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Stemwedel K, Haase N, Christ S, Bogdanova N, Rudorf S. Synonymous rpsH variants: the common denominator in Escherichia coli adapting to ionizing radiation. NAR Genom Bioinform 2024; 6:lqae110. [PMID: 39184377 PMCID: PMC11344242 DOI: 10.1093/nargab/lqae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/18/2024] [Accepted: 08/08/2024] [Indexed: 08/27/2024] Open
Abstract
Ionizing radiation (IR) in high doses is generally lethal to most organisms. Investigating mechanisms of radiation resistance is crucial for gaining insights into the underlying cellular responses and understanding the damaging effects of IR. In this study, we conducted a comprehensive analysis of sequencing data from an evolutionary experiment aimed at understanding the genetic adaptations to ionizing radiation in Escherichia coli. By including previously neglected synonymous mutations, we identified the rpsH c.294T > G variant, which emerged in all 17 examined isolates across four subpopulations. The identified variant is a synonymous mutation affecting the 30S ribosomal protein S8, and consistently exhibited high detection and low allele frequencies in all subpopulations. This variant, along with two additional rpsH variants, potentially influences translational control of the ribosomal spc operon. The early emergence and stability of these variants suggest their role in adapting to environmental stress, possibly contributing to radiation resistance. Our findings shed light on the dynamics of ribosomal variants during the evolutionary process and their potential role in stress adaptation, providing valuable implications for understanding clinical radiation sensitivity and improving radiotherapy.
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Affiliation(s)
- Katharina Stemwedel
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
| | - Nadin Haase
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
| | - Simon Christ
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
| | | | - Sophia Rudorf
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
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2
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Aseev LV, Koledinskaya LS, Boni IV. Extraribosomal Functions of Bacterial Ribosomal Proteins-An Update, 2023. Int J Mol Sci 2024; 25:2957. [PMID: 38474204 DOI: 10.3390/ijms25052957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein-protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria.
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Affiliation(s)
- Leonid V Aseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
| | | | - Irina V Boni
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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3
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Pavan M, Bassani D, Sturlese M, Moro S. Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations. NAR Genom Bioinform 2022; 4:lqac088. [PMID: 36458023 PMCID: PMC9706429 DOI: 10.1093/nargab/lqac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/20/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
Ribonucleic acid (RNA) plays a key regulatory role within the cell, cooperating with proteins to control the genome expression and several biological processes. Due to its characteristic structural features, this polymer can mold itself into different three-dimensional structures able to recognize target biomolecules with high affinity and specificity, thereby attracting the interest of drug developers and medicinal chemists. One successful example of the exploitation of RNA's structural and functional peculiarities is represented by aptamers, a class of therapeutic and diagnostic tools that can recognize and tightly bind several pharmaceutically relevant targets, ranging from small molecules to proteins, making use of the available structural and conformational freedom to maximize the complementarity with their interacting counterparts. In this scientific work, we present the first application of Supervised Molecular Dynamics (SuMD), an enhanced sampling Molecular Dynamics-based method for the study of receptor-ligand association processes in the nanoseconds timescale, to the study of recognition pathways between RNA aptamers and proteins, elucidating the main advantages and limitations of the technique while discussing its possible role in the rational design of RNA-based therapeutics.
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Affiliation(s)
- Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- To whom correspondence should be addressed. Tel: +39 0498275704; Fax: +39 0498275366;
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4
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Nikulin AD. Characteristic Features of Protein Interaction with Single- and Double-Stranded RNA. BIOCHEMISTRY (MOSCOW) 2021; 86:1025-1040. [PMID: 34488578 DOI: 10.1134/s0006297921080125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses differences between the specific protein interactions with single- and double-stranded RNA molecules using the data on the structure of RNA-protein complexes. Proteins interacting with the single-stranded RNAs form contacts with RNA bases, which ensures recognition of specific nucleotide sequences. Formation of such contacts with the double-stranded RNAs is hindered, so that the proteins recognize unique conformations of the RNA spatial structure and interact mainly with the RNA sugar-phosphate backbone.
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Affiliation(s)
- Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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5
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Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing. mBio 2021; 12:e0104921. [PMID: 34126767 PMCID: PMC8262987 DOI: 10.1128/mbio.01049-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium abscessus is an emerging opportunistic human pathogen that naturally resists most major classes of antibiotics, making infections difficult to treat. Thus far, little is known about M. abscessus physiology, pathogenesis, and drug resistance. Genome-wide analyses have comprehensively catalogued genes with essential functions in Mycobacterium tuberculosis and Mycobacterium avium subsp. hominissuis (here, M. avium) but not in M. abscessus. By optimizing transduction conditions, we achieved full saturation of TA insertion sites with Himar1 transposon mutagenesis in the M. abscessus ATCC 19977T genome, as confirmed by deep sequencing prior to essentiality analyses of annotated genes and other genomic features. The overall densities of inserted TA sites (85.7%), unoccupied TA sites (14.3%), and nonpermissive TA sites (8.1%) were similar to results in M. tuberculosis and M. avium. Of the 4,920 annotated genes, 326 were identified as essential, 269 (83%) of which have mutual homology with essential M. tuberculosis genes, while 39 (12%) are homologous to genes that are not essential in M. tuberculosis and M. avium, and 11 (3.4%) only have homologs in M. avium. Interestingly, 7 (2.1%) essential M. abscessus genes have no homologs in either M. tuberculosis or M. avium, two of which were found in phage-like elements. Most essential genes are involved in DNA replication, RNA transcription and translation, and posttranslational events to synthesize important macromolecules. Some essential genes may be involved in M. abscessus pathogenesis and antibiotics response, including certain essential tRNAs and new short open reading frames. Our findings will help to pave the way for better understanding of M. abscessus and benefit development of novel bactericidal drugs against M. abscessus. IMPORTANCE Limited knowledge regarding Mycobacterium abscessus pathogenesis and intrinsic resistance to most classes of antibiotics is a major obstacle to developing more effective strategies to prevent and mitigate disease. Using optimized procedures for Himar1 transposon mutagenesis and deep sequencing, we performed a comprehensive analysis to identify M. abscessus genetic elements essential for in vitro growth and compare them to similar data sets for M. tuberculosis and M. avium subsp. hominissuis. Most essential M. abscessus genes have mutual homology with essential M. tuberculosis genes, providing a foundation for leveraging available knowledge from M. tuberculosis to develop more effective drugs and other interventions against M. abscessus. A small number of essential genes unique to M. abscessus deserve further attention to gain insights into what makes M. abscessus different from other mycobacteria. The essential genes and other genomic features such as short open reading frames and noncoding RNA identified here will provide useful information for future study of M. abscessus pathogenicity and new drug development.
