Phylogenomics and genetic analysis of solvent-producing Clostridium species.

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

Prenatal exposure to environmental toxins and comprehensive dental findings in a population cohort of children.

Environmental toxins are known to have many impacts on growth and development in humans, starting in utero. Alterations in amelogenesis, caused by chemical and physical trauma that occur during the antenatal, perinatal and postnatal time periods, may result in developmental defects in deciduous and permanent tooth enamel, as demonstrated in animal studies. These defects can be clinically visible and result in a variety of morphological and functional problems in the dentition. Since enamel does not remodel after formation, it may serve as a permanent record of insults during organ development.Our primary purpose was to investigate any possible relationship between intrauterine exposure to endocrine disrupting chemicals (phenols and phthalates) and developmental defects in enamel in children, while also accounting for fluoride exposure. Our secondary purpose was to report descriptively on findings from comprehensive dental examinations performed on 356 children that were drawn from the general paediatric population. A cohort of children from the Utah Children's Project (N = 356) that had full medical exams, comprehensive medical and family histories and available biospecimens were given extraoral and intraoral examinations. They also completed an oral health questionnaire. Standardized intraoral photographs were taken of the teeth and viewed by standardised examiners and the dental observations were recorded for a full inventory of findings, including: tooth morphology, caries, restorations, colorations, attrition, erosion, fractures and hypomineralization. Perinatal maternal urine samples were assessed for the concentration of fluoride, phenols and phthalates, including bisphenol A (BPA).Pairwise statistical analyses were done to correlate the dental findings with one another and with the presence of environment chemicals found in the urine samples. Hypomineralization was the most common finding (96% of children; 37% of deciduous teeth, 42% of permanent teeth), consistent with molar incisor hypomineralization (MIH) described in other human populations. No consistent correlations were seen between dental findings and the presence of phenols and phthalates in prenatal urine, but the number of samples available for the assessment was limited (n = 35).In conclusion, we found a high proportion of dental hypomineralization in a population based paediatric cohort, but did not find an association with prenatal exposure to phenols and phthalates.

First-in-Human Dose-Escalation Study of the Novel Oral Depsipeptide Class I-Targeting HDAC Inhibitor Bocodepsin (OKI-179) in Patients with Advanced Solid Tumors.

(1) Background: Histone deacetylases (HDACs) play a critical role in epigenetic signaling in cancer; however, available HDAC inhibitors have limited therapeutic windows and suboptimal pharmacokinetics (PK). This first-in-human phase I dose escalation study evaluated the safety, PK, pharmacodynamics (PDx), and efficacy of the oral Class I-targeting HDAC inhibitor bocodepsin (OKI-179). (2) Patients and Methods: Patients (n = 34) with advanced solid tumors were treated with OKI-179 orally once daily in three schedules: 4 days on 3 days off (4:3), 5 days on 2 days off (5:2), or continuous in 21-day cycles until disease progression or unacceptable toxicity. Single-patient escalation cohorts followed a standard 3 + 3 design. (3) Results: The mean duration of treatment was 81.2 (range 11-447) days. The most frequent adverse events in all patients were nausea (70.6%), fatigue (47.1%), and thrombocytopenia (41.2%). The maximum tolerated dose (MTD) of OKI-179 was 450 mg with 4:3 and 200 mg with continuous dosing. Dose-limiting toxicities included decreased platelet count and nausea. Prolonged disease control was observed, including two patients with platinum-resistant ovarian cancer. Systemic exposure to the active metabolite exceeded the preclinical efficacy threshold at doses lower than the MTD and was temporally associated with increased histone acetylation in circulating T cells. (4) Conclusions: OKI-179 has a manageable safety profile at the recommended phase 2 dose (RP2D) of 300 mg daily on a 4:3 schedule with prophylactic oral antiemetics. OKI-179 is currently being investigated with the MEK inhibitor binimetinib in patients with NRAS-mutated melanoma in the phase 2 Nautilus trial.

Cross-cultural adaptation of a Spanish version of a previously validated HPV survey that evaluates dental students' knowledge, perception and clinical practices in Latin America.

