1
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Payá G, Bautista V, Pastor-Soler S, Camacho M, Esclapez J, Bonete MJ. Analysis of Lsm Protein-Mediated Regulation in the Haloarchaeon Haloferax mediterranei. Int J Mol Sci 2024; 25:580. [PMID: 38203750 PMCID: PMC10779274 DOI: 10.3390/ijms25010580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq found in the Eukarya, Archaea, and Bacteria domains. Archaeal Lsm proteins have been shown to bind sRNAs and are probably involved in various cellular processes, suggesting a similar function in regulating sRNAs by Hfq in bacteria. Moreover, archaeal Lsm proteins probably represent the ancestral Lsm domain from which eukaryotic Sm proteins have evolved. In this work, Haloferax mediterranei was used as a model organism because it has been widely used to investigate the nitrogen cycle and its regulation in Haloarchaea. Predicting this protein's secondary and tertiary structures has resulted in a three-dimensional model like the solved Lsm protein structure of Archaeoglobus fulgidus. To obtain information on the oligomerization state of the protein, homologous overexpression and purification by means of molecular exclusion chromatography have been performed. The results show that this protein can form hexameric complexes, which can aggregate into 6 or 12 hexameric rings depending on the NaCl concentration and without RNA. In addition, the study of transcriptional expression via microarrays has allowed us to obtain the target genes regulated by the Lsm protein under nutritional stress conditions: nitrogen or carbon starvation. Microarray analysis has shown the first universal stress proteins (USP) in this microorganism that mediate survival in situations of nitrogen deficiency.
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Affiliation(s)
| | | | | | | | | | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; (G.P.); (V.B.); (S.P.-S.); (M.C.); (J.E.)
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2
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Reichelt R, Rothmeier T, Grünberger F, Willkomm S, Bruckmann A, Hausner W, Grohmann D. The archaeal Lsm protein from Pyrococcus furiosus binds co-transcriptionally to poly(U)-rich target RNAs. Biol Chem 2023; 404:1085-1100. [PMID: 37709673 DOI: 10.1515/hsz-2023-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Posttranscriptional processes in Bacteria include the association of small regulatory RNAs (sRNA) with a target mRNA. The sRNA/mRNA annealing process is often mediated by an RNA chaperone called Hfq. The functional role of bacterial and eukaryotic Lsm proteins is partially understood, whereas knowledge about archaeal Lsm proteins is scarce. Here, we used the genetically tractable archaeal hyperthermophile Pyrococcus furiosus to identify the protein interaction partners of the archaeal Sm-like proteins (PfuSmAP1) using mass spectrometry and performed a transcriptome-wide binding site analysis of PfuSmAP1. Most of the protein interaction partners we found are part of the RNA homoeostasis network in Archaea including ribosomal proteins, the exosome, RNA-modifying enzymes, but also RNA polymerase subunits, and transcription factors. We show that PfuSmAP1 preferentially binds messenger RNAs and antisense RNAs recognizing a gapped poly(U) sequence with high affinity. Furthermore, we found that SmAP1 co-transcriptionally associates with target RNAs. Our study reveals that in contrast to bacterial Hfq, PfuSmAP1 does not affect the transcriptional activity or the pausing behaviour of archaeal RNA polymerases. We propose that PfuSmAP1 recruits antisense RNAs to target mRNAs and thereby executes its putative regulatory function on the posttranscriptional level.
