1
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Brauns F, Iñigo de la Cruz L, Daalman WKG, de Bruin I, Halatek J, Laan L, Frey E. Redundancy and the role of protein copy numbers in the cell polarization machinery of budding yeast. Nat Commun 2023; 14:6504. [PMID: 37845215 PMCID: PMC10579396 DOI: 10.1038/s41467-023-42100-0] [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: 02/05/2022] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
How can a self-organized cellular function evolve, adapt to perturbations, and acquire new sub-functions? To make progress in answering these basic questions of evolutionary cell biology, we analyze, as a concrete example, the cell polarity machinery of Saccharomyces cerevisiae. This cellular module exhibits an intriguing resilience: it remains operational under genetic perturbations and recovers quickly and reproducibly from the deletion of one of its key components. Using a combination of modeling, conceptual theory, and experiments, we propose that multiple, redundant self-organization mechanisms coexist within the protein network underlying cell polarization and are responsible for the module's resilience and adaptability. Based on our mechanistic understanding of polarity establishment, we hypothesize that scaffold proteins, by introducing new connections in the existing network, can increase the redundancy of mechanisms and thus increase the evolvability of other network components. Moreover, our work gives a perspective on how a complex, redundant cellular module might have evolved from a more rudimental ancestral form.
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Affiliation(s)
- Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Leila Iñigo de la Cruz
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Werner K-G Daalman
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Ilse de Bruin
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jacob Halatek
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539, Munich, Germany.
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2
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Theodosiou L, Farr AD, Rainey PB. Barcoding Populations of Pseudomonas fluorescens SBW25. J Mol Evol 2023; 91:254-262. [PMID: 37186220 PMCID: PMC10275814 DOI: 10.1007/s00239-023-10103-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/13/2023] [Indexed: 05/17/2023]
Abstract
In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.
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Affiliation(s)
- Loukas Theodosiou
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding, Cologne, Germany.
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
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3
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Römling U, Cao LY, Bai FW. Evolution of cyclic di-GMP signalling on a short and long term time scale. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001354. [PMID: 37384391 PMCID: PMC10333796 DOI: 10.1099/mic.0.001354] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Lian-Ying Cao
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
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4
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Characterizing a novel CMK-EngA fusion protein from Bifidobacterium: Implications for inter-domain regulation. Biochem Biophys Rep 2022; 33:101410. [PMID: 36578527 PMCID: PMC9791819 DOI: 10.1016/j.bbrep.2022.101410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
EngA is an essential and unique bacterial GTPase involved in ribosome biogenesis. The essentiality and species-specific variations among EngA homologues make the protein a potential target for future drug development. In this aspect, it is important to understand the variations of EngA among probiotic organisms and non-probiotic bacteria to understand species specificity. The search for variations among EngA homologues revealed a unique variant, exclusively found in Bifidobacterium and a few Actinobacteria species. Bifidobacterium possesses a multifunctional fusion protein, wherein EngA is fused with an N-terminal CMK (Cytidylate Monophosphate Kinase) domain. The resulting protein is therefore a large (70kDa size) with 3 consecutive P-loops and a 50 amino acid long linker connecting the EngA and CMK domains. EngA is known to regulate ribosome biogenesis via nucleotide-dependent conformational changes. The additional domain may introduce further intricate regulation in ribosome biogenesis or participate in newer biological processes. This study is the first attempt to characterise this novel class of bacterial EngA found in the Genus of Bifidobacteria.