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Zakrevsky P, Calkins E, Kao YL, Singh G, Keleshian VL, Baudrey S, Jaeger L. In vitro selected GUAA tetraloop-binding receptors with structural plasticity and evolvability towards natural RNA structural modules. Nucleic Acids Res 2021; 49:2289-2305. [PMID: 33524109 PMCID: PMC7913685 DOI: 10.1093/nar/gkab021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/05/2021] [Accepted: 01/26/2021] [Indexed: 11/24/2022] Open
Abstract
GNRA tetraloop-binding receptor interactions are key components in the macromolecular assembly of a variety of functional RNAs. In nature, there is an apparent bias for GAAA/11nt receptor and GYRA/helix interactions, with the former interaction being thermodynamically more stable than the latter. While past in vitro selections allowed isolation of novel GGAA and GUGA receptors, we report herein an in vitro selection that revealed several novel classes of specific GUAA receptors with binding affinities comparable to those from natural GAAA/11nt interactions. These GUAA receptors have structural homology with double-locked bulge RNA modules naturally occurring in ribosomal RNAs. They display mutational robustness that enables exploration of the sequence/phenotypic space associated to GNRA/receptor interactions through epistasis. Their thermodynamic self-assembly fitness landscape is characterized by a rugged neutral network with possible evolutionary trajectories toward natural GNRA/receptor interactions. High throughput sequencing analysis revealed synergetic mutations located away from the tertiary interactions that positively contribute to assembly fitness. Our study suggests that the repertoire of GNRA/receptor interactions is much larger than initially thought from the analysis of natural stable RNA molecules and also provides clues for their evolution towards natural GNRA/receptors.
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Affiliation(s)
- Paul Zakrevsky
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Erin Calkins
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Yi-Ling Kao
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Gurkeerat Singh
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Vasken L Keleshian
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Stephanie Baudrey
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
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7
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Mikhaylina AO, Nikonova EY, Kostareva OS, Tishchenko SV. Regulation of Ribosomal Protein Synthesis in Prokaryotes. Mol Biol 2021. [DOI: 10.1134/s0026893321010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Abstract
Production and expression of RNA requires the action of multiple RNA-binding proteins (RBPs). New RBPs are most often created by novel combinations of dedicated RNA-binding modules. However, recruiting existing genes to create new RBPs is also an important evolutionary strategy. In this report, we analyzed the eight-member uL18 ribosomal protein family in Arabidopsis uL18 proteins share a short structurally conserved domain that binds the 5S ribosomal RNA (rRNA) and allows its incorporation into ribosomes. Our results indicate that Arabidopsis uL18-Like proteins are targeted to either mitochondria or chloroplasts. While two members of the family are found in organelle ribosomes, we show here that two uL18-type proteins function as factors necessary for the splicing of certain mitochondrial and plastid group II introns. These two proteins do not cosediment with mitochondrial or plastid ribosomes but instead associate with the introns whose splicing they promote. Our study thus reveals that the RNA-binding capacity of uL18 ribosomal proteins has been repurposed to create factors that facilitate the splicing of organellar introns.
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Discovery of 20 novel ribosomal leader candidates in bacteria and archaea. BMC Microbiol 2020; 20:130. [PMID: 32448158 PMCID: PMC7247131 DOI: 10.1186/s12866-020-01823-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNAs perform many functions in addition to supplying coding templates, such as binding proteins. RNA-protein interactions are important in multiple processes in all domains of life, and the discovery of additional protein-binding RNAs expands the scope for studying such interactions. To find such RNAs, we exploited a form of ribosomal regulation. Ribosome biosynthesis must be tightly regulated to ensure that concentrations of rRNAs and ribosomal proteins (r-proteins) match. One regulatory mechanism is a ribosomal leader (r-leader), which is a domain in the 5' UTR of an mRNA whose genes encode r-proteins. When the concentration of one of these r-proteins is high, the protein binds the r-leader in its own mRNA, reducing gene expression and thus protein concentrations. To date, 35 types of r-leaders have been validated or predicted. RESULTS By analyzing additional conserved RNA structures on a multi-genome scale, we identified 20 novel r-leader structures. Surprisingly, these included new r-leaders in the highly studied organisms Escherichia coli and Bacillus subtilis. Our results reveal several cases where multiple unrelated RNA structures likely bind the same r-protein ligand, and uncover previously unknown r-protein ligands. Each r-leader consistently occurs upstream of r-protein genes, suggesting a regulatory function. That the predicted r-leaders function as RNAs is supported by evolutionary correlations in the nucleotide sequences that are characteristic of a conserved RNA secondary structure. The r-leader predictions are also consistent with the locations of experimentally determined transcription start sites. CONCLUSIONS This work increases the number of known or predicted r-leader structures by more than 50%, providing additional opportunities to study structural and evolutionary aspects of RNA-protein interactions. These results provide a starting point for detailed experimental studies.
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10
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Knöppel A, Andersson DI, Näsvall J. Synonymous Mutations in rpsT Lead to Ribosomal Assembly Defects That Can Be Compensated by Mutations in fis and rpoA. Front Microbiol 2020; 11:340. [PMID: 32210939 PMCID: PMC7069363 DOI: 10.3389/fmicb.2020.00340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/17/2020] [Indexed: 11/21/2022] Open
Abstract
We previously described how four deleterious synonymous mutations in the Salmonella enterica rpsT gene (encoding ribosomal protein S20) result in low S20 levels that can be compensated by mutations that restore [S20]. Here, we have further studied the cause for the deleterious effects of S20 deficiency and found that the S20 mutants were also deficient in four other 30S proteins (S1, S2, S12, and S21), which is likely due to an assembly defect of the S20 deficient 30S subunits. We examined the compensatory effect by six additional mutations affecting the global regulator Fis and the C-terminal domain of the α subunit of RNA polymerase (encoded by rpoA). The fis and rpoA mutations restored the S20 levels, concomitantly restoring the assembly defect and the levels of S1, S2, S12, and S21. These results illustrate the complexity of compensatory evolution and how the negative effects of deleterious mutations can be suppressed by a multitude of mechanisms. Additionally, we found that the mutations in fis and rpoA caused reduced expression of other ribosomal components. Notably, some of the fis mutations and the rpoA mutation corrected the fitness of the rpsT mutants to wild-type levels, although expression of other ribosomal components was reduced compared to wild-type. This finding raises new questions regarding the relation between translation capacity and growth rate.
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11
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Chiaruttini C, Guillier M. On the role of mRNA secondary structure in bacterial translation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1579. [PMID: 31760691 DOI: 10.1002/wrna.1579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 11/07/2022]
Abstract
Messenger RNA (mRNA) is no longer considered as a mere informational molecule whose sole function is to convey the genetic information specified by DNA to the ribosome. Beyond this primary function, mRNA also contains additional instructions that influence the way and the extent to which this message is translated by the ribosome into protein(s). Indeed, owing to its intrinsic propensity to quickly and dynamically fold and form higher order structures, mRNA exhibits a second layer of structural information specified by the sequence itself. Besides influencing transcription and mRNA stability, this additional information also affects translation, and more precisely the frequency of translation initiation, the choice of open reading frame by recoding, the elongation speed, and the folding of the nascent protein. Many studies in bacteria have shown that mRNA secondary structure participates to the rapid adaptation of these versatile organisms to changing environmental conditions by efficiently tuning translation in response to diverse signals, such as the presence of ligands, regulatory proteins, or small RNAs. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Translation Regulation.
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12
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Abstract
RNA-binding proteins (RBPs) are central to most if not all cellular processes, dictating the fate of virtually all RNA molecules in the cell. Starting with pioneering work on ribosomal proteins, studies of bacterial RBPs have paved the way for molecular studies of RNA-protein interactions. Work over the years has identified major RBPs that act on cellular transcripts at the various stages of bacterial gene expression and that enable their integration into post-transcriptional networks that also comprise small non-coding RNAs. Bacterial RBP research has now entered a new era in which RNA sequencing-based methods permit mapping of RBP activity in a truly global manner in vivo. Moreover, the soaring interest in understudied members of host-associated microbiota and environmental communities is likely to unveil new RBPs and to greatly expand our knowledge of RNA-protein interactions in bacteria.
