Long term adaptation of a microbial population to a permanent metabolic constraint: overcoming thymineless death by experimental evolution of Escherichia coli

In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology

Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.

Does the Semiconservative Nature of DNA Replication Facilitate Coherent Phenotypic Diversity?

It has been clear for over sixty years that the principal method whereby cells replicate and segregate their DNA is semiconservative. It is much less clear why it should be like this rather than, say, conservative. Recently, evidence has accumulated that supports the hypothesis that one of the functions of the cell cycle is to generate phenotypically different daughter cells, even in nondifferentiating bacteria such as Escherichia coli Evidence has also accumulated that the bacterial phenotype is determined by the functioning of extended assemblies of macromolecules termed hyperstructures. One class of these hyperstructures is attached dynamically to a DNA strand by the coupling of transcription and translation. Previously, we proposed in the strand segregation model that one set of hyperstructures accompanies one parental strand into one daughter cell while another set of hyperstructures accompanies the other parental strand into the other daughter cell. This epigenetic mechanism results in daughter cells having different phenotypes. Here, I propose that one of the reasons why semiconservative replication has been selected is because it allows the generation of a population containing cells with very different growth rates even in steady-state conditions.

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

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.

A nanoliter microfluidic serial dilution bioreactor

Bacterial culture is a basic technique in both fundamental and applied microbiology. The excessive reagent consumption and laborious maintenance of bulk bioreactors for microbial culture have prompted the development of miniaturized on-chip bioreactors. With the minimal choice of two compartments (N = 2) and discrete time, periodic dilution steps, we realize a microfluidic bioreactor that mimics macroscopic serial dilution transfer culture. This device supports automated, long-term microbial cultures with a nanoliter-scale working volume and real-time monitoring of microbial populations at single-cell resolution. Because of the high surface-to-volume ratio, the device also operates as an effective biofilm-flow reactor to support cogrowth of planktonic and biofilm populations. We expect that such devices will open opportunities in many fields of microbiology.

Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion

One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the fundamental chemistry of life is the inclusion of amino acid building blocks beyond the canonical 20 (i.e. expanding the genetic code). This strategy would allow the transfer of numerous chemical functionalities and reactions from the synthetic laboratory into the cellular environment. Due to limitations in terms of both efficiency and practical applicability, state-of-the-art nonsense suppression- or frameshift suppression-based methods are less suitable for such engineering. Consequently, we set out to achieve this goal by sense codon emancipation, that is, liberation from its natural decoding function – a prerequisite for the reassignment of degenerate sense codons to a new 21st amino acid. We have achieved this by redesigning of several features of the post-transcriptional modification machinery which are directly involved in the decoding process. In particular, we report first steps towards the reassignment of 5797 AUA isoleucine codons in Escherichia coli using efficient tools for tRNA nucleotide modification pathway engineering.

Long-term diversity and genome adaptation of Acinetobacter baylyi in a minimal-medium chemostat

Laboratory-based evolution experiments on microorganisms that do not recombine frequently show two distinct phases: an initial rapid increase in fitness followed by a slower regime. To explore the population structure and the evolutionary tree in the later stages of adaptation, we evolved a very large population (∼3 × 10) of Acinetobacter baylyi bacteria for approximately 2,800 generations from a single clone. The population was maintained in a chemostat at a high dilution rate. Nitrate in limiting amount and as the sole nitrogen source was used as a selection pressure. Analysis via resequencing of genomes extracted from populations at different generations provides evidence that long-term diversity can be established in the chemostat in a very simple medium. To find out which biological parameters were targeted by adaptation, we measured the maximum growth rate, the nitrate uptake, and the resistance to starvation. Overall, we find that maximum growth rate could be a reasonably good proxy for fitness. The late slow adaptation is compatible with selection coefficients spanning a typical range of 10–10 per generation as estimated by resequencing, pointing to a possible subpopulations structuring.

Plasmids as scribbling pads for operon formation and propagation

Many bacterial genes are in operons and the process whereby operons are formed is therefore fundamental. To help elucidate this process, we propose in the Scribbling Pad hypothesis that bacteria have been constantly using plasmids for genetic experimentation and, in particular, for the construction of operons. This hypothesis simultaneously solves the problems of the creation of operons and the way operons are propagated. We cite results in the literature to support the hypothesis and make experimental predictions to test it.

