The principle of uncertainty in biology: Will machine learning/artificial intelligence lead to the end of mechanistic studies?

Molecular Biology has long tried to discover mechanisms, considering that unless we understand the principles, we cannot develop applications. Now machine learning and artificial intelligence enable direct leaps to application without understanding the principles. Will this herald a decline in mechanistic studies?

Genome-wide protein-DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase

DNA-protein interactions are central to fundamental cellular processes, yet widely implemented technologies for measuring these interactions on a genome scale in bacteria are laborious and capture only a snapshot of binding events. We devised a facile method for mapping DNA-protein interaction sites in vivo using the double-stranded DNA-specific cytosine deaminase toxin DddA. In 3D-seq (DddA-sequencing), strains containing DddA fused to a DNA-binding protein of interest accumulate characteristic mutations in DNA sequence adjacent to sites occupied by the DNA-bound fusion protein. High-depth sequencing enables detection of sites of increased mutation frequency in these strains, yielding genome-wide maps of DNA-protein interaction sites. We validated 3D-seq for four transcription regulators in two bacterial species, Pseudomonas aeruginosa and Escherichia coli. We show that 3D-seq offers ease of implementation, the ability to record binding event signatures over time and the capacity for single-cell resolution.

Molecular biology for green recovery-A call for action

Molecular biology holds a vast potential for tackling climate change and biodiversity loss. Yet, it is largely absent from the current strategies. We call for a community-wide action to bring molecular biology to the forefront of climate change solutions.

Automated design and implementation of a NOR gate in Pseudomonas putida

Boolean NOR gates have been widely implemented in Escherichia coli as transcriptional regulatory devices for building complex genetic circuits. Yet, their portability to other bacterial hosts/chassis is generally hampered by frequent changes in the parameters of the INPUT/OUTPUT response functions brought about by new genetic and biochemical contexts. Here, we have used the circuit design tool CELLO for assembling a NOR gate in the soil bacterium and the metabolic engineering platform Pseudomonas putida with components tailored for E. coli. To this end, we capitalized on the functional parameters of 20 genetic inverters for each host and the resulting compatibility between NOT pairs. Moreover, we added to the gate library three inducible promoters that are specific to P. putida, thus expanding cross-platform assembly options. While the number of potential connectable inverters decreased drastically when moving the library from E. coli to P. putida, the CELLO software was still able to find an effective NOR gate in the new chassis. The automated generation of the corresponding DNA sequence and in vivo experimental verification accredited that some genetic modules initially optimized for E. coli can indeed be reused to deliver NOR logic in P. putida as well. Furthermore, the results highlight the value of creating host-specific collections of well-characterized regulatory inverters for the quick assembly of genetic circuits to meet complex specifications.

MIXed plastics biodegradation and UPcycling using microbial communities: EU Horizon 2020 project MIX-UP started January 2020

This article introduces the EU Horizon 2020 research project MIX-UP, "Mixed plastics biodegradation and upcycling using microbial communities". The project focuses on changing the traditional linear value chain of plastics to a sustainable, biodegradable based one. Plastic mixtures contain five of the top six fossil-based recalcitrant plastics [polyethylene (PE), polyurethane (PUR), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS)], along with upcoming bioplastics polyhydroxyalkanoate (PHA) and polylactate (PLA) will be used as feedstock for microbial transformations. Consecutive controlled enzymatic and microbial degradation of mechanically pre-treated plastics wastes combined with subsequent microbial conversion to polymers and value-added chemicals by mixed cultures. Known plastic-degrading enzymes will be optimised by integrated protein engineering to achieve high specific binding capacities, stability, and catalytic efficacy towards a broad spectrum of plastic polymers under high salt and temperature conditions. Another focus lies in the search and isolation of novel enzymes active on recalcitrant polymers. MIX-UP will formulate enzyme cocktails tailored to specific waste streams and strives to enhance enzyme production significantly. In vivo and in vitro application of these cocktails enable stable, self-sustaining microbiomes to convert the released plastic monomers selectively into value-added products, key building blocks, and biomass. Any remaining material recalcitrant to the enzymatic activities will be recirculated into the process by physicochemical treatment. The Chinese-European MIX-UP consortium is multidisciplinary and industry-participating to address the market need for novel sustainable routes to valorise plastic waste streams. The project's new workflow realises a circular (bio)plastic economy and adds value to present poorly recycled plastic wastes where mechanical and chemical plastic recycling show limits.

