1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Kusebauch U, Lorenzetti APR, Campbell DS, Pan M, Shteynberg D, Kapil C, Midha MK, López García de Lomana A, Baliga NS, Moritz RL. A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS. Sci Data 2023; 10:697. [PMID: 37833331 PMCID: PMC10575869 DOI: 10.1038/s41597-023-02590-5] [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: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon. Data and spectral assay libraries are available via ProteomeXchange (PXD042770, PXD042774) and SWATHAtlas (SAL00312-SAL00319).
Collapse
Affiliation(s)
- Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | | | - David S Campbell
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Min Pan
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - David Shteynberg
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Charu Kapil
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Mukul K Midha
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Adrián López García de Lomana
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | - Nitin S Baliga
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA.
| |
Collapse
|