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing-alias bioputing-has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating.

Bacterial physiology, regulation and mutational adaptation in a chemostat environment

The chemostat was devised over 50 years ago and rapidly adopted for studies of bacterial physiology and mutation. Despite the long history and earlier analyses, the complexity of events in continuous cultures is only now beginning to be resolved. The application of techniques for following regulatory and mutational changes and the identification of mutated genes in chemostat populations has provided new insights into bacterial behaviour. Inoculation of bacteria into a chemostat culture results in a population competing for a limiting amount of a particular resource. Any utilizable carbon source or ion can be a limiting nutrient and bacteria respond to limitation through a regulated nutrient-specific hunger response. In addition to transcriptional responses to nutrient limitation, a second regulatory influence in a chemostat culture is the reduced growth rate fixed by the dilution rate in individual experiments. Sub-maximal growth rates and hunger result in regulation involving sigma factors and alarmones like cAMP and ppGpp. Reduced growth rate also results in increased mutation frequencies. The combination of a strongly selective environment (where mutants able to compete for limiting nutrient have a major fitness advantage) and elevated mutation rates (both endogenous and through the secondary enrichment of mutators) results in a population that changes rapidly and persistently over many generations. Contrary to common belief, the chemostat environment is never in "steady state" with fixed bacterial characteristics usable for clean comparisons of physiological or regulatory states. Adding to the complexity, chemostat populations do not simply exhibit a succession of mutational sweeps leading to a dominant winner clone. Instead, within 100 generations large populations become heterogeneous and evolving bacteria adopt alternative, parallel fitness strategies. Transport physiology, metabolism and respiration, as well as growth yields, are highly diverse in chemostat-evolved bacteria. The rich assortment of changes in an evolving chemostat provides an excellent experimental system for understanding bacterial evolution. The adaptive radiation or divergence of populations into a collection of individuals with alternative solutions to the challenge of chemostat existence provides an ideal model system for testing evolutionary and ecological theories on adaptive radiations and the generation of bacterial diversity.

Development of a novel continuous culture device for experimental evolution of bacterial populations

The availability of a robust and reliable continuous culture apparatus that eliminates wall growth problems would lead to many applications in the microbial field, including allowing genetically engineered strains to recover high fitness, improving biodegradation strains, and predicting likely antibiotic resistance mechanisms. We describe the design and implementation of a novel automated continuous culture machine that can be used both in time-dependent mode (similar to a chemostat) and turbidostat modes, in which wall growth is circumvented through the use of a long, variably divisible tube of growth medium. This tube can be restricted with clamps to create a mobile growth chamber region in which static portions of the tube and the associated medium are replaced together at equal rates. To functionally test the device as a tool for re-adaptation of engineered strains, we evolved a strain carrying a highly deleterious deletion of Elongation Factor P, a gene involved in translation. In 200 generations over 2 weeks of dilution cycles, the evolved strain improved in generation time by a factor of three, with no contaminations and easy manipulation.

Clostridium cellulolyticum: model organism of mesophilic cellulolytic clostridia

Clostridium cellulolyticum ATCC 35319 is a non-ruminal mesophilic cellulolytic bacterium originally isolated from decayed grass. As with most truly cellulolytic clostridia, C. cellulolyticum possesses an extracellular multi-enzymatic complex, the cellulosome. The catalytic components of the cellulosome release soluble cello-oligosaccharides from cellulose providing the primary carbon substrates to support bacterial growth. As most cellulolytic bacteria, C. cellulolyticum was initially characterised by limited carbon consumption and subsequent limited growth in comparison to other saccharolytic clostridia. The first metabolic studies performed in batch cultures suggested nutrient(s) limitation and/or by-product(s) inhibition as the reasons for this limited growth. In most recent investigations using chemostat cultures, metabolic flux analysis suggests a self-intoxication of bacterial metabolism resulting from an inefficiently regulated carbon flow. The investigation of C. cellulolyticum physiology with cellobiose, as a model of soluble cellodextrin, and with pure cellulose, as a carbon source more closely related to lignocellulosic compounds, strengthen the idea of a bacterium particularly well adapted, and even restricted, to a cellulolytic lifestyle. The metabolic flux analysis from continuous cultures revealed that (i) in comparison to cellobiose, the cellulose hydrolysis by the cellulosome introduces an extra regulation of entering carbon flow resulting in globally lower metabolic fluxes on cellulose than on cellobiose, (ii) the glucose 1-phosphate/glucose 6-phosphate branch point controls the carbon flow directed towards glycolysis and dissipates carbon excess towards the formation of cellodextrins, glycogen and exopolysaccharides, (iii) the pyruvate/acetyl-CoA metabolic node is essential to the regulation of electronic and energetic fluxes. This in-depth analysis of C. cellulolyticum metabolism has permitted the first attempt to engineer metabolically a cellulolytic microorganism.