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Affiliation(s)
- Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany. .,Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
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13
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Abstract
The rRNA is the largest and most abundant RNA in bacterial and archaeal cells. It is also one of the best-characterized RNAs in terms of its structural motifs and sequence variation. Production of ribosome components including >50 ribosomal proteins (r-proteins) consumes significant cellular resources. Thus, RNA cis-regulatory structures that interact with r-proteins to repress further r-protein synthesis play an important role in maintaining appropriate stoichiometry between r-proteins and rRNA. Classically, such mRNA structures were thought to directly mimic the rRNA. However, more than 30 years of research has demonstrated that a variety of different recognition and regulatory paradigms are present. This review will demonstrate how structural mimicry between the rRNA and mRNA cis-regulatory structures may take many different forms. The collection of mRNA structures that interact with r-proteins to regulate r-protein operons are best characterized in Escherichia coli, but are increasingly found within species from nearly all phyla of bacteria and several archaea. Furthermore, they represent a unique opportunity to assess the plasticity of RNA structure in the context of RNA-protein interactions. The binding determinants imposed by r-proteins to allow regulation can be fulfilled in many ways. Some r-protein-interacting mRNAs are immediately obvious as rRNA mimics from primary sequence similarity, others are identifiable only after secondary or tertiary structure determination, and some show no obvious similarity. In addition, across different bacterial species a host of different mechanisms of action have been characterized, showing that there is no simple one-size-fits-all solution.
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14
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Crowther CV, Jones LE, Morelli JN, Mastrogiacomo EM, Porterfield C, Kent JL, Serra MJ. Influence of two bulge loops on the stability of RNA duplexes. RNA (NEW YORK, N.Y.) 2017; 23:217-228. [PMID: 27872162 PMCID: PMC5238796 DOI: 10.1261/rna.056168.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 11/13/2016] [Indexed: 05/24/2023]
Abstract
Fifty-three RNA duplexes containing two single nucleotide bulge loops were optically melted in 1 M NaCl in order to determine the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each duplex. Because of the large number of possible combinations and lack of sequence effects observed previously, we limited our initial investigation to adenosine bulges, the most common naturally occurring bulge. For example, the following duplexes were investigated: 5'GGCAXYAGGC/3'CCG YX CCG, 5'GGCAXY GCC/3'CCG YXACGG, and 5'GGC XYAGCC/3'CCGAYX CGG. The identity of XY (where XY are Watson-Crick base pairs) and the total number of base pairs in the terminal and central stems were varied. As observed for duplexes with a single bulge loop, the effect of the two bulge loops on duplex stability is primarily influenced by non-nearest neighbor interactions. In particular, the stability of the stems influences the destabilization of the duplex by the inserted bulge loops. The model proposed to predict the influence of multiple bulge loops on duplex stability suggests that the destabilization of each bulge is related to the stability of the adjacent stems. A database of RNA secondary structures was examined to determine the naturally occurring abundance of duplexes containing multiple bulge loops. Of the 2000 examples found in the database, over 65% of the two bulge loops occur within 3 base pairs of each other. A database of RNA three-dimensional structures was examined to determine the structure of duplexes containing two single nucleotide bulge loops. The structures of the bulge loops are described.
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Affiliation(s)
- Claire V Crowther
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Laura E Jones
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Jessica N Morelli
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | | | - Claire Porterfield
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Jessica L Kent
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
| | - Martin J Serra
- Department of Chemistry, Allegheny College, Meadville, Pennsylvania 16335, USA
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15
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The ribosome as a missing link in prebiotic evolution II: Ribosomes encode ribosomal proteins that bind to common regions of their own mRNAs and rRNAs. J Theor Biol 2016; 397:115-27. [DOI: 10.1016/j.jtbi.2016.02.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 11/18/2022]
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16
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Virtanen JJ, Sosnick TR, Freed KF. Ionic strength independence of charge distributions in solvation of biomolecules. J Chem Phys 2015; 141:22D503. [PMID: 25494774 DOI: 10.1063/1.4895522] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). Although water provides the dominant contribution to the charge density distribution and to the electrostatic potential even in 1M NaCl solutions, the contributions of water molecules and of ions to the total electrostatic interaction free energy with the solvated biomolecule are comparable. The electrostatic biomolecule/solvent interaction energies and the total charge distribution exhibit a remarkable insensitivity to salt concentrations over a huge range of salt concentrations (20 mM to 1M NaCl). The electrostatic potentials near the biomolecule's surface obtained from the MD simulations differ markedly, as expected, from the potentials predicted by continuum dielectric models, even though the total electrostatic interaction free energies are within 11% of each other.
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Affiliation(s)
- J J Virtanen
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
| | - T R Sosnick
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - K F Freed
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
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17
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Duval M, Simonetti A, Caldelari I, Marzi S. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 2015; 114:18-29. [PMID: 25792421 DOI: 10.1016/j.biochi.2015.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/15/2022]
Abstract
To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.
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Affiliation(s)
- Mélodie Duval
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
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18
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Davlieva M, Donarski J, Wang J, Shamoo Y, Nikonowicz EP. Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis. Nucleic Acids Res 2014; 42:10795-808. [PMID: 25140011 PMCID: PMC4176348 DOI: 10.1093/nar/gku743] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.
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Affiliation(s)
- Milya Davlieva
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - James Donarski
- Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - Jiachen Wang
- Department of Physics, East China Normal University, 200062 Shanghai, P. R. China
| | - Yousif Shamoo
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
| | - Edward P Nikonowicz
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
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19
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Dienst D, Georg J, Abts T, Jakorew L, Kuchmina E, Börner T, Wilde A, Dühring U, Enke H, Hess WR. Transcriptomic response to prolonged ethanol production in the cyanobacterium Synechocystis sp. PCC6803. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:21. [PMID: 24502290 PMCID: PMC3925133 DOI: 10.1186/1754-6834-7-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 01/17/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND The production of biofuels in photosynthetic microalgae and cyanobacteria is a promising alternative to the generation of fuels from fossil resources. To be economically competitive, producer strains need to be established that synthesize the targeted product at high yield and over a long time. Engineering cyanobacteria into forced fuel producers should considerably interfere with overall cell homeostasis, which in turn might counteract productivity and sustainability of the process. Therefore, in-depth characterization of the cellular response upon long-term production is of high interest for the targeted improvement of a desired strain. RESULTS The transcriptome-wide response to continuous ethanol production was examined in Synechocystis sp. PCC6803 using high resolution microarrays. In two independent experiments, ethanol production rates of 0.0338% (v/v) ethanol d-1 and 0.0303% (v/v) ethanol d-1 were obtained over 18 consecutive days, measuring two sets of biological triplicates in fully automated photobioreactors. Ethanol production caused a significant (~40%) delay in biomass accumulation, the development of a bleaching phenotype and a down-regulation of light harvesting capacity. However, microarray analyses performed at day 4, 7, 11 and 18 of the experiment revealed only three mRNAs with a strongly modified accumulation level throughout the course of the experiment. In addition to the overexpressed adhA (slr1192) gene, this was an approximately 4 fold reduction in cpcB (sll1577) and 3 to 6 fold increase in rps8 (sll1809) mRNA levels. Much weaker modifications of expression level or modifications restricted to day 18 of the experiment were observed for genes involved in carbon assimilation (Ribulose bisphosphate carboxylase and Glutamate decarboxylase). Molecular analysis of the reduced cpcB levels revealed a post-transcriptional processing of the cpcBA operon mRNA leaving a truncated mRNA cpcA* likely not competent for translation. Moreover, western blots and zinc-enhanced bilin fluorescence blots confirmed a severe reduction in the amounts of both phycocyanin subunits, explaining the cause of the bleaching phenotype. CONCLUSIONS Changes in gene expression upon induction of long-term ethanol production in Synechocystis sp. PCC6803 are highly specific. In particular, we did not observe a comprehensive stress response as might have been expected.
