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Romeyer Dherbey J, Parab L, Gallie J, Bertels F. Stepwise evolution of E. coli C and ΦX174 reveals unexpected lipopolysaccharide (LPS) diversity. Mol Biol Evol 2023:msad154. [PMID: 37399035 PMCID: PMC10368449 DOI: 10.1093/molbev/msad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/21/2023] [Accepted: 06/28/2023] [Indexed: 07/04/2023] Open
Abstract
Phage therapy is a promising method for the treatment of multi-drug-resistant bacterial infections. However, its long-term efficacy depends on understanding the evolutionary effects of the treatment. Current knowledge of such evolutionary effects is lacking, even in well-studied systems. We used the bacterium Escherichia coli C and its bacteriophage ΦX174, which infects cells using host lipopolysaccharide (LPS) molecules. We first generated 31 bacterial mutants resistant to ΦX174 infection. Based on the genes disrupted by these mutations, we predicted that these E. coli C mutants collectively produce eight unique LPS structures. We then developed a series of evolution experiments to select for ΦX174 mutants capable of infecting the resistant strains. During phage adaptation, we distinguished two types of phage resistance: one that was easily overcome by ΦX174 with few mutational steps ("easy" resistance), and one that was more difficult to overcome ("hard" resistance). We found that increasing the diversity of the host and phage populations could accelerate the adaptation of phage ΦX174 to overcome the hard resistance phenotype. From these experiments, we isolated 16 ΦX174 mutants that, together, can infect all 31 initially resistant E. coli C mutants. Upon determining the infectivity profiles of these 16 evolved phages, we uncovered 14 distinct profiles. Given that only eight profiles are anticipated if the LPS predictions are correct, our findings highlight that the current understanding of LPS biology is insufficient to accurately forecast the evolutionary outcomes of bacterial populations infected by phage.
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Affiliation(s)
- Jordan Romeyer Dherbey
- Department Microbial Population Biology, Research Group Microbial Molecular Evolution, Max Planck Institute for Evolutionary Biology, Plön (24306), Germany
| | - Lavisha Parab
- Department Microbial Population Biology, Research Group Microbial Molecular Evolution, Max Planck Institute for Evolutionary Biology, Plön (24306), Germany
| | - Jenna Gallie
- Department for Evolutionary Theory, Research Group Microbial Evolutionary Dynamics, Max Planck Institute for Evolutionary Biology, Plön (24306), Germany
| | - Frederic Bertels
- Department Microbial Population Biology, Research Group Microbial Molecular Evolution, Max Planck Institute for Evolutionary Biology, Plön (24306), Germany
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Abstract
The landscape paradigm is revisited in the light of evolution in simple systems. A brief overview of different classes of fitness landscapes is followed by a more detailed discussion of the RNA model, which is currently the only evolutionary model that allows for a comprehensive molecular analysis of a fitness landscape. Neutral networks of genotypes are indispensable for the success of evolution. Important insights into the evolutionary mechanism are gained by considering the topology of sequence and shape spaces. The dynamic concept of molecular quasispecies is viewed in the light of the landscape paradigm. The distribution of fitness values in state space is mirrored by the population structures of mutant distributions. Two classes of thresholds for replication error or mutations are important: (i) the-conventional-genotypic error threshold, which separates ordered replication from random drift on neutral networks, and (ii) a phenotypic error threshold above which the molecular phenotype is lost. Empirical landscapes are reviewed and finally, the implications of the landscape concept for virus evolution are discussed.
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Affiliation(s)
- Peter Schuster
- Institut für Theoretische Chemie der Universität Wien, Währingerstraße 17, 1090, Wien, Austria.
| | - Peter F Stadler
- Institut für Informatik der Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.,The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Hallgrimsson B, Green RM, Katz DC, Fish JL, Bernier FP, Roseman CC, Young NM, Cheverud JM, Marcucio RS. The developmental-genetics of canalization. Semin Cell Dev Biol 2018; 88:67-79. [PMID: 29782925 DOI: 10.1016/j.semcdb.2018.05.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 10/16/2022]
Abstract
Canalization, or robustness to genetic or environmental perturbations, is fundamental to complex organisms. While there is strong evidence for canalization as an evolved property that varies among genotypes, the developmental and genetic mechanisms that produce this phenomenon are very poorly understood. For evolutionary biology, understanding how canalization arises is important because, by modulating the phenotypic variation that arises in response to genetic differences, canalization is a determinant of evolvability. For genetics of disease in humans and for economically important traits in agriculture, this subject is important because canalization is a potentially significant cause of missing heritability that confounds genomic prediction of phenotypes. We review the major lines of thought on the developmental-genetic basis for canalization. These fall into two groups. One proposes specific evolved molecular mechanisms while the other deals with robustness or canalization as a more general feature of development. These explanations for canalization are not mutually exclusive and they overlap in several ways. General explanations for canalization are more likely to involve emergent features of development than specific molecular mechanisms. Disentangling these explanations is also complicated by differences in perspectives between genetics and developmental biology. Understanding canalization at a mechanistic level will require conceptual and methodological approaches that integrate quantitative genetics and developmental biology.
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Affiliation(s)
- Benedikt Hallgrimsson
- Dept. of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Rebecca M Green
- Dept. of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - David C Katz
- Dept. of Cell Biology & Anatomy, Alberta Children's Hospital Research Institute and McCaig Bone and Joint Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jennifer L Fish
- Dept. of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Francois P Bernier
- Dept of Medical Genetics, Alberta Children's Hospital Research Institute Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Charles C Roseman
- Dept. of Animal Biology, University of Illinois Urbana Champaign, Urbana, IL, 61801, USA
| | - Nathan M Young
- Dept. of Orthopaedic Surgery, School of Medicine, University of California San Francisco, San Francisco, CA, 94110, USA
| | - James M Cheverud
- Dept. of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Ralph S Marcucio
- Dept. of Orthopaedic Surgery, School of Medicine, University of California San Francisco, San Francisco, CA, 94110, USA.
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