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5
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Wu J, Wu C, Rong C, Tian J, Jiang N, Wu R, Yue X, Shi H. Catalytic mechanisms underlying fungal fatty acid desaturases activities. Crit Rev Biotechnol 2022:1-17. [PMID: 35658758 DOI: 10.1080/07388551.2022.2063106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Polyunsaturated fatty acids (PUFAs) have beneficial roles in a variety of human pathologies and disorders. Owing to the limited source of PUFAs in animals and plants, microorganisms, especially fungi, have become a new source of PUFAs. In fungi, fatty acid desaturases (F-FADS) are the main enzymes that convert saturated fatty acids (SFAs) into PUFAs. Their catalytic activities and substrate specificities, which are directly dependent on the structure of the FADS proteins, determine their efficiency to convert SFAs to PUFAs. Catalytic mechanisms underlying F-FADS activities can be determined from the findings of the relationship between their structure and function. In this review, the advances made in the past decade in terms of catalytic activities and substrate specificities of the fungal FADS cluster are summarized. The relationship between the key domain(s) and site(s) in F-FADS proteins and their catalytic activity is highlighted, and the FADS cluster is analyzed phylogenetically. In addition, subcellular localization of F-FADS is discussed. Finally, we provide prospective crystal structures of F-FADSs. The findings may provide a reference for the resolution of the crystal structures of F-FADS proteins and facilitate the increase in fungal PUFA production for human health.
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Affiliation(s)
- Junrui Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, China
| | - Chen Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Chunchi Rong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Jinlong Tian
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Nan Jiang
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang, China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, China
| | - Haisu Shi
- College of Food Science, Shenyang Agricultural University, Shenyang, China.,Liaoning Engineering Research Center of Food Fermentation Technology, Shenyang Agricultural University, Shenyang, China.,Shenyang Key Laboratory of Microbial Fermentation Technology Innovation, Shenyang Agricultural University, Shenyang, China
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6
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Abstract
Microbes rely on signal transduction systems to sense and respond to environmental changes for survival and reproduction. It is generally known that niche adaptation plays an important role in shaping the signaling repertoire. However, the evolution of bacterial signaling capacity lacks systematic studies with a temporal direction. In particular, it is unclear how complexity evolved from simplicity or vice versa for signaling networks. Here, we examine the evolutionary processes of major signal transduction systems in Campylobacterota (formerly Epsilonproteobacteria), a phylum with sufficient evolutionary depth and ecological diversity. We discovered that chemosensory system increases complexity by horizontal gene transfer (HGT) of entire chemosensory classes, and different chemosensory classes rarely mix their components. Two-component system gains complexity by atypical histidine kinases fused with receiver domain to achieve multistep or branched signal transduction process. The presence and complexity of c-di-GMP-mediated system is related to the size of signaling network, and c-di-GMP pathways are easy to rewire, since enzymes and effectors can be linked without direct protein-protein interaction. Overall, signaling capacity and complexity rise and drop together in Campylobacterota, determined by sensory demand, genetic resources, and coevolution within the genomic context. These findings reflect plausible evolutionary principles for other cellular networks and genome evolution of the Bacteria domain.
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7
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Warsi O, Knopp M, Surkov S, Jerlström Hultqvist J, Andersson DI. Evolution of a New Function by Fusion between Phage DNA and a Bacterial Gene. Mol Biol Evol 2021; 37:1329-1341. [PMID: 31977019 PMCID: PMC7182210 DOI: 10.1093/molbev/msaa007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mobile genetic elements, such as plasmids, phages, and transposons, are important sources for evolution of novel functions. In this study, we performed a large-scale screening of metagenomic phage libraries for their ability to suppress temperature-sensitivity in Salmonella enterica serovar Typhimurium strain LT2 mutants to examine how phage DNA could confer evolutionary novelty to bacteria. We identified an insert encoding 23 amino acids from a phage that when fused with a bacterial DNA-binding repressor protein (LacI) resulted in the formation of a chimeric protein that localized to the outer membrane. This relocalization of the chimeric protein resulted in increased membrane vesicle formation and an associated suppression of the temperature sensitivity of the bacterium. Both the host LacI protein and the extracellular 23-amino acid stretch are necessary for the generation of the novel phenotype. Furthermore, mutational analysis of the chimeric protein showed that although the native repressor function of the LacI protein is maintained in this chimeric structure, it is not necessary for the new function. Thus, our study demonstrates how a gene fusion between foreign DNA and bacterial DNA can generate novelty without compromising the native function of a given gene.
