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Tieng FYF, Abdullah-Zawawi MR, Md Shahri NAA, Mohamed-Hussein ZA, Lee LH, Mutalib NSA. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Brief Bioinform 2023; 25:bbad421. [PMID: 38040490 PMCID: PMC10753535 DOI: 10.1093/bib/bbad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023] Open
Abstract
RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA-RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA-RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | | | - Nur Alyaa Afifah Md Shahri
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), UKM, Selangor 43600, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, UKM, Selangor 43600, Malaysia
| | - Learn-Han Lee
- Sunway Microbiomics Centre, School of Medical and Life Sciences, Sunway University, Sunway City 47500, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, UKM, Kuala Lumpur 50300, Malaysia
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2
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Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021; 17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022] Open
Abstract
Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.
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Affiliation(s)
- Bikash K. Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniela M. Remus
- Callaghan Innovation Protein Science and Engineering, University of Canterbury, Christchurch, New Zealand
| | - Augustine Chen
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Craig van Dolleweerd
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
| | - Paul P. Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
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3
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Bhandari BK, Lim CS, Gardner PP. TISIGNER.com: web services for improving recombinant protein production. Nucleic Acids Res 2021; 49:W654-W661. [PMID: 33744969 PMCID: PMC8265118 DOI: 10.1093/nar/gkab175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/17/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022] Open
Abstract
Experiments that are planned using accurate prediction algorithms will mitigate failures in recombinant protein production. We have developed TISIGNER (https://tisigner.com) with the aim of addressing technical challenges to recombinant protein production. We offer three web services, TIsigner (Translation Initiation coding region designer), SoDoPE (Soluble Domain for Protein Expression) and Razor, which are specialised in synonymous optimisation of recombinant protein expression, solubility and signal peptide analysis, respectively. Importantly, TIsigner, SoDoPE and Razor are linked, which allows users to switch between the tools when optimising genes of interest.
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Affiliation(s)
- Bikash K Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Paul P Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
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4
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Soo VWC, Swadling JB, Faure AJ, Warnecke T. Fitness landscape of a dynamic RNA structure. PLoS Genet 2021; 17:e1009353. [PMID: 33524037 PMCID: PMC7877785 DOI: 10.1371/journal.pgen.1009353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/11/2021] [Accepted: 01/12/2021] [Indexed: 11/24/2022] Open
Abstract
RNA structures are dynamic. As a consequence, mutational effects can be hard to rationalize with reference to a single static native structure. We reasoned that deep mutational scanning experiments, which couple molecular function to fitness, should capture mutational effects across multiple conformational states simultaneously. Here, we provide a proof-of-principle that this is indeed the case, using the self-splicing group I intron from Tetrahymena thermophila as a model system. We comprehensively mutagenized two 4-bp segments of the intron. These segments first come together to form the P1 extension (P1ex) helix at the 5' splice site. Following cleavage at the 5' splice site, the two halves of the helix dissociate to allow formation of an alternative helix (P10) at the 3' splice site. Using an in vivo reporter system that couples splicing activity to fitness in E. coli, we demonstrate that fitness is driven jointly by constraints on P1ex and P10 formation. We further show that patterns of epistasis can be used to infer the presence of intramolecular pleiotropy. Using a machine learning approach that allows quantification of mutational effects in a genotype-specific manner, we demonstrate that the fitness landscape can be deconvoluted to implicate P1ex or P10 as the effective genetic background in which molecular fitness is compromised or enhanced. Our results highlight deep mutational scanning as a tool to study alternative conformational states, with the capacity to provide critical insights into the structure, evolution and evolvability of RNAs as dynamic ensembles. Our findings also suggest that, in the future, deep mutational scanning approaches might help reverse-engineer multiple alternative or successive conformations from a single fitness landscape.
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Affiliation(s)
- Valerie W. C. Soo
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Jacob B. Swadling
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Andre J. Faure
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tobias Warnecke
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
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5
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Abstract
MicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in coexpressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of nontarget sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analyzed ancestral target sites, the derived (nontarget) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyze separately target sites in which the target allele is ancestral to the population, the proportion of single-nucleotide polymorphisms with high Fst significantly increases. These findings support that population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences.