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Affiliation(s)
- Robert Reichelt
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Tamara Rothmeier
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Felix Grünberger
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Sarah Willkomm
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology (Biochemistry I), Protein Mass Spectrometry Laboratory, University of Regensburg, D-93053 Regensburg, Germany
| | - Winfried Hausner
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, D-93053 Regensburg, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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3
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Payá G, Bautista V, Camacho M, Esclapez J, Bonete MJ. Comprehensive Bioinformatics Analysis of the Biodiversity of Lsm Proteins in the Archaea Domain. Microorganisms 2023; 11:1196. [PMID: 37317170 DOI: 10.3390/microorganisms11051196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 06/16/2023] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq proteins. Sm and Lsm proteins are found in the Eukarya and Archaea domains, respectively, while Hfq proteins exist in the Bacteria domain. Even though Sm and Hfq proteins have been extensively studied, archaeal Lsm proteins still require further exploration. In this work, different bioinformatics tools are used to understand the diversity and distribution of 168 Lsm proteins in 109 archaeal species to increase the global understanding of these proteins. All 109 archaeal species analyzed encode one to three Lsm proteins in their genome. Lsm proteins can be classified into two groups based on molecular weight. Regarding the gene environment of lsm genes, many of these genes are located adjacent to transcriptional regulators of the Lrp/AsnC and MarR families, RNA-binding proteins, and ribosomal protein L37e. Notably, only proteins from species of the class Halobacteria conserved the internal and external residues of the RNA-binding site identified in Pyrococcus abyssi, despite belonging to different taxonomic orders. In most species, the Lsm genes show associations with 11 genes: rpl7ae, rpl37e, fusA, flpA, purF, rrp4, rrp41, hel308, rpoD, rpoH, and rpoN. We propose that most archaeal Lsm proteins are related to the RNA metabolism, and the larger Lsm proteins could perform different functions and/or act through other mechanisms of action.
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Affiliation(s)
- Gloria Payá
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Vanesa Bautista
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Mónica Camacho
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain
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4
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Lorenzetti APR, Kusebauch U, Zaramela LS, Wu WJ, de Almeida JPP, Turkarslan S, L. G. de Lomana A, Gomes-Filho JV, Vêncio RZN, Moritz RL, Koide T, Baliga NS. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. mSystems 2023; 8:e0081622. [PMID: 36912639 PMCID: PMC10134880 DOI: 10.1128/msystems.00816-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net). IMPORTANCE While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas (https://halodata.systemsbiology.net).
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Affiliation(s)
- Alan P. R. Lorenzetti
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- Institute for Systems Biology, Seattle, Washington, USA
| | | | - Lívia S. Zaramela
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, Washington, USA
| | - João P. P. de Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | | | - José V. Gomes-Filho
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Ricardo Z. N. Vêncio
- Department of Computation and Mathematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Tie Koide
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
- Lawrence Berkeley National Lab, Berkeley, California, USA
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5
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Tishchenko SV, Mikhailina AO, Lekontseva NV, Stolboushkina EA, Nikonova EY, Nikonov OS, Nikulin AD. Structural Investigations of RNA–Protein Complexes in Post-Ribosomal Era. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Structural studies of RNA–protein complexes are important for understanding many molecular mechanisms occurring in cells (e.g., regulation of protein synthesis and RNA-chaperone activity of proteins). Various objects investigated at the Institute of Protein Research of the Russian Academy of Sciences are considered. Based on the analysis of the structures of the complexes of the ribosomal protein L1 with specific regions on both mRNA and rRNA, the principles of regulation of the translation of the mRNA of its own operon are presented. The studies of the heterotrimeric translation initiation factor IF2 of archaea and eukaryotes are described, and the data on the interaction of glycyl-tRNA-synthetase with viral IRES are reported. The results of studying the interaction of RNA molecules with one of functionally important sites of the Hfq protein are presented, and the differences in the RNA-binding properties of the Hfq and archaeal Lsm proteins are revealed.
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6
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Payá G, Bautista V, Camacho M, Bonete MJ, Esclapez J. Functional analysis of Lsm protein under multiple stress conditions in the extreme haloarchaeon Haloferax mediterranei. Biochimie 2021; 187:33-47. [PMID: 33992715 DOI: 10.1016/j.biochi.2021.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 01/24/2023]
Abstract
The Sm, like-Sm, and Hfq proteins belonging to the Sm superfamily of proteins are represented in all domains of life. These proteins are involved in several RNA metabolism pathways. The functions of bacterial Hfq and eukaryotic Sm proteins have been described, but knowledge about the in vivo functions of archaeal Sm proteins remains limited. This study aims to improve the understanding of Lsm proteins and their role using the haloarchaeon Haloferax mediterranei as a model microorganism. The Haloferax mediterranei genome contains one lsm gene that overlaps with the rpl37e gene. To determine the expression of lsm and rpl37e genes and the co-transcription of both, reverse transcription-polymerase chain reaction (RT-PCR) analyses were performed under different standard and stress conditions. The results suggest that the expression of lsm and rpl37e is constitutive. Co-transcription occurs at sub-optimal salt concentrations and temperatures, depending on the growth phase. The halophilic Lsm protein contains two Sm motifs, Sm1 and Sm2, and the sequence encoding the Sm2 motif also constitutes the promoter of the rpl37e gene. To investigate their biological functions, the lsm deletion mutant and the Sm1 motif deletion mutant, where the Sm2 motif remained intact, were generated and characterised. Comparison of the lsm deletion mutant, Sm1 deletion mutant, and the parental strain HM26 under standard and stress growth conditions revealed growth differences. Finally, swarming assays in complex and defined media showed greater swarming capacity in the deletion mutants.