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Affiliation(s)
- Omar Warsi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Michael Knopp
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Serhiy Surkov
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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8
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Updegrove TB, Harke J, Anantharaman V, Yang J, Gopalan N, Wu D, Piszczek G, Stevenson DM, Amador-Noguez D, Wang JD, Aravind L, Ramamurthi KS. Reformulation of an extant ATPase active site to mimic ancestral GTPase activity reveals a nucleotide base requirement for function. eLife 2021; 10:65845. [PMID: 33704064 PMCID: PMC7952092 DOI: 10.7554/elife.65845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/05/2021] [Indexed: 12/23/2022] Open
Abstract
Hydrolysis of nucleoside triphosphates releases similar amounts of energy. However, ATP hydrolysis is typically used for energy-intensive reactions, whereas GTP hydrolysis typically functions as a switch. SpoIVA is a bacterial cytoskeletal protein that hydrolyzes ATP to polymerize irreversibly during Bacillus subtilis sporulation. SpoIVA evolved from a TRAFAC class of P-loop GTPases, but the evolutionary pressure that drove this change in nucleotide specificity is unclear. We therefore reengineered the nucleotide-binding pocket of SpoIVA to mimic its ancestral GTPase activity. SpoIVAGTPase functioned properly as a GTPase but failed to polymerize because it did not form an NDP-bound intermediate that we report is required for polymerization. Further, incubation of SpoIVAGTPase with limiting ATP did not promote efficient polymerization. This approach revealed that the nucleotide base, in addition to the energy released from hydrolysis, can be critical in specific biological functions. We also present data suggesting that increased levels of ATP relative to GTP at the end of sporulation was the evolutionary pressure that drove the change in nucleotide preference in SpoIVA.
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Affiliation(s)
- Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Jailynn Harke
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | - Nikhil Gopalan
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | | | - Jue D Wang
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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9
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Escudero JA, Nivina A, Kemble HE, Loot C, Tenaillon O, Mazel D. Primary and promiscuous functions coexist during evolutionary innovation through whole protein domain acquisitions. eLife 2020; 9:58061. [PMID: 33319743 PMCID: PMC7790495 DOI: 10.7554/elife.58061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular examples of evolutionary innovation are scarce and generally involve point mutations. Innovation can occur through larger rearrangements, but here experimental data is extremely limited. Integron integrases innovated from double-strand- toward single-strand-DNA recombination through the acquisition of the I2 α-helix. To investigate how this transition was possible, we have evolved integrase IntI1 to what should correspond to an early innovation state by selecting for its ancestral activity. Using synonymous alleles to enlarge sequence space exploration, we have retrieved 13 mutations affecting both I2 and the multimerization domains of IntI1. We circumvented epistasis constraints among them using a combinatorial library that revealed their individual and collective fitness effects. We obtained up to 104-fold increases in ancestral activity with various asymmetrical trade-offs in single-strand-DNA recombination. We show that high levels of primary and promiscuous functions could have initially coexisted following I2 acquisition, paving the way for a gradual evolution toward innovation.
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Affiliation(s)
- José Antonio Escudero
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France.,Molecular Basis of Adaptation, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.,VISAVET Health Surveillance Centre. Universidad Complutense Madrid. Avenida Puerta de Hierro, Madrid, Spain
| | - Aleksandra Nivina
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Harry E Kemble
- Infection, Antimicrobials, Modelling, Evolution, INSERM, UMR 1137, Université Paris Diderot, Université Paris Nord, Paris, France
| | - Céline Loot
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France
| | - Olivier Tenaillon
- Infection, Antimicrobials, Modelling, Evolution, INSERM, UMR 1137, Université Paris Diderot, Université Paris Nord, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France
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10
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Horizontal Gene Transfer in Eukaryotes: Not if, but How Much? Trends Genet 2020; 36:915-925. [DOI: 10.1016/j.tig.2020.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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11
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Gallant J, Mouton J, Ummels R, Ten Hagen-Jongman C, Kriel N, Pain A, Warren RM, Bitter W, Heunis T, Sampson SL. Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins. NAR Genom Bioinform 2020; 2:lqaa033. [PMID: 33575588 PMCID: PMC7671302 DOI: 10.1093/nargab/lqaa033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis is a facultative intracellular pathogen responsible for causing tuberculosis. The harsh environment in which M. tuberculosis survives requires this pathogen to continuously adapt in order to maintain an evolutionary advantage. However, the apparent absence of horizontal gene transfer in M. tuberculosis imposes restrictions in the ways by which evolution can occur. Large-scale changes in the genome can be introduced through genome reduction, recombination events and structural variation. Here, we identify a functional chimeric protein in the ppe38-71 locus, the absence of which is known to have an impact on protein secretion and virulence. To examine whether this approach was used more often by this pathogen, we further develop software that detects potential gene fusion events from multigene deletions using whole genome sequencing data. With this software we could identify a number of other putative gene fusion events within the genomes of M. tuberculosis isolates. We were able to demonstrate the expression of one of these gene fusions at the protein level using mass spectrometry. Therefore, gene fusions may provide an additional means of evolution for M. tuberculosis in its natural environment whereby novel chimeric proteins and functions can arise.