Refactoring the Conjugation Machinery of Promiscuous Plasmid RP4 into a Device for Conversion of Gram-Negative Isolates to Hfr Strains

Chromosomal exchange and subsequent recombination of the cognate DNA between bacteria was one of the most useful genetic tools (e.g., Hfr strains) for genetic analyses of E. coli before the genomic era. In this paper, yeast assembly has been used to recruit the conjugation machinery of environmentally promiscuous RP4 plasmid into a minimized, synthetic construct that enables transfer of chromosomal segments between donor/recipient strains of P. putida KT2440 and potentially many other Gram-negative bacteria. The synthetic device features [i] a R6K suicidal plasmid backbone, [ii] a mini-Tn5 transposon vector, and [iii] the minimal set of genes necessary for active conjugation (RP4 Tra1 and Tra2 clusters) loaded as cargo in the mini-Tn5 mobile element. Upon insertion of the transposon in different genomic locations, the ability of P. putida-TRANS (transference of RP4-activated nucleotide segments) donor strains to mobilize genomic stretches of DNA into neighboring bacteria was tested. To this end, a P. putida double mutant ΔpyrF (uracil auxotroph) Δedd (unable to grow on glucose) was used as recipient in mating experiments, and the restoration of the pyrF+/edd+ phenotypes allowed for estimation of chromosomal transfer efficiency. Cells with the inserted transposon behaved in a manner similar to Hfr-like strains and were able to transfer up to 23% of their genome at frequencies close to 10-6 exconjugants per recipient cell. The hereby described TRANS device not only expands the molecular toolbox for P. putida, but it also enables a suite of genomic manipulations which were thus far only possible with domesticated laboratory strains and species.

Low CyaA expression and anti-cooperative binding of cAMP to CRP frames the scope of the cognate regulon of Pseudomonas putida

Although the soil bacterium Pseudomonas putida KT2440 bears a bona fide adenylate cyclase gene (cyaA), intracellular concentrations of 3',5'-cyclic adenosine monophosphate (cAMP) are barely detectable. By using reporter technology and direct quantification of cAMP under various conditions, we show that such low levels of the molecule stem from the stringent regulation of its synthesis, efflux and degradation. Poor production of cAMP was the result of inefficient translation of cyaA mRNA. Moreover, deletion of the cAMP-phosphodiesterase pde gene led to intracellular accumulation of the cyclic nucleotide, exposing an additional cause of cAMP drain in vivo. But even such low levels of the signal sustained activation of promoters dependent on the cAMP-receptor protein (CRP). Genetic and biochemical evidence indicated that the phenomenon ultimately rose from the unusual binding parameters of cAMP to CRP. This included an ultratight cAMP-Crp_{P. putida} affinity (K_D of 45.0 ± 3.4 nM) and an atypical 1:1 effector/dimer stoichiometry that obeyed an infrequent anti-cooperative binding mechanism. It thus seems that keeping the same regulatory parts and their relational logic but changing the interaction parameters enables genetic devices to take over entirely different domains of the functional landscape.

Contextual dependencies expand the re-usability of genetic inverters

The implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, the context in which the circuit performs is crucial for its outcome. We characterise 20 genetic NOT logic gates in up to 7 bacterial-based contexts each, to generate 135 different functions. The contexts we focus on are combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each gate shows seven different dynamic behaviours, depending on the context. That is, gates can be fine-tuned by changing only contextual parameters, thus improving the compatibility between gates. Finally, we analyse portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expands functionality, and advocate for considering context as a fundamental design parameter.