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

Cells must abide by a number of constraints. The environmental constrains of cellular behavior and physicochemical limitations affect cellular processes. To regulate and adapt their functions, cells impose constraints on themselves. Enumerating, understanding, and applying these constraints leads to a constraints-based modeling formalism that has been helpful in converting conceptual models to computational models in biology. The continued success of the constraints-based approach depends upon identification and incorporation of new constraints to more accurately define cellular capabilities. This review considers constraints in terms of environmental, physicochemical, and self-imposed regulatory and evolutionary constraints with the purpose of refining current constraints-based models of cell phenotype.

Artificially ambiguous genetic code confers growth yield advantage

A primitive genetic code is thought to have encoded statistical, ambiguous proteins in which more than one amino acid was inserted at a given codon. The relative vitality of organisms bearing ambiguous proteins and the kinds of pressures that forced development of the highly specific modern genetic code are unknown. Previous work demonstrated that, in the absence of selective pressure, enforced ambiguity in cells leads to death or to sequence reversion to eliminate the ambiguous phenotype. Here, we report the creation of a nonreverting strain of bacteria that produced statistical proteins. Ablating the editing activity of isoleucyl-tRNA synthetase resulted in an ambiguous code in which, through supplementation of a limited supply of isoleucine with an alternative amino acid that was noncoding, the mutant generating statistical proteins was favored over the wild-type isogenic strain. Such organisms harboring statistical proteins could have had an enhanced adaptive capacity and could have played an important role in the early development of living systems.

Group I aptazymes as genetic regulatory switches

BACKGROUND

Allosteric ribozymes (aptazymes) that have extraordinary activation parameters have been generated in vitro by design and selection. For example, hammerhead and ligase ribozymes that are activated by small organic effectors and protein effectors have been selected from random sequence pools appended to extant ribozymes. Many ribozymes, especially self-splicing introns, are known control gene regulation or viral replication in vivo. We attempted to generate Group I self-splicing introns that were activated by a small organic effector, theophylline, and to show that such Group I aptazymes could mediate theophylline-dependent splicing in vivo.

RESULTS

By appending aptamers to the Group I self-splicing intron, we have generated a Group I aptazyme whose in vivo splicing is controlled by exogenously added small molecules. Substantial differences in gene regulation could be observed with compounds that differed by as little as a single methyl group. The effector-specificity of the Group I aptazyme could be rationally engineered for new effector molecules.

CONCLUSION

Group I aptazymes may find applications as genetic regulatory switches for generating conditional knockouts at the level of mRNA or for developing economically viable gene therapies.

Bacteriophage resistance of a deltathyA mutant of Lactococcus lactis blocked in DNA replication

The thyA gene, which encodes thymidylate synthase (TS), of Lactococcus lactis CHCC373 was sequenced, including the upstream and downstream regions. We then deleted part of thyA by gene replacement. The resulting strain, MBP71 deltathyA, was devoid of TS activity, and in media without thymidine, such as milk, there was no detectable dTTP pool in the cells. Hence, DNA replication was abolished, and acidification by MBP71 was completely unaffected by the presence of nine different phages tested at a multiplicity of infection (MOI) of 0.1. Nonreplicating MBP71 must be inoculated at a higher level than CHCC373 to achieve a certain pH within a specified time. For a pH of 5.2 to be reached in 6 h, the inoculation level of MBP71 must be 17-fold higher than for CHCC373. However, by adding a limiting amount of thymidine this could be lowered to just 5-fold the normal amount, while acidification was unaffected with MBP71 up to an MOI of 0.01. It was found that nonreplicating MBP71 produced largely the same products as CHCC373, though the acetaldehyde production of the former was higher.