevant in untranslated mRNA regions, where base pairing is less affected by interactions with the translation machinery. Relatively large stem-loops significantly contribute to the formation of more complex secondary structures, often important for the activity of sequence elements controlling gene expression. RESULTS Systematic analysis of the distribution of stem-loop structures (SLSs) in 40 wholly-sequenced bacterial genomes is presented. SLSs were searched as stems measuring at least 12 bp, bordering loops 5 to 100 nt in length. G-U pairing in the stems was allowed. SLSs found in natural genomes are constantly more numerous and stable than those expected to randomly form in sequences of comparable size and composition. The large majority of SLSs fall within protein-coding regions but enrichment of specific, non random, SLS sub-populations of higher stability was observed within the intergenic regions of the chromosomes of several species. In low-GC firmicutes, most higher stability intergenic SLSs resemble canonical rho-independent transcriptional terminators, but very frequently feature at the 5'-end an additional A-rich stretch complementary to the 3' uridines. In all species, a clearly biased SLS distribution was observed within the intergenic space, with most concentrating at the 3'-end side of flanking CDSs. Some intergenic SLS regions are members of novel repeated sequence families. CONCLUSION In depth analysis of SLS features and distribution in 40 different bacterial genomes showed the presence of non random populations of such structures in all species. Many of these structures are plausibly transcribed, and might be involved in the control of transcription termination, or might serve as RNA elements which can enhance either the stability or the turnover of cotranscribed mRNAs. Three previously undescribed families of repeated sequences were found in Yersiniae, Bordetellae and Enterococci.
Collapse
Affiliation(s)
- Mauro Petrillo
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
| | - Giustina Silvestro
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
| | - Pier Paolo Di Nocera
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate scarl Via Comunale Margherita 482, 80145 Napoli, Italy
- Dipartimento SAVA Università del Molise Via De Sanctis, 86100 Campobasso, Italy
- Dipartimento di Biochimica e Biotecnologie Mediche, Università Federico II Via S. Pansini 5, 80131 Napoli, Italy
| |
Collapse
|
10
|
Bermúdez-Cruz RM, Chamberlin MJ, Montañez C. Nus A is involved in transcriptional termination on lambda tI. Biochimie 1999; 81:757-64. [PMID: 10492023 DOI: 10.1016/s0300-9084(99)80134-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The transcriptional terminator tI generates the 3'end of the integrase (int) gene transcript that is read from the lambda PI promoter in lambda phage. We have studied the factors that affect transcription termination in vitro and in vivo at the lambda tI terminator. In vitro transcriptional studies showed that tI is about 80% efficient in the presence of purified NusA protein, whereas it is only about 50% efficient in its absence. In vivo studies, where the readthrough transcript of lambda tI was measured by quantitative dot blot analysis, gave about 80% efficiency in wild-type strains, but only 60% in the nusA1 mutant strain at non-permissive temperatures. These results support the idea that termination at lambda tI in vivo involves interaction with the NusA factor.
Collapse
Affiliation(s)
- R M Bermúdez-Cruz
- Departmento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del I.P.N., Mexico City, D.F.C.P., Mexico
| | | | | |
Collapse
|
11
|
García-Mena J, Das A, Sánchez-Trujillo A, Portier C, Montañez C. A novel mutation in the KH domain of polynucleotide phosphorylase affects autoregulation and mRNA decay in Escherichia coli. Mol Microbiol 1999; 33:235-48. [PMID: 10411741 DOI: 10.1046/j.1365-2958.1999.01451.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Polynucleotide phosphorylase (PNPase) is a key 3'-5' exonuclease for mRNA decay in bacteria. Here, we report the isolation of a novel mutant of Escherichia coli PNPase that affects autogenous control and mRNA decay. We show that the inactivation of PNPase by a transposon insertion increases the half-life of galactokinase mRNA encoded by a plasmid. When the bacteriophage lambda int gene retroregulator (sib/tI ) is placed between pgal and galK, it severely diminishes galactokinase expression because of transcription termination. The expression of galK from this construct is increased by a single base mutation, sib1, which causes a partial readthrough of transcription at tI. We have used this plasmid system with sib1 to select E. coli mutants that depress galK expression. Genetic and molecular analysis of one such mutant revealed that it contains a mutation in the pnp gene, which encodes the PNPase catalytic subunit alpha. The mutation responsible (pnp-71 ) has substituted a highly conserved glycine residue in the KH domain of PNPase with aspartate. We show that this G-570D substitution causes a higher accumulation of the alpha-subunit as a result of defective autoregulation, thereby increasing the PNPase activity in the cell. The purified mutant alpha-subunit shows the same electrophoretic mobility in denaturing gels as the wild-type subunit, as expected. However, the mutant protein present in crude extracts displays an altered electrophoretic mobility in non-denaturing gels that is indicative of a novel enzyme complex. We present a model for how the pnp-71 mutation might affect autoregulation and mRNA decay based on the postulated role of the KH domain in RNA-protein and protein-protein interactions.
Collapse
Affiliation(s)
- J García-Mena
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Apdo Postal 14-740, México DF 07000, México
| | | | | | | | | |
Collapse
|