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Affiliation(s)
- Dennis Dienst
- Algenol Biofuels Germany GmbH, Magnusstraße 1, Berlin D-12489, Germany
- Institute of Biology, Humboldt-University Berlin, Chausseestr 117, Berlin D-10115, Germany
| | - Jens Georg
- Faculty of Biology, Inst. Biology III, University of Freiburg, Schänzlestr 1, Freiburg D-79104, Germany
| | - Thomas Abts
- Algenol Biofuels Germany GmbH, Magnusstraße 1, Berlin D-12489, Germany
| | - Lew Jakorew
- Institute of Biology, Humboldt-University Berlin, Chausseestr 117, Berlin D-10115, Germany
- Current address: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Ekaterina Kuchmina
- Faculty of Biology, Inst. Biology III, University of Freiburg, Schänzlestr 1, Freiburg D-79104, Germany
| | - Thomas Börner
- Institute of Biology, Humboldt-University Berlin, Chausseestr 117, Berlin D-10115, Germany
| | - Annegret Wilde
- Faculty of Biology, Inst. Biology III, University of Freiburg, Schänzlestr 1, Freiburg D-79104, Germany
| | - Ulf Dühring
- Algenol Biofuels Germany GmbH, Magnusstraße 1, Berlin D-12489, Germany
| | - Heike Enke
- Algenol Biofuels Germany GmbH, Magnusstraße 1, Berlin D-12489, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Inst. Biology III, University of Freiburg, Schänzlestr 1, Freiburg D-79104, Germany
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20
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Fu Y, Deiorio-Haggar K, Soo MW, Meyer MM. Bacterial RNA motif in the 5' UTR of rpsF interacts with an S6:S18 complex. RNA (NEW YORK, N.Y.) 2014; 20:168-76. [PMID: 24310371 PMCID: PMC3895269 DOI: 10.1261/rna.041285.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Approximately half the transcripts encoding ribosomal proteins in Escherichia coli include a structured RNA motif that interacts with a specific ribosomal protein to inhibit gene expression, thus allowing stoichiometric production of ribosome components. However, many of these RNA structures are not widely distributed across bacterial phyla. It is increasingly common for RNA motifs associated with ribosomal protein genes to be identified using comparative genomic methods, yet these are rarely experimentally validated. In this work, we characterize one such motif that precedes operons containing rpsF and rpsR, which encode ribosomal proteins S6 and S18. This RNA structure is widely distributed across many phyla of bacteria despite differences within the downstream operon, and examples are present in both E. coli and Bacillus subtilis. We demonstrate a direct interaction between an example of the RNA from B. subtilis and an S6:S18 complex using in vitro binding assays, verify our predicted secondary structure, and identify a putative protein-binding site. The proposed binding site bears a strong resemblance to the S18 binding site within the 16S rRNA, suggesting molecular mimicry. This interaction is a valuable addition to the canon of ribosomal protein mRNA interactions. This work shows how experimental verification translates computational results into concrete knowledge of biological systems.
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21
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Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S. S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA. RNA (NEW YORK, N.Y.) 2013; 19:1341-8. [PMID: 23980204 PMCID: PMC3854524 DOI: 10.1261/rna.038794.113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/05/2013] [Indexed: 05/24/2023]
Abstract
Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5' untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism.
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MESH Headings
- 5' Untranslated Regions/genetics
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Pairing
- Base Sequence
- Binding Sites
- Electrophoretic Mobility Shift Assay
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Operon/genetics
- Protein Binding
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Protein S6/chemistry
- Ribosomal Protein S6/genetics
- Ribosomal Protein S6/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Sequence Homology, Nucleic Acid
- Thermus thermophilus/genetics
- Thermus thermophilus/metabolism
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Affiliation(s)
- Dorota Matelska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Sylwia Panek
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Michal J. Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, 61-614, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
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22
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Fu Y, Deiorio-Haggar K, Anthony J, Meyer MM. Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria. Nucleic Acids Res 2013; 41:3491-503. [PMID: 23396277 PMCID: PMC3616713 DOI: 10.1093/nar/gkt055] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/02/2013] [Accepted: 01/10/2013] [Indexed: 01/30/2023] Open
Abstract
In Escherichia coli, 12 distinct RNA structures within the transcripts encoding ribosomal proteins interact with specific ribosomal proteins to allow autogenous regulation of expression from large multi-gene operons, thus coordinating ribosomal protein biosynthesis across multiple operons. However, these RNA structures are typically not represented in the RNA Families Database or annotated in genomic sequences databases, and their phylogenetic distribution is largely unknown. To investigate the extent to which these RNA structures are conserved across eubacterial phyla, we created multiple sequence alignments representing 10 of these messenger RNA (mRNA) structures in E. coli. We find that while three RNA structures are widely distributed across many phyla of bacteria, seven of the RNAs are narrowly distributed to a few orders of Gammaproteobacteria. To experimentally validate our computational predictions, we biochemically confirmed dual L1-binding sites identified in many Firmicute species. This work reveals that RNA-based regulation of ribosomal protein biosynthesis is used in nearly all eubacterial phyla, but the specific RNA structures that regulate ribosomal protein biosynthesis in E. coli are narrowly distributed. These results highlight the limits of our knowledge regarding ribosomal protein biosynthesis regulation outside of E. coli, and the potential for alternative RNA structures responsible for regulating ribosomal proteins in other eubacteria.
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Affiliation(s)
| | | | | | - Michelle M. Meyer
- Department of Biology, Boston College, 140 Commonwealth Ave. Chestnut Hill, MA 02467, USA
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23
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Boutorine YI, Steinberg SV. Twist-joints and double twist-joints in RNA structure. RNA (NEW YORK, N.Y.) 2012; 18:2287-98. [PMID: 23060425 PMCID: PMC3504679 DOI: 10.1261/rna.030940.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Analysis of available RNA crystal structures has allowed us to identify a new family of RNA arrangements that we call double twist-joints, or DTJs. Each DTJ is composed of a double helix that contains two bulges incorporated into different strands and separated from each other by 2 or 3 bp. At each bulge, the double helix is over-twisted, while the unpaired nucleotides of both bulges form a complex network of stacking and hydrogen-bonding with nucleotides of helical regions. In total, we identified 14 DTJ cases, which can be combined in three groups based on common structural characteristics. One DTJ is found in a functional center of the ribosome, another DTJ mediates binding of the pre-tRNA to the RNase P, and two more DTJs form the sensing domains in the glycine riboswitch.
