Biofuels and Bioproducts Data

Multiple annotated DNA sequences, DNA design and assembly files, primers, plasmids and strains have been produced, validated, and shared. Explore these and microarray datasets for yeast responses to biofuel-related stress. Image from Chertkov O, et al., Stand. Genomic Sci. 5:1 (2011).

Functional genomics for strain engineering

Developing improved microbial strains for bioconversion routinely uses functional genomics data from RNA-seq, Proteomics and RB-TnSeq.Eng et. al., 2021 evaluated P. putida KT2440 in a bioreactor using RB-TnSeq to identify genes that provide fitness. The RB-TnSeq P. putida reactor data is available from the fitness browser. Banerjee et al 2020 showed the use of RNA-seq data (from the Join Genome institute) to curate Genome Scale Metabolic Models. All RNA-seq data from this study is available via NCBI Bioproject PRJNA580539 and also the JGI Gold site. 

Genome sequence of bioproduction strains

Research at JBEI uncovered a strain variant of the commonly used Corynebacterium glutamicum strain; C. glutamicum BRC-JBEI 1.1.2 that was used to engineer the production of isoprenol (Sasaki et. al., 2019), TMP (Srinivasan et. al., 2024) and most recently to develop robust additional tools for bioproduction (Luckie et. al., 2024). The BRC-JBEI 1.1.2 was resequenced at the JGI and is available via NCBI Genome Assembly ID: GCA_011761195.1. Additional omics data for BRC-JBEI 1.1.2 tolerance to Cholinium lysinate is also available from NCBI listed in Banerjee et al 2021. 

JBEI ALE data

To develop improved microbial chassis for bioproduction, JBEI researchers use ALE to obtain strain with improved tolerance to deconstruction reagents (), catabolism of aromatics (), sugars (). When high throughput automated ALE is used, routine sequencing allows us to capture genome wide mutations that accumulate in evolved strain lines. These data are organized and available via the ALE DB. Here are links to recent projects that led to publications: 

• Pputida_carbon_ALE  – 10.1021/acssuschemeng.1c03765
• Pputida_carbon_ALE_2 – 10.1021/acssuschemeng.1c03765
• P. putida Hydroxycinnamic TALE – 10.1016/j.mec.2020.e00143
• ILTolerance – 10.1186/s12934-017-0819-1

 

High-throughput and automated DBTL cycle for polyketide synthase reprogramming: Retrobiosynthesis of unnatural lactams

High-throughput and automated DBTL cycles were developed for PKS-based retrobiosynthesis, as partially demonstrated by Nava et al., 2023. Unnatural lactams were selected as the initial target compounds and successfully produced from biomass using P. putida KT2440. Hundreds of chimeric PKSs were constructed by exchanging domains or modules at various junction sites to produce unnatural lactams. The resulting production data will be presented in an upcoming paper.

Biosynthetic platforms for industrial diols and derivatives

Developing retrobiosynthetic platforms suitable for biomanufacturing petroleum-derived industrial molecules. Using integrative approaches in genome mining, biochemistry, structural biology and metabolic engineering, Dan et al. identified hundreds of candidate polyketide synthase (PKS) thioreductases (TRs), characterized PKS TR catalysis, incorporated TRs into assembly-line PKS engineering, and enabled biosynthetic access to seventeen diols and derivatives in Streptomyces albus. These products include 1,3-butanediol (humectant) and 2-ethyl-1,3-hexanediol (insect repellent). The coordinates of CpkC TR crystal structure are available on Protein Data Bank (PDB 8V1X). All proteomics data from this study are also available via the ProteomeXchange Consortium (PXD055149).

Functional genomics for strain engineering

To better understand the metabolism of a JBEI host organism and aid in metabolic engineering efforts, JBEI researchers leveraged RB-TnSeq to obtain functional evidence for the genetic basis of nitrogen metabolism in Pseudomonas putida KT2440 (Schmidt and Pearson et al 2022). Researchers tested 52 nitrogen sources and 19 amino acid drop-out conditions, resulting in significant phenotypes in 672 different genes. These data can be browsed through an interactive figure or the full dataset can be accessed through the fitness browser.

Improving the production of value-added products in different host organisms using codon optimization

Protein engineering and heterologous expression in host organisms holds enormous potential as a rational production platform for the biosynthesis of specialty chemicals. However, choosing the wrong codon optimization strategy for expression in a heterologous host can have detrimental effects on protein and product levels. (Schmidt et. al., 2023) investigated the relationship between codon optimization strategies and the resulting transcript, protein, and product expression levels. By employing the strategies developed in their study, JBEI researchers successfully produced unnatural polyketides across three different hosts. This research also led to the development of a free, transparent, and customizable codon optimization tool, available at basebuddy.lbl.gov.

A bio-based platform for renewable and recyclable plastics with customizable properties

Traditional plastics are almost exclusively produced from non-renewable feedstocks and face considerable challenges in recycling. In this recent work by (Wang et. al., 2024), researchers took an interdisciplinary approach that combined computational materials design, polymer chemistry, synthetic biology, and systems analysis. This integrated effort enabled the design of customizable, biorenewable plastics with tailored properties, contributing to a circular bioeconomy. The microbial strains used to produce the monomers in this work are accessible through the JBEI Public Registry. 

Adaptive Evolution of E. coli strains for Malonyl-CoA Production

Heterologous expression of polyketide synthase (PKS) genes in Escherichia coli enables the production of valuable natural and synthetic products, but limited malonyl-CoA (M-CoA) availability hinders high-titer production. Introducing an orthogonal malonate transport and CoA ligation pathway significantly enhanced M-CoA-derived polyketide titers (Klass et al., 2024 ; Wang et al., 2023). Disrupting the native M-CoA pathway and reconstituting it through malonate supplementation enabled adaptive laboratory evolution (ALE), revealing mutations though whole genome sequencing and proteomic analysis that increased M-CoA and polyketide levels. This approach not only improves E. coli as a polyketide host but also provides insights into M-CoA modulation dynamics.

 

 

Archived Data:

*Please note: Any user can create an account on the public instance of the JBEI Registry by going to https://public-registry.jbei.org/.