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Affiliation(s)
- Andrea Hatlen
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Antonio Marco
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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6
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Wang SE, Brooks AES, Poole AM, Simoes-Barbosa A. Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis. BMC Mol Cell Biol 2020; 21:54. [PMID: 32689943 PMCID: PMC7370421 DOI: 10.1186/s12860-020-00297-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Trichomonas vaginalis, the causative agent of a prevalent urogenital infection in humans, is an evolutionarily divergent protozoan. Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5' UTRs. The specific mechanisms adopted by T. vaginalis to fine-tune the translation efficiency (TE) of mRNAs remain largely unknown. RESULTS Using both computational and experimental approaches, this study investigated two key factors influencing TE in T. vaginalis: codon usage and mRNA secondary structure. Statistical dependence between TE and codon adaptation index (CAI) highlighted the impact of codon usage on mRNA translation in T. vaginalis. A genome-wide interrogation revealed that low structural complexity at the 5' end of mRNA followed closely by a highly structured downstream region correlates with TE variation in this organism. To validate these findings, a synthetic library of 15 synonymous iLOV genes was created, representing five mRNA folding profiles and three codon usage profiles. Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions. CONCLUSIONS This study demonstrates the role of codon usage bias and mRNA secondary structure in TE of T. vaginalis mRNAs, contributing to a better understanding of the factors that influence, and possibly regulate, gene expression in this human pathogen.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, USA
| | - Anna E S Brooks
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
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7
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Soulé A, Steyaert JM, Waldispühl J. A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae. J Comput Biol 2020; 27:390-402. [PMID: 32160035 DOI: 10.1089/cmb.2019.0464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The growing number of RNA-mediated regulation mechanisms identified in the past decades suggests a widespread impact of RNA-RNA interactions. The efficiency of the regulation relies on highly specific and coordinated interactions while simultaneously repressing the formation of opportunistic complexes. However, the analysis of RNA interactomes is highly challenging because of the large number of potential partners, discrepancy of the size of RNA families, and the inherent noise in interaction predictions. We designed a recursive two-step cross-validation pipeline to capture the specificity of noncoding RNA (ncRNA) messenger RNA (mRNA) interactomes. Our method has been designed to detect significant loss or gain of specificity between ncRNA-mRNA interaction profiles. Applied to small nucleolar RNA-mRNA in Saccharomyces cerevisiae, our results suggest the existence of a repression of ncRNA affinities with mRNAs and thus the existence of an evolutionary pressure leveling down such interactions.
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Affiliation(s)
- Antoine Soulé
- School of Computer Science, McGill University, Montreal, Canada.,LiX, École Polytechnique, Palaiseau, France
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8
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Hockenberry AJ, Jewett MC, Amaral LAN, Wilke CO. Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function. Mol Biol Evol 2019; 35:2487-2498. [PMID: 30085185 DOI: 10.1093/molbev/msy150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Shine-Dalgarno (SD) sequence motif facilitates translation initiation and is frequently found upstream of bacterial start codons. However, thousands of instances of this motif occur throughout the middle of protein coding genes in a typical bacterial genome. Here, we use comparative evolutionary analysis to test whether SD sequences located within genes are functionally constrained. We measure the conservation of SD sequences across Enterobacteriales, and find that they are significantly less conserved than expected. Further, the strongest SD sequences are the least conserved whereas we find evidence of conservation for the weakest possible SD sequences given amino acid constraints. Our findings indicate that most SD sequences within genes are likely to be deleterious and removed via selection. To illustrate the origin of these deleterious costs, we show that ATG start codons are significantly depleted downstream of SD sequences within genes, highlighting the constraint that these sequences impose on the surrounding nucleotides to minimize the potential for erroneous translation initiation.
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Affiliation(s)
- Adam J Hockenberry
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL.,Center for Synthetic Biology, Northwestern University, Evanston, IL.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL.,Simpson Querrey Institute, Northwestern University, Evanston, IL
| | - Luís A N Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL.,Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX
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9
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Transcriptional noise and exaptation as sources for bacterial sRNAs. Biochem Soc Trans 2019; 47:527-539. [PMID: 30837318 DOI: 10.1042/bst20180171] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
Understanding how new genes originate and integrate into cellular networks is key to understanding evolution. Bacteria present unique opportunities for both the natural history and experimental study of gene origins, due to their large effective population sizes, rapid generation times, and ease of genetic manipulation. Bacterial small non-coding RNAs (sRNAs), in particular, many of which operate through a simple antisense regulatory logic, may serve as tractable models for exploring processes of gene origin and adaptation. Understanding how and on what timescales these regulatory molecules arise has important implications for understanding the evolution of bacterial regulatory networks, in particular, for the design of comparative studies of sRNA function. Here, we introduce relevant concepts from evolutionary biology and review recent work that has begun to shed light on the timescales and processes through which non-functional transcriptional noise is co-opted to provide regulatory functions. We explore possible scenarios for sRNA origin, focusing on the co-option, or exaptation, of existing genomic structures which may provide protected spaces for sRNA evolution.