Concomitant prediction of environmental fate and toxicity of chemical compounds

The environmental fate of many functional molecules that are produced on a large scale as precursors or as additives to specialty goods (plastics, fibers, construction materials, etc.), let alone those synthesized by the pharmaceutical industry, is generally unknown. Assessing their environmental fate is crucial when taking decisions on the manufacturing, handling, usage, and release of these substances, as is the evaluation of their toxicity in humans and other higher organisms. While this data are often hard to come by, the experimental data already available on the biodegradability and toxicity of many unusual compounds (including genuinely xenobiotic molecules) make it possible to develop machine learning systems to predict these features. As such, we have created a predictor of the "risk" associated with the use and release of any chemical. This new system merges computational methods to predict biodegradability with others that assess biological toxicity. The combined platform, named BiodegPred (https://sysbiol.cnb.csic.es/BiodegPred/), provides an informed prognosis of the chance a given molecule can eventually be catabolized in the biosphere, as well as of its eventual toxicity, all available through a simple web interface. While the platform described does not give much information about specific degradation kinetics or particular biodegradation pathways, BiodegPred has been instrumental in anticipating the probable behavior of a large number of new molecules (e.g. antiviral compounds) for which no biodegradation data previously existed.

SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards

Robust synthetic biology applications rely heavily on the design and assembly of DNA parts with specific functionalities based on engineering principles. However, the assembly standards adopted by different communities vary considerably, thus limiting the interoperability of parts, vectors and methods. We hereby introduce the SEVA 3.1 platform consisting of the SEVA 3.1 vectors and the Golden Gate-based 'SevaBrick Assembly'. This platform enables the convergence of standard processes between the SEVA platform, the BioBricks and the Type IIs-mediated DNA assemblies to reduce complexity and optimize compatibility between parts and methods. It features a wide library of cloning vectors along with a core set of standard SevaBrick primers that allow multipart assembly and exchange of short functional genetic elements (promoters, RBSs) with minimal cloning and design effort. As proof of concept, we constructed, among others, multiple sfGFP expression vectors under the control of eight RBSs, eight promoters and four origins of replication as well as an inducible four-gene operon expressing the biosynthetic genes for the black pigment proviolacein. To demonstrate the interoperability of the SEVA 3.1 vectors, all constructs were characterized in both Pseudomonas putida and Escherichia coli. In summary, the SEVA 3.1 platform optimizes compatibility and modularity of inserts and backbones with a cost- and time-friendly DNA assembly method, substantially expanding the toolbox for successful synthetic biology applications in Gram-negative bacteria.

Synthetic Biology for Terraformation Lessons from Mars, Earth, and the Microbiome

What is the potential for synthetic biology as a way of engineering, on a large scale, complex ecosystems? Can it be used to change endangered ecological communities and rescue them to prevent their collapse? What are the best strategies for such ecological engineering paths to succeed? Is it possible to create stable, diverse synthetic ecosystems capable of persisting in closed environments? Can synthetic communities be created to thrive on planets different from ours? These and other questions pervade major future developments within synthetic biology. The goal of engineering ecosystems is plagued with all kinds of technological, scientific and ethic problems. In this paper, we consider the requirements for terraformation, i.e., for changing a given environment to make it hospitable to some given class of life forms. Although the standard use of this term involved strategies for planetary terraformation, it has been recently suggested that this approach could be applied to a very different context: ecological communities within our own planet. As discussed here, this includes multiple scales, from the gut microbiome to the entire biosphere.

Omnipresent Maxwell's demons orchestrate information management in living cells

The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information‐managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy‐efficient way that is vastly better than our contemporary computers.

Toward unrestricted use of public genomic data

Publication interests should not limit access to public data

An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth

The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.

The contribution of microbial biotechnology to sustainable development goals

The signature and almost unique characteristic of microbial technology is the exceptional diversity of applications it can address, and the exceptional range of human activities and needs to which it is and can be applied. Precisely because sustainability goals have very diverse and complex components and requirements, microbial technology has the ability to contribute substantively on many levels in many arenas to global efforts to achieve sustainability. Indeed, microbial technology could be viewed as a unifying element in our progress towards sustainability.