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Affiliation(s)
- Yury I. Boutorine
- Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Sergey V. Steinberg
- Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
- Corresponding authorE-mail
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24
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Yruela I, Contreras-Moreira B. Protein disorder in plants: a view from the chloroplast. BMC PLANT BIOLOGY 2012; 12:165. [PMID: 22970728 PMCID: PMC3460767 DOI: 10.1186/1471-2229-12-165] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/10/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND The intrinsically unstructured state of some proteins, observed in all living organisms, is essential for basic cellular functions. In this field the available information from plants is limited but it has been reached a point where these proteins can be comprehensively classified on the basis of disorder, function and evolution. RESULTS Our analysis of plant genomes confirms that nuclear-encoded proteins follow the same trend than other multi-cellular eukaryotes; however, chloroplast- and mitochondria- encoded proteins conserve the patterns of Archaea and Bacteria, in agreement with their phylogenetic origin. Based on current knowledge about gene transference from the chloroplast to the nucleus, we report a strong correlation between the rate of disorder of transferred and nuclear-encoded proteins, even for polypeptides that play functional roles back in the chloroplast. We further investigate this trend by reviewing the set of chloroplast ribosomal proteins, one of the most representative transferred gene clusters, finding that the ribosomal large subunit, assembled from a majority of nuclear-encoded proteins, is clearly more unstructured than the small one, which integrates mostly plastid-encoded proteins. CONCLUSIONS Our observations suggest that the evolutionary dynamics of the plant nucleus adds disordered segments to genes alike, regardless of their origin, with the notable exception of proteins currently encoded in both genomes, probably due to functional constraints.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda. Montañana, 1005, Zaragoza, 50059, Spain
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Avda. Montañana, 1005, Zaragoza, 50059, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Mariano Esquillor, Edificio I + D, Zaragoza, 50018, Spain
- Fundación ARAID, Zaragoza, Spain
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25
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Tishchenko S, Gabdulkhakov A, Nevskaya N, Sarskikh A, Kostareva O, Nikonova E, Sycheva A, Moshkovskii S, Garber M, Nikonov S. High-resolution crystal structure of the isolated ribosomal L1 stalk. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1051-7. [PMID: 22868771 DOI: 10.1107/s0907444912020136] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/04/2012] [Indexed: 11/11/2022]
Abstract
The crystal structure of the isolated full-length ribosomal L1 stalk, consisting of Thermus thermophilus ribosomal protein L1 in complex with a specific 80-nucleotide fragment of 23S rRNA, has been solved for the first time at high resolution. The structure revealed details of protein-RNA interactions in the L1 stalk. Analysis of the crystal packing enabled the identification of sticky sites on the protein and the 23S rRNA which may be important for ribosome assembly and function. The structure was used to model different conformational states of the ribosome. This approach provides an insight into the roles of domain II of L1 and helix 78 of rRNA in ribosome function.
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Affiliation(s)
- S Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
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26
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Abstract
The purpose of Reflections articles, it seems, is to give elderly scientists a chance to write about the "good old days," when everyone walked to school in the snow. They enjoy this activity so much that your editor, Martha Fedor, must have known that I would accept her invitation to write such an article, no matter how much I demurred at first. As everyone knows, flattery will get you everywhere. It may comfort the apprehensive reader to learn that there is not going to be much walking to school in the snow in this story. On the contrary, rather than thinking how hard I had it during my scientific career, I find it inconceivable that anyone could have had a smoother ride. At the time I began my career, science was an expanding enterprise in the United States that welcomed the young. Only in such an opportunity-rich environment would someone like me have stood a chance. The contrast between that world and the dog-eat-dog world young scientists confront today is stark.
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Affiliation(s)
- Peter B Moore
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
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27
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Menichelli E, Edgcomb SP, Recht MI, Williamson JR. The structure of Aquifex aeolicus ribosomal protein S8 reveals a unique subdomain that contributes to an extremely tight association with 16S rRNA. J Mol Biol 2011; 415:489-502. [PMID: 22079365 DOI: 10.1016/j.jmb.2011.10.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 10/14/2011] [Accepted: 10/26/2011] [Indexed: 12/01/2022]
Abstract
The assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. The ribosomal protein S8 from Aquifex aeolicus (AS8) is unique in that there is a 41-residue insertion in the consensus S8 sequence. In addition, AS8 exhibits an unusually high affinity for the 16S ribosomal RNA, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than the equivalent interaction from Escherichia coli. Deletion analysis demonstrated that binding to the minimal site on helix 21 occurred at the same nanomolar affinity found for other bacterial species. The additional affinity required the presence of a three-helix junction between helices 20, 21, and 22. The crystal structure of AS8 was solved, revealing the helix-loop-helix geometry of the unique AS8 insertion region, while the core of the molecule is conserved with known S8 structures. The AS8 structure was modeled onto the structure of the 30S ribosomal subunit from E. coli, suggesting the possibility that the unique subdomain provides additional backbone and side-chain contacts between the protein and an unpaired base within the three-way junction of helices 20, 21, and 22. Point mutations in the protein insertion subdomain resulted in a significantly reduced RNA binding affinity with respect to wild-type AS8. These results indicate that the AS8-specific subdomain provides additional interactions with the three-way junction that contribute to the extremely tight binding to ribosomal RNA.
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Affiliation(s)
- Elena Menichelli
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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28
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29
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Siibak T, Peil L, Dönhöfer A, Tats A, Remm M, Wilson DN, Tenson T, Remme J. Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins. Mol Microbiol 2011; 80:54-67. [PMID: 21320180 DOI: 10.1111/j.1365-2958.2011.07555.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inhibitors of protein synthesis cause defects in the assembly of ribosomal subunits. In response to treatment with the antibiotics erythromycin or chloramphenicol, precursors of both large and small ribosomal subunits accumulate. We have used a pulse-labelling approach to demonstrate that the accumulating subribosomal particles maturate into functional 70S ribosomes. The protein content of the precursor particles is heterogeneous and does not correspond with known assembly intermediates. Mass spectrometry indicates that production of ribosomal proteins in the presence of the antibiotics correlates with the amounts of the individual ribosomal proteins within the precursor particles. Thus, treatment of cells with chloramphenicol or erythromycin leads to an unbalanced synthesis of ribosomal proteins, providing the explanation for formation of assembly-defective particles. The operons for ribosomal proteins show a characteristic pattern of antibiotic inhibition where synthesis of the first proteins is inhibited weakly but gradually increases for the subsequent proteins in the operon. This phenomenon most likely reflects translational coupling and allows us to identify other putative coupled non-ribosomal operons in the Escherichia coli chromosome.
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Affiliation(s)
- Triinu Siibak
- Institutes of Molecular and Cell Biology Technology, University of Tartu, Tartu, Estonia
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30
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Abstract
RNA binding proteins are capable of regulating translation initiation by a variety of mechanisms. Although the vast majority of these regulatory mechanisms involve translational repression, one example of translational activation has been characterized in detail. The RNA recognition targets of these regulatory proteins exhibit a wide range in structural complexity, with some proteins recognizing complex pseudoknot structures and others binding to simple RNA hairpins and/or short repeated single-stranded sequences. In some instances the bound protein directly competes with ribosome binding, and in other instances the bound protein promotes formation of an RNA structure that inhibits ribosome binding. Examples also exist in which the bound protein traps the ribosome in a complex that is incapable of initiating translation.
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Affiliation(s)
- Paul Babitzke
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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31
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Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'. BMC Genomics 2009; 10:268. [PMID: 19531245 PMCID: PMC2704228 DOI: 10.1186/1471-2164-10-268] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 06/16/2009] [Indexed: 02/04/2023] Open
Abstract
Background Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content. Results To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of 'Cand. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from 'Cand. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data. Conclusion This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.
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Affiliation(s)
- Michelle M Meyer
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.