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10
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RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics. Molecules 2018; 23:molecules23123329. [PMID: 30558267 PMCID: PMC6321275 DOI: 10.3390/molecules23123329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 11/25/2022] Open
Abstract
Cells frequently simultaneously express RNAs and cognate antisense transcripts without necessarily leading to the formation of RNA duplexes. Here, we present a novel transcriptome-wide experimental approach to ascertain the presence of accessible double-stranded RNA structures based on sequencing of RNA fragments longer than 18 nucleotides that were not degraded by single-strand cutting nucleases. We applied this approach to four different cell lines with respect to three different treatments (native cell lysate, removal of proteins, and removal of ribosomal RNA and proteins). We found that long accessible RNA duplexes were largely absent in native cell lysates, while the number of RNA duplexes was dramatically higher when proteins were removed. The majority of RNA duplexes involved ribosomal transcripts. The duplex formation between different non-ribosomal transcripts appears to be largely of a stochastic nature. These results suggest that cells are—via RNA-binding proteins—mostly devoid of long RNA duplexes, leading to low “noise” in the molecular patterns that are utilized by the innate immune system. These findings have implications for the design of RNA interference (RNAi)-based therapeutics by imposing structural constraints on designed RNA complexes that are intended to have specific properties with respect to Dicer cleavage and target gene downregulation.
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11
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Abstract
It is widely assumed that there is a clear distinction between eukaryotes, with cell nuclei, and prokaryotes, which lack nuclei. This suggests the evolution of nuclear compartmentation is a singular event. However, emerging knowledge of the diversity of bacterial internal cell structures suggests the picture may not be as black-and-white as previously thought. For instance, some members of the bacterial PVC superphylum appear to have nucleus-like compartmentation, where transcription and translation are physically separated, and some jumbophages have recently been shown to create nucleus-like structures within their Pseudomonad hosts. Moreover, there is also tantalizing metagenomic identification of new Archaea that carry homologs of genes associated with internal cell membrane structure in eukaryotes. All these cases invite comparison with eukaryote cell biology. While the bacterial cases of genetic compartmentation are likely convergent, and thus viewed by many as not germane to the question of eukaryote origins, we argue here that, in addressing the broader question of the evolution of compartmentation, other instances are at least as important: they provide us with a point of comparison which is critical for a more general understanding of both the conditions favoring the emergence of intracellular compartmentation of DNA and the evolutionary consequences of such cellular architecture. Finally, we consider three classes of explanation for the emergence of compartmentation: physical protection, crosstalk avoidance and nonadaptive origins.
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Affiliation(s)
- Heather L. Hendrickson
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Anthony M. Poole
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
- Te Ao Mârama/Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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12
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Quandt EM, Traverse CC, Ochman H. Local genic base composition impacts protein production and cellular fitness. PeerJ 2018; 6:e4286. [PMID: 29362699 PMCID: PMC5774297 DOI: 10.7717/peerj.4286] [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: 08/18/2017] [Accepted: 01/01/2018] [Indexed: 01/25/2023] Open
Abstract
The maintenance of a G + C content that is higher than the mutational input to a genome provides support for the view that selection serves to increase G + C contents in bacteria. Recent experimental evidence from Escherichia coli demonstrated that selection for increasing G + C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G + C content acts across all sites within a gene or is confined to particular genic regions or nucleotide positions. We systematically altered the G + C contents of the GFP gene and assayed its effects on the fitness of strains harboring each variant. Fitness differences were attributable to the base compositional variation in the terminal portion of the gene, suggesting a connection to the folding of a specific protein feature. Variants containing sequence features that are thought to result in rapid translation, such as low G + C content and high levels of codon adaptation, displayed highly reduced growth rates. Taken together, our results show that purifying selection acting against A and T mutations most likely results from their tendency to increase the rate of translation, which can perturb the dynamics of protein folding.