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Affiliation(s)
- James Gallant
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.,Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Jomien Mouton
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Roy Ummels
- Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Corinne Ten Hagen-Jongman
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Nastassja Kriel
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, 001-0020, N20 W10 Kita-ku, Sapporo, Japan
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Wilbert Bitter
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.,Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Tiaan Heunis
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Samantha L Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
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12
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Noirot-Gros MF, Forrester S, Malato G, Larsen PE, Noirot P. CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens. Sci Rep 2019; 9:15954. [PMID: 31685917 PMCID: PMC6828691 DOI: 10.1038/s41598-019-52400-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 10/12/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial biofilm formation involves signaling and regulatory pathways that control the transition from motile to sessile lifestyle, production of extracellular polymeric matrix, and maturation of the biofilm 3D structure. Biofilms are extensively studied because of their importance in biomedical, ecological and industrial settings. Gene inactivation is a powerful approach for functional studies but it is often labor intensive, limiting systematic gene surveys to the most tractable bacterial hosts. Here, we adapted the CRISPR interference (CRISPRi) system for use in diverse strain isolates of P. fluorescens, SBW25, WH6 and Pf0-1. We found that CRISPRi is applicable to study complex phenotypes such as cell morphology, motility and biofilm formation over extended periods of time. In SBW25, CRISPRi-mediated silencing of genes encoding the GacA/S two-component system and regulatory proteins associated with the cylic di-GMP signaling messenger produced swarming and biofilm phenotypes similar to those obtained after gene inactivation. Combined with detailed confocal microscopy of biofilms, our study also revealed novel phenotypes associated with extracellular matrix biosynthesis as well as the potent inhibition of SBW25 biofilm formation mediated by the PFLU1114 operon. We conclude that CRISPRi is a reliable and scalable approach to investigate gene networks in the diverse P. fluorescens group.
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Affiliation(s)
| | - Sara Forrester
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
| | - Grace Malato
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
| | - Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States.,Department of Bioengineering, University of Illinois Chicago, Chicago, IL60607, United States
| | - Philippe Noirot
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
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13
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Willson BJ, Chapman LNM, Thomas GH. Evolutionary dynamics of membrane transporters and channels: enhancing function through fusion. Curr Opin Genet Dev 2019; 58-59:76-86. [DOI: 10.1016/j.gde.2019.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 02/05/2023]
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14
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Remigi P, Ferguson GC, McConnell E, De Monte S, Rogers DW, Rainey PB. Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase. Mol Biol Evol 2019; 36:1056-1070. [PMID: 30835283 PMCID: PMC6501884 DOI: 10.1093/molbev/msz041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Observations of bacteria at the single-cell level have revealed many instances of phenotypic heterogeneity within otherwise clonal populations, but the selective causes, molecular bases, and broader ecological relevance remain poorly understood. In an earlier experiment in which the bacterium Pseudomonas fluorescens SBW25 was propagated under a selective regime that mimicked the host immune response, a genotype evolved that stochastically switched between capsulation states. The genetic cause was a mutation in carB that decreased the pyrimidine pool (and growth rate), lowering the activation threshold of a preexisting but hitherto unrecognized phenotypic switch. Genetic components surrounding bifurcation of UTP flux toward DNA/RNA or UDP-glucose (a precursor of colanic acid forming the capsules) were implicated as key components. Extending these molecular analyses-and based on a combination of genetics, transcriptomics, biochemistry, and mathematical modeling-we show that pyrimidine limitation triggers an increase in ribosome biosynthesis and that switching is caused by competition between ribosomes and CsrA/RsmA proteins for the mRNA transcript of a positively autoregulated activator of colanic acid biosynthesis. We additionally show that in the ancestral bacterium the switch is part of a program that determines stochastic entry into a semiquiescent capsulated state, ensures that such cells are provisioned with excess ribosomes, and enables provisioned cells to exit rapidly from stationary phase under permissive conditions.
