DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

Journal Article · · Microbial Cell Factories
ORCiD logo [1];  [2];  [3];  [4];  [4];  [5];  [3];  [6];  [7];  [8]; ORCiD logo [5];  [9];  [8]
  1. Univ. of Sao Paulo (Brazil); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Technische Univ. Braunschweig, Brunswick (Germany)
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Univ. of Sao Paulo (Brazil)
  8. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  9. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States). QB3-Berkeley

BACKGROUND:Rhodosporidium toruloides is a promising host for the production of bioproducts from lignocellulosic biomass. A key prerequisite for efficient pathway engineering is the availability of robust genetic tools and resources. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering in R. toruloides. RESULTS:This data describes a set of native R. toruloides promoters, characterized over time in four different media commonly used for cultivation of this yeast. The promoter sequences were selected using transcriptional analysis and several of them were found to drive expression bidirectionally. Promoter expression strength was determined by measurement of EGFP and mRuby2 reporters by flow cytometry. A total of 20 constitutive promoters (12 monodirectional and 8 bidirectional) were found, and are expected to be of potential value for genetic engineering of R. toruloides. CONCLUSIONS:A set of robust and constitutive promoters to facilitate genetic engineering of R. toruloides is presented here, ranging from a promoter previously used for this purpose (P7, glyceraldehyde 3-phosphate dehydrogenase, GAPDH) to stronger monodirectional (e.g., P15, mitochondrial adenine nucleotide translocator, ANT) and bidirectional (e.g., P9 and P9R, histones H3 and H4, respectively) promoters. We also identified promoters that may be useful for specific applications such as late-stage expression (e.g., P3, voltage-dependent anion channel protein 2, VDAC2). This set of characterized promoters significantly expands the range of engineering tools available for this yeast and can be applied in future metabolic engineering studies.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1545318
Journal Information:
Microbial Cell Factories, Journal Name: Microbial Cell Factories Journal Issue: 1 Vol. 18; ISSN 1475-2859
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (54)

Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides collection January 2018
Engineered bidirectional promoters enable rapid multi-gene co-expression optimization journal September 2018
Causes and Effects of N-Terminal Codon Bias in Bacterial Genes journal September 2013
Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae journal January 2016
HISAT: a fast spliced aligner with low memory requirements journal March 2015
The art of vector engineering: towards the construction of next-generation genetic tools journal September 2018
Bidirectional promoters generate pervasive transcription in yeast journal January 2009
Functional integration of multiple genes into the genome of the oleaginous yeast Rhodosporidium toruloides journal February 2014
ARS2/MAGL signaling in glioblastoma stem cells promotes self-renewal and M2-like polarization of tumor-associated macrophages journal June 2020
Engineering an efficient and tight d-amino acid-inducible gene expression system in Rhodosporidium/Rhodotorula species journal October 2015
Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides journal March 2019
Characterization of glyceraldehyde-3-phosphate dehydrogenase gene RtGPD1 and development of genetic transformation method by dominant selection in oleaginous yeast Rhodosporidium toruloides journal June 2012
Engineering metabolism through dynamic control journal August 2015
Four Inducible Promoters for Controlled Gene Expression in the Oleaginous Yeast Rhodotorula toruloides journal October 2016
Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides journal May 2018
HISAT: a fast spliced aligner with low memory requirements journal March 2015
Composability of regulatory sequences controlling transcription and translation in Escherichia coli journal August 2013
Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts journal October 2017
Composability of regulatory sequences controlling transcription and translation in Escherichia coli journal August 2013
The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications journal March 2018
The Impact of Systems Biology on Bioprocessing journal December 2017
Precise and reliable gene expression via standard transcription and translation initiation elements journal March 2013
Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation journal September 2016
Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae journal January 2016
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast journal January 2009
Mitochondrial acetyl-CoA utilization pathway for terpenoid productions journal November 2016
5´-UTR introns enhance protein expression in the yeast Saccharomyces cerevisiae journal October 2016
Engineered bidirectional promoters enable rapid multi-gene co-expression optimization text January 2018
Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation journal September 2016
Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides journal January 2019
The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications journal March 2018
Causes and Effects of N-Terminal Codon Bias in Bacterial Genes journal September 2013
MicroRNA-146a Regulates Perfusion Recovery in Response to Arterial Occlusion via Arteriogenesis journal January 2018
Engineering and application of synthetic nar promoter for fine-tuning the expression of metabolic pathway genes in Escherichia coli journal April 2018
featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features text January 2013
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast journal January 2009
Engineered bidirectional promoters enable rapid multi-gene co-expression optimization journal September 2018
Engineering and application of synthetic nar promoter for fine-tuning the expression of metabolic pathway genes in Escherichia coli journal April 2018
Bidirectional promoters generate pervasive transcription in yeast journal January 2009
IL-1-dependent enteric gliosis guides intestinal inflammation and dysmotility and modulates macrophage function journal August 2022
The Impact of Systems Biology on Bioprocessing journal December 2017
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features journal November 2013
Engineering metabolism through dynamic control journal August 2015
Cloning and evaluation of different constitutive promoters in the oleaginous yeast Rhodosporidium toruloides : Evaluation of five constitutive promoters in journal January 2016
Functional integration of multiple genes into the genome of the oleaginous yeast Rhodosporidium toruloides journal February 2014
Developing a set of strong intronic promoters for robust metabolic engineering in oleaginous Rhodotorula (Rhodosporidium) yeast species collection January 2016
How introns enhance gene expression journal October 2017
Development of a fed-batch process for a recombinant Pichia pastoris Δoch1 strain expressing a plant peroxidase journal January 2015
Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides journal May 2018
Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts [Supplemental Data] collection October 2017
Assembly of a novel biosynthetic pathway for gentamicin B production in Micromonospora echinospora journal January 2016
Assembly of a novel biosynthetic pathway for gentamicin B production in Micromonospora echinospora journal January 2016
Cloning and evaluation of different constitutive promoters in the oleaginous yeast Rhodosporidium toruloides : Evaluation of five constitutive promoters in journal January 2016
5´-UTR introns enhance protein expression in the yeast Saccharomyces cerevisiae journal October 2016

Cited By (1)