1
|
Brück M, Köbel TS, Dittmar S, Ramírez Rojas AA, Georg J, Berghoff BA, Schindler D. A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. iScience 2024; 27:110774. [PMID: 39280619 PMCID: PMC11402225 DOI: 10.1016/j.isci.2024.110774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/14/2024] [Accepted: 08/15/2024] [Indexed: 09/18/2024] Open
Abstract
All organisms must respond to environmental changes. In bacteria, small RNAs (sRNAs) are an important aspect of the regulation network underlying the adaptation to such changes. sRNAs base-pair with their target mRNAs, allowing rapid modulation of the proteome. This post-transcriptional regulation is usually facilitated by RNA chaperones, such as Hfq. sRNAs have a potential as synthetic regulators that can be modulated by rational design. In this study, we use a library-based approach and oxacillin susceptibility assays to investigate the importance of the seed region length for synthetic sRNAs based on RybB and SgrS scaffolds in Escherichia coli. In the presence of Hfq we show that 12 nucleotides are sufficient for regulation. Furthermore, we observe a scaffold-specific Hfq-dependency and processing by RNase E. Our results provide information for design considerations of synthetic sRNAs in basic and applied research.
Collapse
Affiliation(s)
- Michel Brück
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Tania S Köbel
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Sophie Dittmar
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Adán A Ramírez Rojas
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Jens Georg
- Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Daniel Schindler
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Karl-von-Frisch-Straße 14, 35032 Marburg, Germany
| |
Collapse
|
2
|
Ramming L, Stukenberg D, Sánchez Olmos MDC, Glatter T, Becker A, Schindler D. Rationally designed chromosome fusion does not prevent rapid growth of Vibrio natriegens. Commun Biol 2024; 7:519. [PMID: 38698198 PMCID: PMC11066055 DOI: 10.1038/s42003-024-06234-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/23/2024] [Indexed: 05/05/2024] Open
Abstract
DNA replication is essential for the proliferation of all cells. Bacterial chromosomes are replicated bidirectionally from a single origin of replication, with replication proceeding at about 1000 bp per second. For the model organism, Escherichia coli, this translates into a replication time of about 40 min for its 4.6 Mb chromosome. Nevertheless, E. coli can propagate by overlapping replication cycles with a maximum short doubling time of 20 min. The fastest growing bacterium known, Vibrio natriegens, is able to replicate with a generation time of less than 10 min. It has a bipartite genome with chromosome sizes of 3.2 and 1.9 Mb. Is simultaneous replication from two origins a prerequisite for its rapid growth? We fused the two chromosomes of V. natriegens to create a strain carrying one chromosome with a single origin of replication. Compared to the parental, this strain showed no significant deviation in growth rate. This suggests that the split genome is not a prerequisite for rapid growth.
Collapse
Affiliation(s)
- Lea Ramming
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel Stukenberg
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Anke Becker
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
| |
Collapse
|
3
|
Lindeboom TA, Sanchez Olmos MDC, Schulz K, Brinkmann CK, Ramírez Rojas AA, Hochrein L, Schindler D. An Optimized Genotyping Workflow for Identifying Highly SCRaMbLEd Synthetic Yeasts. ACS Synth Biol 2024; 13:1116-1127. [PMID: 38597458 PMCID: PMC11036488 DOI: 10.1021/acssynbio.3c00476] [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: 08/03/2023] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Synthetic Sc2.0 yeast strains contain hundreds to thousands of loxPsym recombination sites that allow restructuring of the Saccharomyces cerevisiae genome by SCRaMbLE. Thus, a highly diverse yeast population can arise from a single genotype. The selection of genetically diverse candidates with rearranged synthetic chromosomes for downstream analysis requires an efficient and straightforward workflow. Here we present loxTags, a set of qPCR primers for genotyping across loxPsym sites to detect not only deletions but also inversions and translocations after SCRaMbLE. To cope with the large number of amplicons, we generated qTagGer, a qPCR genotyping primer prediction tool. Using loxTag-based genotyping and long-read sequencing, we show that light-inducible Cre recombinase L-SCRaMbLE can efficiently generate diverse recombination events when applied to Sc2.0 strains containing a linear or a circular version of synthetic chromosome III.
Collapse
Affiliation(s)
- Timon A Lindeboom
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | | | - Karina Schulz
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Cedric K Brinkmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Adán A Ramírez Rojas
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Lena Hochrein
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 14, 35032Marburg, Germany
| |
Collapse
|
4
|
Ramírez Rojas A, Brinkmann CK, Köbel TS, Schindler D. DuBA.flow─A Low-Cost, Long-Read Amplicon Sequencing Workflow for the Validation of Synthetic DNA Constructs. ACS Synth Biol 2024; 13:457-465. [PMID: 38295293 PMCID: PMC10877597 DOI: 10.1021/acssynbio.3c00522] [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: 08/25/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 02/02/2024]
Abstract
Modern biological science, especially synthetic biology, relies heavily on the construction of DNA elements, often in the form of plasmids. Plasmids are used for a variety of applications, including the expression of proteins for subsequent purification, the expression of heterologous pathways for the production of valuable compounds, and the study of biological functions and mechanisms. For all applications, a critical step after the construction of a plasmid is its sequence validation. The traditional method for sequence determination is Sanger sequencing, which is limited to approximately 1000 bp per reaction. Here, we present a highly scalable in-house method for rapid validation of amplified DNA sequences using long-read Nanopore sequencing. We developed two-step amplicon and transposase strategies to provide maximum flexibility for dual barcode sequencing. We also provide an automated analysis pipeline to quickly and reliably analyze sequencing results and provide easy-to-interpret results for each sample. The user-friendly DuBA.flow start-to-finish pipeline is widely applicable. Furthermore, we show that construct validation using DuBA.flow can be performed by barcoded colony PCR amplicon sequencing, thus accelerating research.
Collapse
Affiliation(s)
- Adán
A. Ramírez Rojas
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Cedric K. Brinkmann
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Tania S. Köbel
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Daniel Schindler
- Max
Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center
for Synthetic Microbiology, Philipps-University
Marburg, Karl-von-Frisch-Str.
14, 35032 Marburg, Germany
| |
Collapse
|
5
|
Brück M, Berghoff BA, Schindler D. In Silico Design, In Vitro Construction, and In Vivo Application of Synthetic Small Regulatory RNAs in Bacteria. Methods Mol Biol 2024; 2760:479-507. [PMID: 38468105 DOI: 10.1007/978-1-0716-3658-9_27] [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] [Indexed: 03/13/2024]
Abstract
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences, for example, to fine-tune genetic circuits or biotechnological processes. Even though sRNAs often have a rather simple and modular structure, the design of functional synthetic sRNAs is not necessarily trivial. This protocol outlines how to use computational predictions and synthetic biology approaches to design, construct, and validate synthetic sRNA functionality for their application in bacteria. The computational tool, SEEDling, matches the optimal seed region with the user-selected sRNA scaffold for repression of target mRNAs. The synthetic sRNAs are assembled using Golden Gate cloning and their functionality is subsequently validated. The protocol uses the acrA mRNA as an exemplary proof-of-concept target in Escherichia coli. Since AcrA is part of a multidrug efflux pump, acrA repression can be revealed by assessing oxacillin susceptibility in a phenotypic screen. However, in case target repression does not result in a screenable phenotype, an alternative validation of synthetic sRNA functionality based on a fluorescence reporter is described.
Collapse
Affiliation(s)
- Michel Brück
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Institute for Microbiology and Molecular Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
| |
Collapse
|