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Affiliation(s)
- Gloria Payá
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Vanesa Bautista
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Mónica Camacho
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - María-José Bonete
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
| | - Julia Esclapez
- Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080, Alicante, Spain.
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7
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Weixlbaumer A, Grünberger F, Werner F, Grohmann D. Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World. Front Microbiol 2021; 12:661827. [PMID: 33995325 PMCID: PMC8116511 DOI: 10.3389/fmicb.2021.661827] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023] Open
Abstract
The lack of a nucleus is the defining cellular feature of bacteria and archaea. Consequently, transcription and translation are occurring in the same compartment, proceed simultaneously and likely in a coupled fashion. Recent cryo-electron microscopy (cryo-EM) and tomography data, also combined with crosslinking-mass spectrometry experiments, have uncovered detailed structural features of the coupling between a transcribing bacterial RNA polymerase (RNAP) and the trailing translating ribosome in Escherichia coli and Mycoplasma pneumoniae. Formation of this supercomplex, called expressome, is mediated by physical interactions between the RNAP-bound transcription elongation factors NusG and/or NusA and the ribosomal proteins including uS10. Based on the structural conservation of the RNAP core enzyme, the ribosome, and the universally conserved elongation factors Spt5 (NusG) and NusA, we discuss requirements and functional implications of transcription-translation coupling in archaea. We furthermore consider additional RNA-mediated and co-transcriptional processes that potentially influence expressome formation in archaea.
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Affiliation(s)
- Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Université de Strasbourg, Strasbourg, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Finn Werner
- RNAP Lab, Division of Biosciences, Institute for Structural and Molecular Biology, London, United Kingdom
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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8
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Zink IA, Fouqueau T, Tarrason Risa G, Werner F, Baum B, Bläsi U, Schleper C. Comparative CRISPR type III-based knockdown of essential genes in hyperthermophilic Sulfolobales and the evasion of lethal gene silencing. RNA Biol 2021; 18:421-434. [PMID: 32957821 PMCID: PMC7951960 DOI: 10.1080/15476286.2020.1813411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/22/2020] [Accepted: 08/16/2020] [Indexed: 02/07/2023] Open
Abstract
CRISPR type III systems, which are abundantly found in archaea, recognize and degrade RNA in their specific response to invading nucleic acids. Therefore, these systems can be harnessed for gene knockdown technologies even in hyperthermophilic archaea to study essential genes. We show here the broader usability of this posttranscriptional silencing technology by expanding the application to further essential genes and systematically analysing and comparing silencing thresholds and escape mutants. Synthetic guide RNAs expressed from miniCRISPR cassettes were used to silence genes involved in cell division (cdvA), transcription (rpo8), and RNA metabolism (smAP2) of the two crenarchaeal model organisms Saccharolobus solfataricus and Sulfolobus acidocaldarius. Results were systematically analysed together with those obtained from earlier experiments of cell wall biogenesis (slaB) and translation (aif5A). Comparison of over 100 individual transformants revealed gene-specific silencing maxima ranging between 40 and 75%, which induced specific knockdown phenotypes leading to growth retardation. Exceedance of this threshold by strong miniCRISPR constructs was not tolerated and led to specific mutation of the silencing miniCRISPR array and phenotypical reversion of cultures. In two thirds of sequenced reverted cultures, the targeting spacers were found to be precisely excised from the miniCRISPR array, indicating a still hypothetical, but highly active recombination system acting on the dynamics of CRISPR spacer arrays. Our results indicate that CRISPR type III - based silencing is a broadly applicable tool to study in vivo functions of essential genes in Sulfolobales which underlies a specific mechanism to avoid malignant silencing overdose.