The contribution of microbial biotechnology to economic growth and employment creation

Our communication discusses the profound impact of bio-based economies - in particular microbial biotechnologies - on SDG 8: Promote sustained, inclusive and sustainable economic growth, full and productive employment and decent work for all. A bio-based economy provides significant potential for improving labour supply, education and investment, and thereby for substantially increasing the demographic dividend. This, in turn, improves the sustainable development of economies.

Nitrogen regulation of the xyl genes of Pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil

The nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by Pseudomonas putida. Nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m‐xylene in soil, the natural habitat of this bacterium. To address this issue, we have developed a test‐tube‐to‐soil model system that exposes the end‐effects of remediation practices influencing gene expression of P. putida mt‐2. We found that NO₃⁻ compared with NH₄⁺ had a stimulating effect on xyl gene expression in pure culture as well as in soil, and that this stimulation was translated into increased m‐xylene mineralization in soil. Furthermore, expression analysis of the nitrogen‐regulated genes amtB and gdhA allowed us to monitor nitrogen sensing status in both experimental systems. Hence, for nitrogen sources, regulatory patterns that emerge in soil reflect those observed in liquid cultures. The current study shows how distinct regulatory traits can lead to discrete environmental consequences; and it underpins that attempts to improve bioremediation by nitrogen amendment should integrate knowledge on their effects on growth and on catabolic gene regulation under natural conditions.

The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42

Some strains of the soil bacterium Pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. Despite availability of many genetic tools for this microorganism, genomic editing of the cell factory P. putida EM42 (a derivative of reference strain KT2440) is still a time-consuming endeavor. In this work we have investigated the in vivo activity of the Ssr protein encoded by the open reading frame T1E_1405 from Pseudomonas putida DOT-T1E, a plausible functional homologue of the β protein of the Red recombination system of λ phage of Escherichia coli. A test based on the phenotypes of pyrF mutants of P. putida (the yeast's URA3 ortholog) was developed for quantifying the ability of Ssr to promote invasion of the genomic DNA replication fork by synthetic oligonucleotides. The efficiency of the process was measured by monitoring the inheritance of the changes entered into pyrF by oligonucleotides bearing mutated sequences. Ssr fostered short and long genomic deletions/insertions at considerable frequencies as well as single-base swaps not affected by mismatch repair. These results not only demonstrate the feasibility of recombineering in P. putida, but they also enable a suite of multiplexed genomic manipulations in this biotechnologically important bacterium.

Tn7-Based Device for Calibrated Heterologous Gene Expression in Pseudomonas putida

The soil bacterium Pseudomonas putida is increasingly attracting considerable interest as a platform for advanced metabolic engineering through synthetic biology approaches. However, genomic context, gene copy number, and transcription/translation interplay often introduce considerable uncertainty to the design of reliable genetic constructs. In this work, we have established a standardized heterologous expression device in which the promoter strength is the only variable; the remaining parameters of the flow have stable default values. To this end, we tailored a mini-Tn7 delivery transposon vector that inserts the constructs in a single genomic locus of P. putida's chromosome. This was then merged with a promoter insertion site, an unvarying translational coupler, and a downstream location for placing the gene(s) of interest under fixed assembly rules. This arrangement was exploited to benchmark a collection of synthetic promoters with low transcriptional noise in this bacterial host. Growth experiments and flow cytometry with single-copy promoter-GFP constructs revealed a robust, constitutive behavior of these promoters, whose strengths and properties could be faithfully compared. This standardized expression device significantly extends the repertoire of tools available for reliable metabolic engineering and other genetic enhancements of P. putida.

Pipelines for New Chemicals: a strategy to create new value chains and stimulate innovation-based economic revival in Southern European countries

Countries of Southern Europe are currently suffering from severe socio-economic pain resulting from high debt levels and austerity measures which constrain investment in innovation-based recovery strategies that are essential for entry into a long-term sustainable period of increasing employment and wealth creation. Young university-educated people are particularly innovative, and hence vital to the development of such strategies, but employment opportunities are poor and many are forced to seek employment that neither profits from their training nor satisfies their justified career expectations, or to emigrate. They are the 'lost generation'. A strategy is proposed here for the creation of Pipelines for New Chemicals, national centre-network partnerships for the discovery-synthesis of new chemicals obtained though harvesting new biological diversity, and their exploitation to develop new medicines, agrochemicals, materials, and other products and applications. The goal is to create new regional motors of economic growth and development, by harnessing the knowledge, motivation and innovation potential of the excellently educated young people of Europe to catalyse the development of new small, medium and large enterprises centred around novel chemicals, and the value chains that will evolve with them, and thereby develop a powerful sector of sustainable growth in employment and social and economic prosperity in Southern Europe.