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32
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Hammond MC, Wachter A, Breaker RR. A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nat Struct Mol Biol 2009; 16:541-9. [PMID: 19377483 PMCID: PMC2680232 DOI: 10.1038/nsmb.1588] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 03/11/2009] [Indexed: 02/07/2023]
Abstract
Transcription factor IIIA (TFIIIA) is required for eukaryotic synthesis of 5S ribosomal RNA by RNA polymerase III. Here we report the discovery of a structured RNA element with striking resemblance to 5S rRNA that is conserved within TFIIIA precursor mRNAs (pre-mRNAs) from diverse plant lineages. TFIIIA protein expression is controlled by alternative splicing of the exon containing the plant 5S rRNA mimic (P5SM). P5SM triggers exon skipping upon binding of ribosomal protein L5, a natural partner of 5S rRNA, which demonstrates the functional adaptation of its structural mimicry. Since the exon-skipped splice product encodes full-length TFIIIA protein, these results reveal a ribosomal protein-mRNA interaction that is involved in 5S rRNA synthesis and has implications for cross-coordination of ribosomal components. This study also provides insight into the origin and function of a newfound class of structured RNA that regulates alternative splicing.
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Affiliation(s)
- Ming C Hammond
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
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33
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Diercks T, AB E, Daniels MA, de Jong RN, Besseling R, Kaptein R, Folkers GE. Solution structure and characterization of the DNA-binding activity of the B3BP-Smr domain. J Mol Biol 2008; 383:1156-70. [PMID: 18804481 DOI: 10.1016/j.jmb.2008.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 09/01/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain.
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Affiliation(s)
- Tammo Diercks
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Faculty of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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34
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Popenda L, Adamiak RW, Gdaniec Z. Bulged Adenosine Influence on the RNA Duplex Conformation in Solution. Biochemistry 2008; 47:5059-67. [DOI: 10.1021/bi7024904] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lukasz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Ryszard W. Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704 Poznań, Poland
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35
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Iben JR, Draper DE. Specific interactions of the L10(L12)4 ribosomal protein complex with mRNA, rRNA, and L11. Biochemistry 2008; 47:2721-31. [PMID: 18247578 DOI: 10.1021/bi701838y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large ribosomal subunit proteins L10 and L12 form a pentameric protein complex, L10(L12) 4, that is intimately involved in the ribosome elongation cycle. Its contacts with rRNA or other ribosomal proteins have been only partially resolved by crystallography. In Escherichia coli, L10 and L12 are encoded from a single operon for which L10(L12) 4 is a translational repressor that recognizes a secondary structure in the mRNA leader. In this study, L10(L12) 4 was expressed from the moderate thermophile Bacillus stearothermophilus to quantitatively compare strategies for binding of the complex to mRNA and ribosome targets. The minimal mRNA recognition structure is widely distributed among bacteria and has the potential to form a kink-turn structure similar to one identified in the rRNA as part of the L10(L12) 4 binding site. Mutations in equivalent positions between the two sequences have similar effects on L10(L12) 4-RNA binding affinity and identify the kink-turn motif and a loop AA sequence as important recognition elements. In contrast to the larger rRNA structure, the mRNA apparently positions the kink-turn motif and loop for protein recognition without the benefit of Mg (2+)-dependent tertiary structure. The mRNA and rRNA fragments bind L10(L12) 4 with similar affinity ( approximately 10 (8) M (-1)), but fluorescence binding studies show that a nearby protein in the ribosome, L11, enhances L10(L12) 4 binding approximately 100-fold. Thus, mRNA and ribosome targets use similar RNA features, held in different structural contexts, to recognize L10(L12) 4, and the ribosome ensures the saturation of its L10(L12) 4 binding site by means of an additional protein-protein interaction.
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Affiliation(s)
- James R Iben
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
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36
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Gilbert SD, Rambo RP, Van Tyne D, Batey RT. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 2008; 15:177-82. [PMID: 18204466 DOI: 10.1038/nsmb.1371] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 11/21/2007] [Indexed: 02/08/2023]
Abstract
In bacteria, numerous genes harbor regulatory elements in the 5' untranslated regions of their mRNA, termed riboswitches, which control gene expression by binding small-molecule metabolites. These sequences influence the secondary and tertiary structure of the RNA in a ligand-dependent manner, thereby directing its transcription or translation. The crystal structure of an S-adenosylmethionine-responsive riboswitch found predominantly in proteobacteria, SAM-II, has been solved to reveal a second means by which RNA interacts with this important cellular metabolite. Notably, this is the first structure of a complete riboswitch containing all sequences associated with both the ligand binding aptamer domain and the regulatory expression platform. Chemical probing of this RNA in the absence and presence of ligand shows how the structure changes in response to S-adenosylmethionine to sequester the ribosomal binding site and affect translational gene regulation.
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Affiliation(s)
- Sunny D Gilbert
- Department of Chemistry and Biochemistry, Campus Box 215, University of Colorado, Boulder, Colorado 80309, USA
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37
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Marzi S, Myasnikov AG, Serganov A, Ehresmann C, Romby P, Yusupov M, Klaholz BP. Structured mRNAs regulate translation initiation by binding to the platform of the ribosome. Cell 2007; 130:1019-31. [PMID: 17889647 DOI: 10.1016/j.cell.2007.07.008] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 05/18/2007] [Accepted: 07/06/2007] [Indexed: 01/04/2023]
Abstract
Gene expression can be regulated at the level of initiation of protein biosynthesis via structural elements present at the 5' untranslated region of mRNAs. These folded mRNA segments may bind to the ribosome, thus blocking translation until the mRNA unfolds. Here, we report a series of cryo-electron microscopy snapshots of ribosomal complexes directly visualizing either the mRNA structure blocked by repressor protein S15 or the unfolded, active mRNA. In the stalled state, the folded mRNA prevents the start codon from reaching the peptidyl-tRNA (P) site inside the ribosome. Upon repressor release, the mRNA unfolds and moves into the mRNA channel allowing translation initiation. A comparative structure and sequence analysis suggests the existence of a universal stand-by site on the ribosome (the 30S platform) dedicated for binding regulatory 5' mRNA elements. Different types of mRNA structures may be accommodated during translation preinitiation and regulate gene expression by transiently stalling the ribosome.
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MESH Headings
- 5' Untranslated Regions
- Amino Acid Sequence
- Base Sequence
- Binding Sites
- Cryoelectron Microscopy
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Gene Expression Regulation, Bacterial
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational
- Protein Binding
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Messenger/metabolism
- RNA, Transfer/metabolism
- Regulatory Sequences, Ribonucleic Acid
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Structural Homology, Protein
- Time Factors
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Affiliation(s)
- Stefano Marzi
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Department of Structural Biology and Genomics, Illkirch, F-67404 France
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38
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Allemand F, Haentjens J, Chiaruttini C, Royer C, Springer M. Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites. Nucleic Acids Res 2007; 35:3016-31. [PMID: 17439971 PMCID: PMC1888825 DOI: 10.1093/nar/gkm197] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Ribosomal protein L20 is crucial for the assembly of the large ribosomal subunit and represses the translation of its own mRNA. L20 mRNA carries two L20-binding sites, the first folding into a pseudoknot and the second into an imperfect stem and loop. These two sites and the L20-binding site on 23S ribosomal RNA are recognized similarly using a single RNA-binding site located on one face of L20. In this work, using gel filtration and fluorescence cross-correlation spectroscopy (FCCS) experiments, we first exclude the possibility that L20 forms a dimer, which would allow each monomer to bind one site of the mRNA. Secondly we show, using affinity purification and FCCS experiments, that only one molecule of L20 binds to the L20 mRNA despite the presence of two potential binding sites. Thirdly, using RNA chemical probing, we show that the two L20-binding sites are in interaction. This interaction provides an explanation for the single occupancy of the mRNA. The two interacting sites could form a single hybrid site or the binding of L20 to a first site may inhibit binding to the second. Models of regulation compatible with our data are discussed.