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Affiliation(s)
- Isabelle Anna Zink
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thomas Fouqueau
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Gabriel Tarrason Risa
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Finn Werner
- RNAP Lab, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Buzz Baum
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Udo Bläsi
- Max Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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9
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Lekontseva N, Mikhailina A, Fando M, Kravchenko O, Balobanov V, Tishchenko S, Nikulin A. Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode. Biochimie 2020; 175:1-12. [PMID: 32422160 DOI: 10.1016/j.biochi.2020.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.
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Affiliation(s)
- N Lekontseva
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - A Mikhailina
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - M Fando
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - O Kravchenko
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - V Balobanov
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - S Tishchenko
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia
| | - A Nikulin
- Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia.
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10
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A journey through the evolutionary diversification of archaeal Lsm and Hfq proteins. Emerg Top Life Sci 2018; 2:647-657. [PMID: 33525833 DOI: 10.1042/etls20180034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 11/17/2022]
Abstract
Sm-like (Lsm) proteins are found in all three domains of life. They are crucially involved in the RNA metabolism of prokaryotic organisms. To exert their function, they assemble into hexa- or heptameric rings and bind RNA via a conserved binding pocket for uridine stretches in the inner pore of the ring. Despite the conserved secondary structure of Lsm proteins, there are several features that lead to a structural diversification of this protein family that mediates their participation in a variety of processes related to RNA metabolism. Until recently, the cellular function of archaeal Sm-like proteins was not well understood. In this review, we discuss structural features of Lsm proteins with a strong focus on archaeal variants, reflect on the evolutionary development of archaeal Lsm proteins and present recent insights into their biological function.
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11
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Abstract
Advances in genome-wide sequence technologies allow for detailed insights into the complexity of RNA landscapes of organisms from all three domains of life. Recent analyses of archaeal transcriptomes identified interaction and regulation networks of noncoding RNAs in this understudied domain. Here, we review current knowledge of small, noncoding RNAs with important functions for the archaeal lifestyle, which often requires adaptation to extreme environments. One focus is RNA metabolism at elevated temperatures in hyperthermophilic archaea, which reveals elevated amounts of RNA-guided RNA modification and virus defense strategies. Genome rearrangement events result in unique fragmentation patterns of noncoding RNA genes that require elaborate maturation pathways to yield functional transcripts. RNA-binding proteins, e.g., L7Ae and LSm, are important for many posttranscriptional control functions of RNA molecules in archaeal cells. We also discuss recent insights into the regulatory potential of their noncoding RNA partners.
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Affiliation(s)
- José Vicente Gomes-Filho
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
| | - Michael Daume
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;, ,
- LOEWE Center for Synthetic Microbiology (Synmikro), 35032 Marburg, Germany
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12
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Bassani F, Romagnoli A, Cacciamani T, Amici A, Benelli D, Londei P, Märtens B, Bläsi U, La Teana A. Modification of translation factor aIF5A from Sulfolobus solfataricus. Extremophiles 2018; 22:769-780. [PMID: 30047030 PMCID: PMC6105217 DOI: 10.1007/s00792-018-1037-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/24/2018] [Indexed: 01/30/2023]
Abstract
Eukaryotic eIF5A and its bacterial orthologue EF-P are translation elongation factors whose task is to rescue ribosomes from stalling during the synthesis of proteins bearing particular sequences such as polyproline stretches. Both proteins are characterized by unique post-translational modifications, hypusination and lysinylation, respectively, which are essential for their function. An orthologue is present in all Archaea but its function is poorly understood. Here, we show that aIF5A of the crenarchaeum Sulfolobus solfataricus is hypusinated and forms a stable complex with deoxyhypusine synthase, the first enzyme of the hypusination pathway. The recombinant enzyme is able to modify its substrate in vitro resulting in deoxyhypusinated aIF5A. Moreover, with the aim to identify the enzyme involved in the second modification step, i.e. hypusination, a set of proteins interacting with aIF5A was identified.