BACKGROUND: The global incidence of oropharyngeal cancer (OPC) is increasing. Dental professionals play a key role in the detection of oral lesions that could lead to cancer. However, scientific-based HPV-OPC visual inspection guidelines are underdeveloped and HPV knowledge and awareness has been reported to be low among dental students and professionals. The present study adapted and performed pretesting of a multi-scale survey evaluating knowledge, perceptions, and clinical practices regarding HPV and HPV-OPC for Latin American Spanish-speaking populations. METHODS: A previously developed questionnaire for English-speaking dental students was translated to Spanish. The questionnaire was administered to first year dental students at two Latin American universities with dental programs. Internal consistencies were measured using Cronbach Alpha. Analyses were conducted in SAS Version 9.4. RESULTS: Data from a total of 114 students, a majority of the which were female (61%), and Hispanic/Latino(a)/Spanish (91%). The HPV, HPV-OPC, and HPV vaccine knowledge subscales demonstrated good internal consistency, the Cronbach's alpha was 0.83, 0.75, and 0.86 respectively. The Barriers subscale had a Cronbach's alpha of 0.93, showing excellent internal consistency. The Clinical Procedures subscale, focused on factors surrounding dental students' hypothetical clinical practice procedures, had a Cronbach's alpha of 0.86. The Scope of Practice scale had a Cronbach's alpha of 0.93. CONCLUSIONS: Ultimately, this survey demonstrated reliability and applicability for the assessment of dental students' knowledge, perceptions, and clinical practices regarding HPV and HPV-OPC in Latin America.

Preclinical Development of the Class-I-Selective Histone Deacetylase Inhibitor OKI-179 for the Treatment of Solid Tumors.

Histone deacetylases (HDACs) play critical roles in epigenomic regulation, and histone acetylation is dysregulated in many human cancers. Although HDAC inhibitors are active in T-cell lymphomas, poor isoform selectivity, narrow therapeutic indices, and a deficiency of reliable biomarkers may contribute to the lack of efficacy in solid tumors. In this article, we report the discovery and preclinical development of the novel, orally bioavailable, class-I-selective HDAC inhibitor, OKI-179. OKI-179 and its cell active predecessor OKI-005 are thioester prodrugs of the active metabolite OKI-006, a unique congener of the natural product HDAC inhibitor largazole. OKI-006, OKI-005, and subsequently OKI-179, were developed through a lead candidate optimization program designed to enhance physiochemical properties without eroding potency and selectivity relative to largazole. OKI-005 displays antiproliferative activity in vitro with induction of apoptosis and increased histone acetylation, consistent with target engagement. OKI-179 showed antitumor activity in preclinical cancer models with a favorable pharmacokinetic profile and on-target pharmacodynamic effects. Based on its potency, desirable class I HDAC inhibition profile, oral bioavailability, and efficacy against a broad range of solid tumors, OKI-179 is currently being evaluated in a first-in-human phase I clinical trial with plans for continued clinical development in solid tumor and hematologic malignancies.

A Multi-state Evaluation of Oral Health Students' Knowledge of Human Papillomavirus-Related Oropharyngeal Cancer and HPV Vaccination.

Human papillomavirus-related oropharyngeal cancers (HPV-OPCs) are on the rise, yet HPV knowledge among dental professionals remains low. The purpose of this multi-state study was to examine sociodemographic factors associated with final year dental hygiene (DH), third year dental (DS3), and fourth year dental (DS4) students' knowledge regarding HPV, HPV-OPC, and HPV vaccination. Twenty dental programs in the USA were approached in the implementation phase to complete an online, 153-item, self-administered questionnaire that was developed and tested in a previous study. Descriptive statistics and chi-square analyses were conducted in SAS version 9.4 to examine the relationship between sociodemographic variables with HPV, HPV-OPC, and HPV vaccination knowledge levels. This study included the participation of students from 15 dental programs (n = 380) with an overall response rate of 28%. Although the results cannot be generalized to the entire population of dental students in the USA, most students had inadequate overall HPV knowledge (65%), HPV-OPC knowledge (80%), and HPV vaccination knowledge (55%). While all student groups displayed adequate general HPV knowledge levels (≥ 70% correct responses), gender, racial, religious, age, and regional differences were observed. Future dental professionals need to have adequate levels of HPV knowledge to aid in reducing the HPV-OPC burden. This study identified sociodemographic factors related to lower knowledge of HPV, HPV-OPC, and HPV vaccination, and highlights groups of students with greater needs for HPV education. This study provides a foundation for future research and interventions to be developed. Dental institutions can use findings to strengthen curricula development.

US oral health students' willingness to train and administer the HPV vaccine in dental practices.