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Affiliation(s)
- F. Allemand
- UPR9073 du CNRS associée à l'Université de Paris VII, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France and INSERM, Unité 554, Montpellier, France and Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - J. Haentjens
- UPR9073 du CNRS associée à l'Université de Paris VII, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France and INSERM, Unité 554, Montpellier, France and Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - C. Chiaruttini
- UPR9073 du CNRS associée à l'Université de Paris VII, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France and INSERM, Unité 554, Montpellier, France and Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - C. Royer
- UPR9073 du CNRS associée à l'Université de Paris VII, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France and INSERM, Unité 554, Montpellier, France and Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
| | - M. Springer
- UPR9073 du CNRS associée à l'Université de Paris VII, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France and INSERM, Unité 554, Montpellier, France and Université de Montpellier, CNRS, UMR 5048, Centre de Biochimie Structurale, Montpellier, France
- *To whom correspondence should be addressed. +33 1 58 41 51 31+33 1 58 41 50 20
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39
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Choonee N, Even S, Zig L, Putzer H. Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res 2007; 35:1578-88. [PMID: 17289755 PMCID: PMC1865079 DOI: 10.1093/nar/gkm011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In contrast to Escherichia coli no molecular mechanism controlling the biosynthesis of ribosomal proteins has been elucidated in Gram-positive organisms. Here we show that the expression of the Bacillus subtilis infC-rpmI-rplT operon encoding translation factor IF3 and the ribosomal proteins L35 and L20 is autoregulated by a complex transcription attenuation mechanism. It implicates a 200-bp leader region upstream of infC which contains two conserved regulatory elements, one of which can act as a transcription terminator. Using in vitro and in vivo approaches we show that expression of the operon is regulated at the level of transcription elongation by a change in the structure of the leader mRNA which depends upon the presence of ribosomal protein L20. L20 binds to a phylogenetically conserved domain and provokes premature transcription termination at the leader terminator. Footprint and toeprint experiments support a regulatory model involving molecular mimicry between the L20-binding sites on 23S rRNA and the mRNA. Our data suggest that Nomura's model of ribosomal protein biosynthesis based on autogenous control and molecular mimicry is also valid in Gram-positive organisms.
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Affiliation(s)
| | | | | | - Harald Putzer
- *To whom correspondence should be addressed. + 33 1 58 41 51 27+ 33 1 58 41 50 20
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40
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41
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Tishchenko SV, Nikonova EY, Nevskaya NA, Nikonov OS, Garber MB, Nikonov SV. Interactions of ribosomal protein L1 with ribosomal and messenger RNAs. Mol Biol 2006. [DOI: 10.1134/s0026893306040108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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42
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Batey RT. Structures of regulatory elements in mRNAs. Curr Opin Struct Biol 2006; 16:299-306. [PMID: 16707260 DOI: 10.1016/j.sbi.2006.05.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 04/21/2006] [Accepted: 05/02/2006] [Indexed: 01/31/2023]
Abstract
Messenger RNAs often contain structures in their 5'-untranslated region that serve to regulate or promote expression of their gene product. Recent structural studies have revealed that riboswitches, which bind a variety of small molecule metabolites, including purine bases, S-adenosylmethionine, amino acids and cofactors, can contain sophisticated tertiary architecture that enables their function, akin to tRNA and rRNA. These structures guide the mRNA to adopt one of two mutually exclusive forms, dictating the outcome of transcription or translation. Another highly structured mRNA element, the viral internal ribosomal entry site, is able to manipulate the ribosome and replace the function of initiation factors to promote gene expression.
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Affiliation(s)
- Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, Colorado 80309, USA.
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43
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McIntosh KB, Bonham-Smith PC. Ribosomal protein gene regulation: what about plants? ACTA ACUST UNITED AC 2006. [DOI: 10.1139/b06-014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ribosome is an intricate ribonucleoprotein complex with a multitude of protein constituents present in equimolar amounts. Coordination of the synthesis of these ribosomal proteins (r-proteins) presents a major challenge to the cell. Although most r-proteins are highly conserved, the mechanisms by which r-protein gene expression is regulated often differ widely among species. While the primary regulatory mechanisms coordinating r-protein synthesis in bacteria, yeast, and animals have been identified, the mechanisms governing the coordination of plant r-protein expression remain largely unexplored. In addition, plants are unique among eukaryotes in carrying multiple (often more than two) functional genes encoding each r-protein, which substantially complicates coordinate expression. A survey of the current knowledge regarding coordinated systems of r-protein gene expression in different model organisms suggests that vertebrate r-protein gene regulation provides a valuable comparison for plants.
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Affiliation(s)
- Kerri B. McIntosh
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Peta C. Bonham-Smith
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
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44
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Abstract
Riboswitches are structured domains that usually reside in the noncoding regions of mRNAs, where they bind metabolites and control gene expression. Like their protein counterparts, these RNA gene control elements form highly specific binding pockets for the target metabolite and undergo allosteric changes in structure. Numerous classes of riboswitches are present in bacteria and they comprise a common and robust metabolite-sensing system.
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Affiliation(s)
- Wade C Winkler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
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45
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Nevskaya N, Tishchenko S, Volchkov S, Kljashtorny V, Nikonova E, Nikonov O, Nikulin A, Köhrer C, Piendl W, Zimmermann R, Stockley P, Garber M, Nikonov S. New insights into the interaction of ribosomal protein L1 with RNA. J Mol Biol 2005; 355:747-59. [PMID: 16330048 DOI: 10.1016/j.jmb.2005.10.084] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Revised: 10/31/2005] [Accepted: 10/31/2005] [Indexed: 11/19/2022]
Abstract
The RNA-binding ability of ribosomal protein L1 is of profound interest, since L1 has a dual function as a ribosomal structural protein that binds rRNA and as a translational repressor that binds its own mRNA. Here, we report the crystal structure at 2.6 A resolution of ribosomal protein L1 from the bacterium Thermus thermophilus in complex with a 38 nt fragment of L1 mRNA from Methanoccocus vannielii. The conformation of RNA-bound T.thermophilus L1 differs dramatically from that of the isolated protein. Analysis of four copies of the L1-mRNA complex in the crystal has shown that domain II of the protein does not contribute to mRNA-specific binding. A detailed comparison of the protein-RNA interactions in the L1-mRNA and L1-rRNA complexes identified amino acid residues of L1 crucial for recognition of its specific targets on the both RNAs. Incorporation of the structure of bacterial L1 into a model of the Escherichia coli ribosome revealed two additional contact regions for L1 on the 23S rRNA that were not identified in previous ribosome models.