Engineering multicellular logic in bacteria with metabolic wires

Aromatic biodegradation pathways of environmental bacteria are vast sources of matching trios of enzymes, substrates and regulators that can be refactored to run logic operations through cell-to-cell communication. As a proof of concept, the connection between two Pseudomonas putida strains using benzoic acid as the wiring molecule is presented. In this system, a sender strain harboring the TOL pathway for biodegradation of aromatics processed toluene as input and generated benzoate as the output signal. Diffusion of such metabolic intermediate to the medium was then sensed by a second strain (the receiver) that used benzoate as input for a new logic gate producing a visual output (i.e., light emission). The setup was functional irrespective of whether sender and receiver cells were in direct contact or in liquid culture. These results highlight the potential of environmental metabolic pathways as sources of building blocks for the engineering of multicellular logic in prokaryotic systems.

Towards functional orthogonalisation of protein complexes: individualisation of GroEL monomers leads to distinct quasihomogeneous single rings

The essential molecular chaperonin GroEL is an example of a functionally highly versatile cellular machine with a wide variety of in vitro applications ranging from protein folding to drug release. Directed evolution of new functions for GroEL is considered difficult, due to its structure as a complex homomultimeric double ring and the absence of obvious molecular engineering strategies. In order to investigate the potential to establish an orthogonal GroEL system in Escherichia coli, which might serve as a basis for GroEL evolution, we first successfully individualised groEL genes by inserting different functional peptide tags into a robustly permissive site identified by transposon mutagenesis. These peptides allowed fundamental aspects of the intracellular GroEL complex stoichiometry to be studied and revealed that GroEL single-ring complexes, which assembled in the presence of several functionally equivalent but biochemically distinct monomers, each consist almost exclusively of only one type of monomer. At least in the case of GroEL, individualisation of monomers thus leads to individualisation of homomultimeric protein complexes, effectively providing the prerequisites for evolving an orthogonal intracellular GroEL folding machine.

Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system

A dual promoter probe system based on a tandem bi-cistronic GFP-luxCDABE reporter cassette is described and implemented. This system is assembled in two synthetic, modular, broad-host range plasmids based on pBBR1 and RK2 origins of replication, allowing its utilization in an extensive number of gram-negative bacteria. We analyze the performance of this dual cassette in two hosts, Escherichia coli and Pseudomonas putida, by examining the induction properties of the lacI(q)-Ptrc expression system in the first host and the Pb promoter of the benzoate degradation pathway in the second host. By quantifying the bioluminescence signal produced through the expression of the lux genes, we explore the dynamic range of induction for the two systems (Ptrc-based and Pb-based) in response to the two inducers. In addition, by quantifying the fluorescence signals produced by GFP expression, we were able to monitor the single-cell expression profile and to explore stochasticity of the same two promoters by flow cytometry. The results provided here demonstrate the power of the dual GFP-luxCDABE cassette as a new, single-step tool to assess promoter properties at both the population and single-cell levels in gram-negative bacteria.

Increasing signal specificity of the TOL network of Pseudomonas putida mt-2 by rewiring the connectivity of the master regulator XylR