HPV oropharyngeal cancers have now surpassed cervical cancer rates in the US. Dental providers' engagement in HPV education and vaccination efforts may help reduce the burden of HPV oropharyngeal cancers. We examined factors associated with oral health students' willingness to train and administer the human papillomavirus (HPV) vaccine in dental settings. US students in 15 oral health programs participated in an online survey in 2016. Unadjusted and adjusted multivariable logistic regression were conducted and odds ratios (OR) and 95% confidence intervals (CI) were reported. Analyses were conducted in SAS Version 9.4. Data from a total of N = 306 students were analyzed to examine sociodemographic, educational, practice, and attitudinal factors associated with willingness to train and administer the HPV vaccine. Majority of the participants were female (70.3%), non-Hispanic/Latino (90.8%), and White (62.1%). Perceiving that HPV vaccination recommendation (OR = 1.95, 95% CI = 1.14-3.35) and administration (OR = 3.79, 95% CI = 1.63-8.81) was in the dental professional's scope was positively associated with outcome measures when other factors were held constant. Students with greater patient contact time (OR = 4.47, 95% CI = 1.14-17.58) and lower role conflict (agreed that HPV vaccine administration was in the dental professional's scope) had higher odds of willingness to administer the HPV vaccine when other factors were held constant (OR = 5.9, 95% CI = 2.27-15.3). The major barrier to engaging oral health students in HPV vaccination efforts was role conflict. Professional organizations and oral health programs should strongly support the role of oral health professionals in HPV oropharyngeal prevention.

Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production.

Multiplex navigation of global regulatory networks (MINR) is an approach for combinatorially reprogramming gene expression to manipulate complex phenotypes. We designed, constructed, and mapped MINR libraries containing 43,020 specific mutations in 25 regulatory genes expected to perturb the yeast regulatory network. We selected growth competition experiments for library mutants conferring increased ethanol and/or glucose tolerance. We identified specific mutants that not only possessed improved ethanol and/or glucose tolerance but also produced ethanol at concentrations up to 2-fold higher than those produced by the wild-type strain. We further determined that mutations increasing ethanol tolerance were transferable to a diploid industrial yeast strain. The facile construction and mapping of 43,020 designer regulatory mutations provide a roadmap for how to access and engineer complex phenotypes in future synthetic biology and broader efforts.

Identification and Characterization of Von Hippel-Lindau-Recruiting Proteolysis Targeting Chimeras (PROTACs) of TANK-Binding Kinase 1.

Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that recruit an E3 ligase to a target protein to facilitate ubiquitination and subsequent degradation of that protein. While the field of targeted degraders is still relatively young, the potential for this modality to become a differentiated and therapeutic reality is strong, such that both academic and pharmaceutical institutions are now entering this interesting area of research. In this article, we describe a broadly applicable process for identifying degrader hits based on the serine/threonine kinase TANK-binding kinase 1 (TBK1) and have generalized the key structural elements associated with degradation activities. Compound 3i is a potent hit (TBK1 DC50 = 12 nM, Dmax = 96%) with excellent selectivity against a related kinase IKKε, which was further used as a chemical tool to assess TBK1 as a target in mutant K-Ras cancer cells.

Pilot Test of Survey to Assess Dental and Dental Hygiene Student Human Papillomavirus-Related Oropharyngeal Cancer Knowledge, Perceptions, and Clinical Practices.

This was the first study to develop and pilot test an assessment tool for the examination of human papillomavirus (HPV)-related oropharyngeal cancer (OPC) knowledge, perceptions, and clinical practices of oral health students. An interdisciplinary team developed the tool using surveys that examined this topic in other populations. The tool was then pilot tested at two different dental programs. Results from the pilot informed revisions to the final version of the tool. Of the 46 student participants, 18 were first-year dental hygiene and 28 were first-year dental students. The majority of participants were female (N = 29, 63%) and ages 18 to 29 years old (N = 41, 89%). Four scales used in the questionnaire were analyzed for reliability. Of these, the HPV and HPV-OPC knowledge and the HPV vaccination knowledge scales had Cronbach alphas of 0.71 and 0.79, respectively. Questions assessing HPV and the role of dental professionals had a correlation coefficient of 0.71. Questions assessing willingness to administer vaccines in the dental office had a correlation coefficient of 0.85. Assessing oral health students' HPV-OPC knowledge, perceptions, and clinical practices are important for future assessment of possible HPV-OPC cases. Dental professionals may be optimally positioned to provide HPV patient education. The tool developed and pilot tested in this study can help schools assess their students' knowledge and guide their dental curriculum to address deficiencies. Since this topic has not been effectively examined with dental health students, the results could help improve dental education and dental care.

Refactoring the Genetic Code for Increased Evolvability.