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MESH Headings
- Amino Acid Sequence
- Hydrogen Bonding
- Kinetics
- Methanococcus/genetics
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/metabolism
- Sequence Alignment
- Surface Plasmon Resonance
- Thermus thermophilus
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Affiliation(s)
- Natalia Nevskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow region, Russian Federation
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46
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Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005; 361:13-37. [PMID: 16213112 DOI: 10.1016/j.gene.2005.06.037] [Citation(s) in RCA: 527] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 05/31/2005] [Accepted: 06/27/2005] [Indexed: 01/19/2023]
Abstract
The mechanism of initiation of translation differs between prokaryotes and eukaryotes, and the strategies used for regulation differ accordingly. Translation in prokaryotes is usually regulated by blocking access to the initiation site. This is accomplished via base-paired structures (within the mRNA itself, or between the mRNA and a small trans-acting RNA) or via mRNA-binding proteins. Classic examples of each mechanism are described. The polycistronic structure of mRNAs is an important aspect of translational control in prokaryotes, but polycistronic mRNAs are not usable (and usually not produced) in eukaryotes. Four structural elements in eukaryotic mRNAs are important for regulating translation: (i) the m7G cap; (ii) sequences flanking the AUG start codon; (iii) the position of the AUG codon relative to the 5' end of the mRNA; and (iv) secondary structure within the mRNA leader sequence. The scanning model provides a framework for understanding these effects. The scanning mechanism also explains how small open reading frames near the 5' end of the mRNA can down-regulate translation. This constraint is sometimes abrogated by changing the structure of the mRNA, sometimes with clinical consequences. Examples are described. Some mistaken ideas about regulation of translation that have found their way into textbooks are pointed out and corrected.
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Affiliation(s)
- Marilyn Kozak
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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47
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Manuell AL, Yamaguchi K, Haynes PA, Milligan RA, Mayfield SP. Composition and structure of the 80S ribosome from the green alga Chlamydomonas reinhardtii: 80S ribosomes are conserved in plants and animals. J Mol Biol 2005; 351:266-79. [PMID: 16005888 DOI: 10.1016/j.jmb.2005.06.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/31/2005] [Accepted: 06/07/2005] [Indexed: 11/29/2022]
Abstract
We have conducted a proteomic analysis of the 80S cytosolic ribosome from the eukaryotic green alga Chlamydomonas reinhardtii, and accompany this with a cryo-electron microscopy structure of the ribosome. Proteins homologous to all but one rat 40S subunit protein, including a homolog of RACK1, and all but three rat 60S subunit proteins were identified as components of the C. reinhardtii ribosome. Expressed Sequence Tag (EST) evidence and annotation of the completed C. reinhardtii genome identified genes for each of the four proteins not identified by proteomic analysis, showing that algae potentially have a complete set of orthologs to mammalian 80S ribosomal proteins. Presented at 25A, the algal 80S ribosome is very similar in structure to the yeast 80S ribosome, with only minor distinguishable differences. These data show that, although separated by billions of years of evolution, cytosolic ribosomes from photosynthetic organisms are highly conserved with their yeast and animal counterparts.
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Affiliation(s)
- Andrea L Manuell
- Department of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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48
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Guillier M, Allemand F, Dardel F, Royer CA, Springer M, Chiaruttini C. Double molecular mimicry in Escherichia coli: binding of ribosomal protein L20 to its two sites in mRNA is similar to its binding to 23S rRNA. Mol Microbiol 2005; 56:1441-56. [PMID: 15916597 DOI: 10.1111/j.1365-2958.2005.04644.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli ribosomal L20 is one of five proteins essential for the first reconstitution step of the 50S ribosomal subunit in vitro. It is purely an assembly protein, because it can be withdrawn from the mature subunit without effect on ribosome activity. In addition, L20 represses the translation of its own gene by binding to two sites in its mRNA. The first site is a pseudoknot formed by a base-pairing interaction between nucleotide sequences separated by more than 280 nucleotides, whereas the second site is an irregular helix formed by base-pairing between neighbouring nucleotide sequences. Despite these differences, the mRNA folds in such a way that both L20 binding sites share secondary structure similarity with the L20 binding site located at the junction between helices H40 and H41 in 23S rRNA. Using a set of genetic, biochemical, biophysical, and structural experiments, we show here that all three sites are recognized similarly by L20.
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MESH Headings
- Base Sequence
- Binding Sites
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Mimicry
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
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Affiliation(s)
- Maude Guillier
- Institut de Biologie Physico-Chimique, CNRS UPR9073, Unité de Régulation de l'Expression Génétique chez les Microorganismes, 13 rue Pierre et Marie Curie, 75005 Paris, France
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49
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Winkler WC. Metabolic monitoring by bacterial mRNAs. Arch Microbiol 2005; 183:151-9. [PMID: 15750802 DOI: 10.1007/s00203-005-0758-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Revised: 01/05/2005] [Accepted: 01/12/2005] [Indexed: 02/04/2023]
Abstract
There is growing appreciation for diversity in the strategies that bacteria utilize in regulating gene expression. Bacteria must be able to respond in different ways to different stresses and thus require unique regulatory solutions for the physiological challenges they encounter. Recent data indicate that bacteria commonly employ a variety of posttranscriptional regulatory mechanisms to coordinate expression of their genes. In many instances, RNA structures embedded at the 5' ends of mRNAs are utilized to sense particular metabolic cues and regulate the encoded genes. These RNA elements are likely to range in structural sophistication, from short sequences recognized by RNA-binding proteins to complex shapes that fold into high-affinity receptors for small organic molecules. Enough examples of RNA-mediated genetic strategies have been found that it is becoming useful to view this overall mode of regulatory control at a genomic level. Eventually, a complete picture of bacterial gene regulation within a single bacterium, from control at transcription initiation to control of mRNA stability, will emerge. But for now, this article seeks to provide a brief overview of the known categories of RNA-mediated genetic mechanisms within the bacterium Bacillus subtilis, with the expectation that it is representative of bacteria as a whole.
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Affiliation(s)
- Wade C Winkler
- Department of Biochemistry, Room L1.404 , University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9038, USA.
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50
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Nevskaya N, Tishchenko S, Gabdoulkhakov A, Nikonova E, Nikonov O, Nikulin A, Platonova O, Garber M, Nikonov S, Piendl W. Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA. Nucleic Acids Res 2005; 33:478-85. [PMID: 15659579 PMCID: PMC548342 DOI: 10.1093/nar/gki194] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Revised: 12/24/2004] [Accepted: 12/24/2004] [Indexed: 11/15/2022] Open
Abstract
The RNA-binding ability of ribosomal protein L1 is of profound interest since the protein has a dual function as a ribosomal protein binding rRNA and as a translational repressor binding its mRNA. Here, we report the crystal structure of ribosomal protein L1 in complex with a specific fragment of its mRNA and compare it with the structure of L1 in complex with a specific fragment of 23S rRNA determined earlier. In both complexes, a strongly conserved RNA structural motif is involved in L1 binding through a conserved network of RNA-protein H-bonds inaccessible to the solvent. These interactions should be responsible for specific recognition between the protein and RNA. A large number of additional non-conserved RNA-protein H-bonds stabilizes both complexes. The added contribution of these non-conserved H-bonds makes the ribosomal complex much more stable than the regulatory one.
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Affiliation(s)
- Natalia Nevskaya
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Svetlana Tishchenko
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Azat Gabdoulkhakov
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Ekaterina Nikonova
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Alexei Nikulin
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Olga Platonova
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences142290 Pushchino, Moscow region, Russia
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
| | - Wolfgang Piendl
- Innsbruck Medical University, BiocentreFritz-Prengl-Str.3, A-6020 Innsbruck, Austria
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