Prokaryotic transcription factors (TFs) that bind small xenobiotic molecules (e.g., TFs that drive genes that respond to environmental pollutants) often display a promiscuous effector profile for analogs of the bona fide chemical signals. XylR, the master TF for expression of the m-xylene biodegradation operons encoded in the TOL plasmid pWW0 of Pseudomonas putida, responds not only to the aromatic compound but also, albeit to a lesser extent, to many other aromatic compounds, such as 3-methylbenzylalcohol (3MBA). We have examined whether such a relaxed regulatory scenario can be reshaped into a high-capacity/high-specificity regime by changing the connectivity of this effector-sensing TF within the rest of the circuit rather than modifying XylR structure itself. To this end, the natural negative feedback loop that operates on xylR transcription was modified with a translational attenuator that brings down the response to 3MBA while maintaining the transcriptional output induced by m-xylene (as measured with a luxCDABE reporter system). XylR expression was then subject to a positive feedback loop in which the TF was transcribed from its own target promoters, each known to hold different input/output transfer functions. In the first case (xylR under the strong promoter of the upper TOL operon, Pu), the reporter system displayed an increased transcriptional capacity in the resulting network for both the optimal and the suboptimal XylR effectors. In contrast, when xylR was expressed under the weaker Ps promoter, the resulting circuit unmistakably discriminated m-xylene from 3MBA. The non-natural connectivity engineered in the network resulted both in a higher promoter activity and also in a much-increased signal-to-background ratio. These results indicate that the working regimes of given genetic circuits can be dramatically altered through simple changes in the way upstream transcription factors are self-regulated by positive or negative feedback loops.

It is generally taken for granted that promoters regulated by transcriptional factors (TFs) that respond to small molecules control their specificity to given effectors by tightening or relaxing the intrinsic dual interaction between the TF and the particular inducer. One such promoter is Pu, which drives expression of an operon for the biodegradation of m-xylene by the soil bacterium P. putida mt-2. While XylR, the chief TF of this system, binds this substrate and activates Pu, the same regulator responds, to a lesser extent, to 3-methylbenzylalcohol and thus also activates the promoter. This work provides evidence that such natural effector promiscuity of the system can be altogether suppressed by replacing the naturally occurring negative autoregulation loop that governs XylR expression with an equivalent positive feedback loop. Based on this result, we argue that signal specificity of a given regulatory device depends not only on the TF involved but also on TF connectivity to upstream signals and downstream targets.

COVER: a priori estimation of coverage for metagenomic sequencing

In any metagenomic project, the coverage obtained for each particular species depends on its abundance. This makes it difficult to determine a priori the amount of DNA sequencing necessary to obtain a high coverage for the dominant genomes in an environment. To aid the design of metagenomic sequencing projects, we have developed COVER, a web-based tool that allows the estimation of the coverage achieved for each species in an environmental sample. COVER uses a set of 16S rRNA sequences to produce an estimate of the number of operational taxonomic units (OTUs) in the sample, provides a taxonomic assignment for them, estimates their genome sizes and, most critically, corrects for the number of unobserved OTUs. COVER then calculates the amount of sequencing needed to achieve a given goal. Our tests and simulations indicate that the results obtained through COVER are in very good agreement with the experimental results.

A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria

Here, we describe a bicistronic reporter system for the analysis of promoter activity in a variety of Gram-negative bacteria at both the population and single-cell levels. This synthetic genetic tool utilizes an artificial operon comprising the gfp and lacZ genes that are assembled in a suicide vector, which is integrated at specific sites within the chromosome of the target bacterium, thereby creating a monocopy reporter system. This tool was instrumental for the complete in vivo characterization of two promoters, Pb and Pc, that drive the expression of the benzoate and catechol degradation pathways, respectively, of the soil bacterium Pseudomonas putida KT2440. The parameterization of these promoters in a population (using β-galactosidase assays) and in single cells (using flow cytometry) was necessary to examine the basic numerical features of these systems, such as the basal and maximal levels and the induction kinetics in response to an inducer (benzoate). Remarkably, GFP afforded a view of the process at a much higher resolution compared with standard lacZ tests; changes in fluorescence faithfully reflected variations in the transcriptional regimes of individual bacteria. The broad host range of the vector/reporter platform is an asset for the characterization of promoters in different bacteria, thereby expanding the diversity of genomic chasses amenable to Synthetic Biology methods.