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Affiliation(s)
- Philippe Remigi
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Laboratoire des Interactions Plantes-Microorganismes (LIPM), Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Gayle C Ferguson
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Ellen McConnell
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Silvia De Monte
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - David W Rogers
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris Tech), CNRS UMR 8231, PSL Research University, Paris, France
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15
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Xu P, Dai X, Wang D, Miao Y, Zhang X, Wang S, Teng L, Dong B, Bao Z, Wang S, Lyu Q, Liu W. The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity. Sci Rep 2018; 8:17082. [PMID: 30459329 PMCID: PMC6244088 DOI: 10.1038/s41598-018-35265-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/31/2018] [Indexed: 01/06/2023] Open
Abstract
Adhesion is essential for many marine sessile organisms. Unraveling the compositions and assembly of marine bioadheisves is the fundamental to understand their physiological roles. Despite the remarkable diversity of animal bioadhesion, our understanding of this biological process remains limited to only a few animal lineages, leaving the majority of lineages remain enigmatic. Our previous study demonstrated that scallop byssus had distinct protein composition and unusual assembly mechanism apart from mussels. Here a novel protein (Sbp9) was discovered from the key part of the byssus (byssal root), which contains two Calcium Binding Domain (CBD) and 49 tandem Epidermal Growth Factor-Like (EGFL) domain repeats. Modular architecture of Sbp9 represents a novel chimeric gene family resulting from a gene fusion event through the acquisition of CBD2 domain by tenascin like (TNL) gene from Na+/Ca2+exchanger 1 (NCX1) gene. Finally, free thiols are present in Sbp9 and the results of a rescue assay indicated that Sbp9 likely plays the cohesive role for byssal root integrity. This study not only aids our understanding of byssus assembly but will also inspire biomimetic material design.
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Affiliation(s)
- Pingping Xu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaoting Dai
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Dandan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yan Miao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaokang Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shuoshuo Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Luyao Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Bo Dong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qianqian Lyu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Weizhi Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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16
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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17
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.Rainey PB, Remigi P, Farr AD, Lind PA. Darwin was right: where now for experimental evolution? Curr Opin Genet Dev 2017; 47:102-109. [DOI: 10.1016/j.gde.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 01/02/2023]
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18
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Fragmentation modes and the evolution of life cycles. PLoS Comput Biol 2017; 13:e1005860. [PMID: 29166656 PMCID: PMC5718564 DOI: 10.1371/journal.pcbi.1005860] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 12/06/2017] [Accepted: 10/31/2017] [Indexed: 11/19/2022] Open
Abstract
Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles. Mode of reproduction is a defining trait of all organisms, including colonial bacteria and multicellular organisms. To produce offspring, aggregates must fragment by splitting into two or more groups. The particular way that a given group fragments defines the life cycle of the organism. For instance, insect colonies can reproduce by splitting or by producing individuals that found new colonies. Similarly, some colonial bacteria propagate by fission or by releasing single cells, while others split in highly sophisticated ways; in multicellular organisms reproduction typically proceeds via a single-cell bottleneck phase. The space of possibilities for fragmentation is so vast that an exhaustive analysis seems daunting. Focusing on fragmentation modes of a simple kind we parametrise all possible modes of group fragmentation and identify those modes leading to the fastest population growth rate. Two kinds of life cycle dominate: one involving division into two equal size groups, and the other involving production of a unicellular propagule. The prevalence of these life cycles in nature is consistent with our null model and suggests that benefits accruing from population growth rate alone may have shaped the evolution of fragmentation mode.
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