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Lipońska A, Lee H, Yap MNF. Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor. Nucleic Acids Res 2024:gkae596. [PMID: 38979572 DOI: 10.1093/nar/gkae596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/05/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
The hibernation-promoting factor (Hpf) in Staphylococcus aureus binds to 70S ribosomes and induces the formation of the 100S complex (70S dimer), leading to translational avoidance and occlusion of ribosomes from RNase R-mediated degradation. Here, we show that the 3'-5' exoribonuclease YhaM plays a previously unrecognized role in modulating ribosome stability. Unlike RNase R, which directly degrades the 16S rRNA of ribosomes in S. aureus cells lacking Hpf, YhaM destabilizes ribosomes by indirectly degrading the 3'-hpf mRNA that carries an intrinsic terminator. YhaM adopts an active hexameric assembly and robustly cleaves ssRNA in a manganese-dependent manner. In vivo, YhaM appears to be a low-processive enzyme, trimming the hpf mRNA by only 1 nucleotide. Deletion of yhaM delays cell growth. These findings substantiate the physiological significance of this cryptic enzyme and the protective role of Hpf in ribosome integrity, providing a mechanistic understanding of bacterial ribosome turnover.
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Affiliation(s)
- Anna Lipońska
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy and Biophysics Core in Research Resources Center, University of Illinois at Chicago (UIC), 1100 S Ashland Ave, Chicago, IL 60607, USA
| | - Mee-Ngan F Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, 320 E Superior St, Chicago, IL 60611, USA
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Wu R, Barnes S, Dahlin H, Khamrui S, Ingle S, Xiang Y, Shi Y, Bechhofer D, Lazarus M. Structural insights into RNA cleavage by a novel family of bacterial RNases. RESEARCH SQUARE 2023:rs.3.rs-3788707. [PMID: 38234822 PMCID: PMC10793500 DOI: 10.21203/rs.3.rs-3788707/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Processing of RNA is a key regulatory mechanism for all living systems. We recently discovered a novel family of endoribonucleases that is conserved across all bacteria. Here, using crystallography, cryo-EM microscopy, biochemical, biophysical, and mass spectrometry techniques, we are able to shed light on a novel RNA cleavage mechanism in bacteria. We show that YicC, the prototypical member of this family, forms a hexameric channel that closes down on a 26-mer RNA substrate, and find that it cleaves across an RNA hairpin to generate several short fragments.
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Affiliation(s)
- Ruoxi Wu
- Icahn School of Medicine at Mount Sinai
| | | | | | | | | | | | - Yi Shi
- Icahn School of Medicine at Mount Sinai
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Myers TM, Ingle S, Weiss CA, Sondermann H, Lee V, Bechhofer D, Winkler W. Bacillus subtilis NrnB is expressed during sporulation and acts as a unique 3'-5' exonuclease. Nucleic Acids Res 2023; 51:9804-9820. [PMID: 37650646 PMCID: PMC10570053 DOI: 10.1093/nar/gkad662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023] Open
Abstract
All cells employ a combination of endo- and exoribonucleases to degrade long RNA polymers to fragments 2-5 nucleotides in length. These short RNA fragments are processed to monoribonucleotides by nanoRNases. Genetic depletion of nanoRNases has been shown to increase abundance of short RNAs. This deleteriously affects viability, virulence, and fitness, indicating that short RNAs are a metabolic burden. Previously, we provided evidence that NrnA is the housekeeping nanoRNase for Bacillus subtilis. Herein, we investigate the biological and biochemical functions of the evolutionarily related protein, B. subtilis NrnB (NrnBBs). These experiments show that NrnB is surprisingly different from NrnA. While NrnA acts at the 5' terminus of RNA substrates, NrnB acts at the 3' terminus. Additionally, NrnA is expressed constitutively under standard growth conditions, yet NrnB is selectively expressed during endospore formation. Furthermore, NrnA processes only short RNAs, while NrnB unexpectedly processes both short RNAs and longer RNAs. Indeed, inducible expression of NrnB can even complement the loss of the known global 3'-5' exoribonucleases, indicating that it acts as a general exonuclease. Together, these data demonstrate that NrnB proteins, which are widely found in Firmicutes, Epsilonproteobacteria and Archaea, are fundamentally different than NrnA proteins and may be used for specialized purposes.
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Affiliation(s)
- Tanner M Myers
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD 20742, USA
| | - Shakti Ingle
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cordelia A Weiss
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Holger Sondermann
- CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Vincent T Lee
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - David H Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wade C Winkler
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, MD 20742, USA
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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Huang L, Tam KS, Xie W. Structural and Biochemical Studies of the Novel Hexameric Endoribonuclease YicC. ACS Chem Biol 2023; 18:1738-1747. [PMID: 37535940 DOI: 10.1021/acschembio.3c00091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The decay of mRNA is an essential process to bacteria. The newly identified E. coli protein YicC is a founding member of the UPF0701 family, and biochemical studies indicated that it is an RNase involved in mRNA degradation. However, its biochemical properties and catalytic mechanism are poorly understood. Here, we report the crystal structure of YicC, which shows an extended shape consisting of modular domains. While the backbone trace of the monomer forms a unique, nearly closed loop, the three monomers present in the asymmetric unit make a "shoulder-by-shoulder" trimer. In vitro RNA cleavage assays indicated that this endoribonuclease mainly recognizes the consensus GUG motif, with a preference for an extended CGUG sequence. Additionally, the active enzyme exists as a hexamer in solution and assumes a funnel shape. Structural analysis indicated that the hexamer interface is mainly formed by the hexamerization domain consisting of D71-D124 and that the disruption of the oligomeric form greatly diminished the enzymatic activity. By studying the surface charge potential and the sequence conservation, we identified a series of residues that play critical functional roles, which helps to reveal the catalytic mechanism of this divalent metal-ion-dependent RNase. Last but not least, we discovered that the catalytic domain of YicC did not share similarity with any known nuclease fold, suggesting that the enzyme adopts a novel fold to perform its catalysis and in vivo functions. In summary, our investigations into YicC provide an in-depth understanding of the functions of the UPF0701 protein family and the DUF1732 domain in general.
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Affiliation(s)
- Lin Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - King Sing Tam
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
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Bremer E, Hoffmann T, Dempwolff F, Bedrunka P, Bange G. The many faces of the unusual biofilm activator RemA. Bioessays 2022; 44:e2200009. [PMID: 35289951 DOI: 10.1002/bies.202200009] [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: 01/11/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022]
Abstract
Biofilms can be viewed as tissue-like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut-shaped octamers with the potential to assemble into dimeric superstructures. The presumed DNA-binding mode suggests that RemA organizes its target DNA into nucleosome-like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic-stress adjustment.
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Affiliation(s)
- Erhard Bremer
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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