The ten grand challenges of synthetic life

The construction of artificial life is one of the main scientific challenges of the Synthetic Biology era. Advances in DNA synthesis and a better understanding of regulatory processes make the goal of constructing the first artificial cell a realistic possibility. This would be both a fundamental scientific milestone and a starting point of a vast range of applications, from biofuel production to drug design. However, several major issues might hamper the objective of achieving an artificial cell. From the bottom-up to the selection-based strategies, this work encompasses the ten grand challenges synthetic biologists will have to be aware of in order to cope with the task of creating life in the lab.

EnvMine: a text-mining system for the automatic extraction of contextual information

BACKGROUND

For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.

RESULTS

EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.

CONCLUSION

EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.

Uncoupling of choline-O-sulphate utilization from osmoprotection in Pseudomonas putida

The genomic context of the recognized bet genes for choline-O-sulphate (COS) utilization in Pseudomonas putida KT2440 is such that betC (choline sulphatase) lies adjacent to an ATP-binding cassette transporter and a LysR type regulator, but well away from betBA, encoding enzymes for transformation of choline into glycine betaine. The consequences of such genetic layout of the functions for COS metabolism have been examined with a suite of genetic and biochemical approaches. An early clue of the utilities of the betencoded products was exposed by the phenotypes of a betC deletion. This mutant still accumulated intact COS but failed to use this compound as carbon or nitrogen source. Furthermore, betC expression was downregulated at high salt concentrations, showing that the principal role of this gene lied in COS metabolism, not in osmoprotection. In contrast, the betBA genes were required for choline transformation into the highly effective compatible solute glycine betaine (and the concomitant endurance to high salt) and also for its utilization as carbon or nitrogen source. Thus, unlike in the cases of Bacillus subtilis and Sinorhizobium meliloti, betC is unrelated to osmoprotection in Pseudomonas putida while the betBA genes are required for both betaine synthesis and tolerance to high osmotic pressure.

Distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from Spain

Hexachlorocyclohexane (HCH)-degrading bacteria are believed to mediate natural attenuation of HCH contamination and have potential for active bioremediation processes. This study addressed the very limited understanding of the distribution, diversity and substrate specificity of such bacteria from 13 soil samples, varying in levels of HCH contamination, from four sites in Spain. Hexachlorocyclohexane removal occurred in 16 of 36 enrichment cultures. Hexachlorocyclohexane-degrading populations were clearly associated with HCH-contaminated soils, and populations growing on the delta-HCH isomer were only found in soil contaminated with delta-HCH. beta-Hexachlorocyclohexane was persistent in enrichment cultures, and there was no evidence for populations growing on beta-HCH. From alpha- and gamma-HCH enrichment cultures, nine HCH-degrading isolates were obtained, which were all Sphingomonas spp. Attempts to isolate organisms from delta-HCH enrichment cultures failed. None of the isolates grew on HCH as a sole organic substrate in pure culture. All isolates degraded alpha- and gamma-HCH, and most degraded beta-HCH. delta-Hexachlorocyclohexane inhibited growth of most isolates, but could be degraded by cell suspensions of at least four strains. Denaturing gradient gel electrophoresis indicated that the isolates represented predominant populations in the enrichment cultures, but additional predominant populations, including some Pseudomonas spp., could not be isolated.

Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray

Microarray technology was used to characterize and compare hexachlorocyclohexane (HCH) contaminated soils from Spain. A library of 2,290 hypervariable 16S rRNA gene sequences was prepared with serial analysis of ribosomal sequence tags (SARST) from a composite of contaminated and uncontaminated soils. By designing hybridization probes specific to the 100 most abundant ribosomal sequence tags (RSTs) in the composite library, the RST array was designed to be habitat-specific and predicted to monitor the most abundant polymerase chain reaction (PCR)-amplified phylotypes in the individual samples. The sensitivity and specificity of the RST array was tested with a series of pure culture-specific probes and hybridized with labelled soil PCR products to generate hybridization patterns for each soil. Sequencing of prominent bands in denaturing gradient gel electrophoresis (DGGE) fingerprints derived from these soils provided a means by which we successfully confirmed the habitat-specific array design and validated the bulk of the probe signals. Non-metric multidimensional scaling revealed correlations between probe signals and soil physicochemical parameters. Among the strongest correlations to total HCH contamination were probe signals corresponding to unknown Gamma Proteobacteria, potential pollutant-degrading phylotypes, and several organisms with acid-tolerant phenotypes. The strongest correlations to alpha-HCH were probe signals corresponding to the genus Sphingomonas, which contains known HCH degraders. This suggests that the population detected was enriched in situ by HCH contamination and may play a role in HCH degradation. Other environmental parameters were also likely instrumental in shaping community composition in these soils. The results highlight the power of habitat-specific microarrays for comparing complex microbial communities.