The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments. We then conclude by evaluating the challenges of constructing such recoded organisms and their potential applications within the field of synthetic biology.IMPORTANCE The conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene via common error-prone methods. Here, we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transitions to a larger pool of amino acids and with a greater extent of chemical differences, based on a single nucleotide replacement within the codon, thus increasing evolvability both at the single-gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement, along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation, and fitness maximization.

The Tolerome: A Database of Transcriptome-Level Contributions to Diverse Escherichia coli Resistance and Tolerance Phenotypes.

Tolerance and resistance are complex biological phenotypes that are desirable bioengineering goals for those seeking to design industrial strains or prevent the spread of antibiotic resistance. Over decades of research, a wealth of information has been generated to attempt to decode a molecular basis for tolerance, but to fully achieve the goal of engineering tolerance, researchers must be able to easily learn from a variety of data sources. To this end, we here describe a resource designed to enable scrutiny of diverse tolerance phenotypes. We have curated hundreds of gene expression studies exploring the response of Escherichia coli to chemical and environmental perturbations, from antibiotics to biofuels and solvents and more. Overall, our efforts give rise to a database encompassing more than 56 000 gene expression changes across 89 different stress conditions. This resource is designed for compatibility with the Resistome database, which includes more than 5000 strains with mutations conferring resistance or sensitivity but no transcriptomic data. Thus, the work here results in the first combined resource specialized to tolerance and resistance in E. coli that supports investigations across genomic, transcriptomic, and phenotypic levels. We leverage the database to identify promising bioengineering targets by searching globally across multiple stress conditions as well as by narrowing the focus to fewer conditions of interest, such as biofuel stress and antibiotic stress. We discuss some of the most frequently differentially expressed or coexpressed genes, and predict which transcription factors and sigma factors most likely contribute to gene expression profiles in a wide array of conditions. We also compare profiles from sensitive and resistant strains, gaining knowledge of how responses differ per overrepresented gene ontology terms. Finally, we search for genes that are frequently differentially expressed but not mutated, with the expectation that these may present interesting targets for future engineering efforts. The curated data presented here is publicly available, and should be advantageous to those studying a variety of bacterial tolerance phenotypes.

Insights on Osmotic Tolerance Mechanisms in Escherichia coli Gained from an rpoC Mutation.

An 84 bp in-frame duplication (K370_A396dup) within the rpoC subunit of RNA polymerase was found in two independent mutants selected during an adaptive laboratory evolution experiment under osmotic stress in Escherichia coli, suggesting that this mutation confers improved osmotic tolerance. To determine the role this mutation in rpoC plays in osmotic tolerance, we reconstructed the mutation in BW25113, and found it to confer improved tolerance to hyperosmotic stress. Metabolite analysis, exogenous supplementation assays, and cell membrane damage analysis suggest that the mechanism of improved osmotic tolerance by this rpoC mutation may be related to the higher production of acetic acid and amino acids such as proline, and increased membrane integrity in the presence of NaCl stress in exponential phase cells. Transcriptional analysis led to the findings that the overexpression of methionine related genes metK and mmuP improves osmotic tolerance in BW25113. Furthermore, deletion of a stress related gene bolA was found to confer enhanced osmotic tolerance in BW25113 and MG1655. These findings expand our current understanding of osmotic tolerance in E. coli, and have the potential to expand the utilization of high saline feedstocks and water sources in microbial fermentation.

Targeted protein degradation by PROTACs.

Targeted protein degradation using the PROTAC technology is emerging as a novel therapeutic method to address diseases driven by the aberrant expression of a disease-causing protein. PROTAC molecules are bifunctional small molecules that simultaneously bind a target protein and an E3-ubiquitin ligase, thus causing ubiquitination and degradation of the target protein by the proteasome. Like small molecules, PROTAC molecules possess good tissue distribution and the ability to target intracellular proteins. Herein, we highlight the advantages of protein degradation using PROTACs, and provide specific examples where degradation offers therapeutic benefit over classical enzyme inhibition. Foremost, PROTACs can degrade proteins regardless of their function. This includes the currently "undruggable" proteome, which comprises approximately 85% of all human proteins. Other beneficial aspects of protein degradation include the ability to target overexpressed and mutated proteins, as well as the potential to demonstrate prolonged pharmacodynamics effect beyond drug exposure. Lastly, due to their catalytic nature and the pre-requisite ubiquitination step, an exquisitely potent molecules with a high degree of degradation selectivity can be designed. Impressive preclinical in vitro and in vivo PROTAC data have been published, and these data have propelled the development of clinically viable PROTACs. With the molecular weight falling in the 700-1000Da range, the delivery and bioavailability of PROTACs remain the largest hurdles on the way to the clinic. Solving these issues and demonstrating proof of concept clinical data will be the focus of many labs over the next few years.

Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution.

Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. IMPORTANCE: Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development.

The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes.

The microbial ability to resist stressful environmental conditions and chemical inhibitors is of great industrial and medical interest. Much of the data related to mutation-based stress resistance, however, is scattered through the academic literature, making it difficult to apply systematic analyses to this wealth of information. To address this issue, we introduce the Resistome database: a literature-curated collection of Escherichia coli genotypes-phenotypes containing over 5,000 mutants that resist hundreds of compounds and environmental conditions. We use the Resistome to understand our current state of knowledge regarding resistance and to detect potential synergy or antagonism between resistance phenotypes. Our data set represents one of the most comprehensive collections of genomic data related to resistance currently available. Future development will focus on the construction of a combined genomic-transcriptomic-proteomic framework for understanding E. coli's resistance biology. The Resistome can be downloaded at https://bitbucket.org/jdwinkler/resistome_release/overview .

PROTAC-induced BET protein degradation as a therapy for castration-resistant prostate cancer.

Prostate cancer has the second highest incidence among cancers in men worldwide and is the second leading cause of cancer deaths of men in the United States. Although androgen deprivation can initially lead to remission, the disease often progresses to castration-resistant prostate cancer (CRPC), which is still reliant on androgen receptor (AR) signaling and is associated with a poor prognosis. Some success against CRPC has been achieved by drugs that target AR signaling, but secondary resistance invariably emerges, and new therapies are urgently needed. Recently, inhibitors of bromodomain and extra-terminal (BET) family proteins have shown growth-inhibitory activity in preclinical models of CRPC. Here, we demonstrate that ARV-771, a small-molecule pan-BET degrader based on proteolysis-targeting chimera (PROTAC) technology, demonstrates dramatically improved efficacy in cellular models of CRPC as compared with BET inhibition. Unlike BET inhibitors, ARV-771 results in suppression of both AR signaling and AR levels and leads to tumor regression in a CRPC mouse xenograft model. This study is, to our knowledge, the first to demonstrate efficacy with a small-molecule BET degrader in a solid-tumor malignancy and potentially represents an important therapeutic advance in the treatment of CRPC.

A Web Interface for Codon Compression.

Saturation mutagenesis is widely used in protein engineering and other experiments. A common practice is to utilize the single degenerate codon NNK. However, this approach suffers from amino acid bias and the presence of a stop codon and of the wild type amino acid. These extra features needlessly increase library size and consequently downstream screening load. Recently, we developed the DYNAMCC algorithms for codon compression that find the minimal set of degenerate codons, covering any defined set of amino acids, with no off-target codons and with redundancy control. Additionally, we experimentally demonstrated the advantages of this approach over the standard NNK method. While the code is freely available from our Web site, we have now made this method more accessible to a broader audience without any computational background by building a user-friendly web-based interface for those algorithms. The Web site can be accessed through: www.dynamcc.com .

Quantifying complexity in metabolic engineering using the LASER database.

We previously introduced the LASER database (Learning Assisted Strain EngineeRing, https://bitbucket.org/jdwinkler/laser_release) (Winkler et al. 2015) to serve as a platform for understanding past and present metabolic engineering practices. Over the past year, LASER has been expanded by 50% to include over 600 engineered strains from 450 papers, including their growth conditions, genetic modifications, and other information in an easily searchable format. Here, we present the results of our efforts to use LASER as a means for defining the complexity of a metabolic engineering "design". We evaluate two complexity metrics based on the concepts of construction difficulty and novelty. No correlation is observed between expected product yield and complexity, allowing minimization of complexity without a performance trade-off. We envision the use of such complexity metrics to filter and prioritize designs prior to implementation of metabolic engineering efforts, thereby potentially reducing the time, labor, and expenses of large-scale projects. Possible future developments based on an expanding LASER database are then discussed.

Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits.

The reliable engineering of biological systems requires quantitative mapping of predictable and context-independent expression over a broad range of protein expression levels. However, current techniques for modifying expression levels are cumbersome and are not amenable to high-throughput approaches. Here we present major improvements to current techniques through the design and construction of E. coli genome-wide libraries using synthetic DNA cassettes that can tune expression over a ∼10(4) range. The cassettes also contain molecular barcodes that are optimized for next-generation sequencing, enabling rapid and quantitative tracking of alleles that have the highest fitness advantage. We show these libraries can be used to determine which genes and expression levels confer greater fitness to E. coli under different growth conditions.