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Affiliation(s)
- F Bassani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - T Cacciamani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Amici
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Via Ranieri 67, 60131, Ancona, Italy
| | - D Benelli
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Rome, Italy
| | - P Londei
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Rome, Italy
| | - B Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030, Vienna, Austria
| | - U Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030, Vienna, Austria
| | - A La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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13
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Märtens B, Sharma K, Urlaub H, Bläsi U. The SmAP2 RNA binding motif in the 3'UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus. Nucleic Acids Res 2017; 45:8957-8967. [PMID: 28911098 PMCID: PMC5587771 DOI: 10.1093/nar/gkx581] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/28/2017] [Indexed: 01/02/2023] Open
Abstract
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism in Pro- and Eukaryotes. In this study, a collection of 53 mRNAs that co-purified with Sulfolobus solfataricus (Sso) SmAP2 were surveyed for a specific RNA binding motif (RBM). SmAP2 was shown to bind with high affinity to the deduced consensus RNA binding motif (SmAP2-cRBM) in vitro. Residues in SmAP2 interacting with the SmAP2-cRBM were mapped by UV-induced crosslinking in combination with mass-spectrometry, and verified by mutational analyses. The RNA-binding site on SmAP2 includes a modified uracil binding pocket containing a unique threonine (T40) located on the L3 face and a second residue, K25, located in the pore. To study the function of the SmAP2-RBM in vivo, three authentic RBMs were inserted in the 3′UTR of a lacS reporter gene. The presence of the SmAP2-RBM in the reporter-constructs resulted in decreased LacS activity and reduced steady state levels of lacS mRNA. Moreover, the presence of the SmAP2-cRBM in and the replacement of the lacS 3′UTR with that of Sso2194 encompassing a SmAP2-RBM apparently impacted on the stability of the chimeric transcripts. These results are discussed in light of the function(s) of eukaryotic Lsm proteins in RNA turnover.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Kundan Sharma
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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14
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Märtens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Bläsi U. The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts. Nucleic Acids Res 2017; 45:7938-7949. [PMID: 28520934 PMCID: PMC5570065 DOI: 10.1093/nar/gkx437] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 05/03/2017] [Indexed: 01/26/2023] Open
Abstract
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated. Moreover, elevated levels of both SmAPs resulted in increased abundance of the soluble exosome fraction, suggesting that they affect the subcellular localization of the exosome in the cell. The increased solubility of the exosome was accompanied by augmented levels of RNAs with A-rich tails that were further characterized using RNASeq. Hence, the observation that the Sso SmAPs impact on the activity of the exosome revealed a hitherto unrecognized function of SmAPs in archaea.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Linlin Hou
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria.,Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria
| | - Elena Evguenieva-Hackenberg
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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15
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Nemchinova M, Balobanov V, Nikonova E, Lekontseva N, Mikhaylina A, Tishchenko S, Nikulin A. An Experimental Tool to Estimate the Probability of a Nucleotide Presence in the Crystal Structures of the Nucleotide-Protein Complexes. Protein J 2017; 36:157-165. [PMID: 28317076 DOI: 10.1007/s10930-017-9709-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A correlation between the ligand-protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements. The estimated stability of the nucleotide-protein complexes has been matched with a presence of the nucleotides in the structures of the proposed nucleotide-protein complexes. It has been shown that the ribonucleotides can be definitely identified in the experimental electron density maps at equilibrium dissociation constant <10 μM. At KD of 20-40 μM, long incubation of the protein crystals in the nucleotide solution is required to obtain the structures of the complexes. The complexes with KD value higher than 50 μM are not stable enough to survive in crystallization conditions.
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Affiliation(s)
- Maria Nemchinova
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | - Vitaly Balobanov
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | | | | | - Alisa Mikhaylina
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | | | - Alexey Nikulin
- Institute of Protein Research RAS, Pushchino, Russian Federation.
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