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Affiliation(s)
- Erik M Quandt
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Charles C Traverse
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
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13
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Frenzel E, Legebeke J, van Stralen A, van Kranenburg R, Kuipers OP. In vivo selection of sfGFP variants with improved and reliable functionality in industrially important thermophilic bacteria. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:8. [PMID: 29371884 PMCID: PMC5771013 DOI: 10.1186/s13068-017-1008-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/29/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Fluorescent reporter proteins (FP) have become an indispensable tool for the optimization of microbial cell factories and in synthetic biology per se. The applicability of the currently available FPs is, however, constrained by species-dependent performance and misfolding at elevated temperatures. To obtain functional reporters for thermophilic, biotechnologically important bacteria such as Parageobacillus thermoglucosidasius, an in vivo screening approach based on a mutational library of superfolder GFP was applied. RESULTS Flow cytometry-based benchmarking of a set of GFPs, sfGFPs and species-specific codon-optimized variants revealed that none of the proteins was satisfyingly detectable in P. thermoglucosidasius at its optimal growth temperature of 60 °C. An undirected mutagenesis approach coupled to fluorescence-activated cell sorting allowed the isolation of sfGFP variants that were extremely well expressed in the chassis background at 60 °C. Notably, a few nucleotide substitutions, including silent mutations, significantly improved the functionality and brightness. The best mutant sfGFP(N39D/A179A) showed an 885-fold enhanced mean fluorescence intensity (MFI) at 60 °C and is the most reliable reporter protein with respect to cell-to-cell variation and signal intensity reported so far. The in vitro spectral and thermostability properties were unaltered as compared to the parental sfGFP protein, strongly indicating that the combination of the amino acid exchange and an altered translation or folding speed, or protection from degradation, contribute to the strongly improved in vivo performance. Furthermore, sfGFP(N39D/A179A) and the newly developed cyan and yellow derivatives were successfully used for labeling several industrially relevant thermophilic bacilli, thus proving their broad applicability. CONCLUSIONS This study illustrates the power of in vivo isolation of thermostable proteins to obtain reporters for highly efficient fluorescence labeling. Successful expression in a variety of thermophilic bacteria proved that the novel FPs are highly suitable for imaging and flow cytometry-based studies. This enables a reliable cell tracking and single-cell-based real-time monitoring of biological processes that are of industrial and biotechnological interest.
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Affiliation(s)
- Elrike Frenzel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jelmer Legebeke
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Atze van Stralen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Corbion, Arkselsedijk 46, 4206 AC Gorinchem, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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14
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RNA search engines empower the bacterial intranet. Biochem Soc Trans 2017; 45:987-997. [PMID: 28710287 PMCID: PMC5652223 DOI: 10.1042/bst20160373] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 11/17/2022]
Abstract
RNA acts not only as an information bearer in the biogenesis of proteins from genes, but also as a regulator that participates in the control of gene expression. In bacteria, small RNA molecules (sRNAs) play controlling roles in numerous processes and help to orchestrate complex regulatory networks. Such processes include cell growth and development, response to stress and metabolic change, transcription termination, cell-to-cell communication, and the launching of programmes for host invasion. All these processes require recognition of target messenger RNAs by the sRNAs. This review summarizes recent results that have provided insights into how bacterial sRNAs are recruited into effector ribonucleoprotein complexes that can seek out and act upon target transcripts. The results hint at how sRNAs and their protein partners act as pattern-matching search engines that efficaciously regulate gene expression, by performing with specificity and speed while avoiding off-target effects. The requirements for efficient searches of RNA patterns appear to be common to all domains of life.
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15
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Umu SU, Gardner PP. A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Bioinformatics 2017; 33:988-996. [PMID: 27993777 PMCID: PMC5408919 DOI: 10.1093/bioinformatics/btw728] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 11/13/2016] [Indexed: 12/15/2022] Open
Abstract
Motivation The aim of this study is to assess the performance of RNA-RNA interaction prediction tools for all domains of life. Results Minimum free energy (MFE) and alignment methods constitute most of the current RNA interaction prediction algorithms. The MFE tools that include accessibility (i.e. RNAup, IntaRNA and RNAplex) to the final predicted binding energy have better true positive rates (TPRs) with a high positive predictive values (PPVs) in all datasets than other methods. They can also differentiate almost half of the native interactions from background. The algorithms that include effects of internal binding energies to their model and alignment methods seem to have high TPR but relatively low associated PPV compared to accessibility based methods. Availability and Implementation We shared our wrapper scripts and datasets at Github (github.com/UCanCompBio/RNA_Interactions_Benchmark). All parameters are documented for personal use. Contact sinan.umu@pg.canterbury.ac.nz. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sinan Ugur Umu
- School of Biological Sciences.,Biomolecular Interaction Centre
| | - Paul P Gardner
- School of Biological Sciences.,Biomolecular Interaction Centre.,Bio-Protection Research Centre, University of Canterbury, Christchurch, New Zealand
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Corley M, Laederach A. Selecting against accidental RNA interactions. eLife 2016; 5. [PMID: 27642846 PMCID: PMC5028187 DOI: 10.7554/elife.20686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 11/13/2022] Open
Abstract
Random base-pairing interactions between messenger RNAs and noncoding RNAs can reduce translation efficiency.
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Affiliation(s)
- Meredith Corley
- Department of Biology, University of North Carolina, Chapel Hill, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, United States
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