Genetically modified organisms for the environment: stories of success and failure and what we have learned from them

The expectations raised in the mid-1980s on the potential of genetic engineering for in situ remediation of environmental pollution have not been entirely fulfilled. Yet, we have learned a good deal about the expression of catabolic pathways by bacteria in their natural habitats, and how environmental conditions dictate the expression of desired catalytic activities. The many different choices between nutrients and responses to stresses form a network of transcriptional switches which, given the redundance and robustness of the regulatory circuits involved, can be neither unraveled through standard genetic analysis nor artificially programmed in a simple manner. Available data suggest that population dynamics and physiological control of catabolic gene expression prevail over any artificial attempt to engineer an optimal performance of the wanted catalytic activities. In this review, several valuable spin-offs of past research into genetically modified organisms with environmental applications are discussed, along with the impact of Systems Biology and Synthetic Biology in the future of environmental biotechnology.

Getting out: protein traffic in prokaryotes

Protein secretion systems in prokaryotes are increasingly shifting from being considered as experimental models for 'more complex' processes (i.e. eukaryotes) to being a major source of key biological questions in their own right. The pathways by which proteins move between compartments or insert into membranes in prokaryotic cells are certainly less numerous than in eukaryotes (though not dramatically so). However, the quality and complexity of bacterial protein targeting systems indicate that virtually all mechanistic problems associated with protein traffic were solved very efficiently well before eukaryotes appeared on the Earth crust. Indeed, recent studies have both increased the number of known prokaryotic protein traffic systems and indicated new layers of complexity for those that were already well characterized. This report describes some recent developments in bacterial protein traffic that were presented at two meetings in the autumn of 2003.

Deciphering environmental signal integration in sigma54-dependent promoters with a simple mathematical model

A mathematical model was developed to describe the physiological co-regulation of two Pseudomonas sigma54-dependent promoter/regulator systems, Pu/XylR and Po/DmpR of Pseudomonas strains mt2 and CF600, respectively. Five ordinary differential equations and six algebraic equations were developed to describe the following processes of transcription initiation: binding of the activator protein to the upstream activating sequence, union of the sigma factor with the core polymerase, formation of the open complex, and escape of the transcription machinery from the promoter region. In addition, growth-phase control of the integration host factor (IHF), sigma-70 regulation during stationary phase, and the contribution of (p)ppGpp to both sigma factor selectivity and promoter escape were hypothesized. By including any three of these four effects, the model predicted that expression from both promoters is repressed during exponential growth and sharply increases as the cells enter stationary phase. The difference in behavior of the two systems during overexpression of either sigma54 or (p)ppGpp could be explained by different values of two model parameters. To accurately represent the behavior of both promoters in (p)ppGpp null strains, an additional parameter must be varied. Although numerical data available for this system is scarce, the model has proved useful for helping to interpret the experimental observations and to evaluate four hypotheses that have been proposed to explain the phenomenon of exponential silencing.

Transcription regulation and environmental adaptation in bacteria

Lifestyle can be viewed as the environment surrounding an organism and the relationships that it establishes with other species. It is one of the driving forces that contribute to the final shape of bacterial genomes. To assess how these forces affect global cellular functions, we investigated the fraction of the genome devoted to transcription-related proteins, small-molecule metabolism enzymes, and transport, for 60 bacterial genomes classified by lifestyle. Larger genomes were found to harbour more transcription factors per gene than smaller ones. In addition, free-living bacteria (with a few exceptions) are clearly enriched for transcription factors, beyond the expected proportion based on their genome size. This suggests that under complex conditions, gene expression regulation and signal integration have been strongly selected for to enable rapid adaptation to environmental conditions.