Identification and Characterization of Phlorizin Transporter from Arabidopsis 2 Thaliana and Its Application for Phlorizin Production in Saccharomyces Cerevisiae
Total Page:16
File Type:pdf, Size:1020Kb
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.248047; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Identification and characterization of phlorizin transporter from Arabidopsis 2 thaliana and its application for phlorizin production in Saccharomyces cerevisiae 3 Zeinu Mussa Belew1, Christoph Crocoll1, Iben Møller-Hansen2, Michael Naesby3, Irina Borodina2, Hussam 4 Hassan Nour-Eldin1* 5 6 1DynaMo Center, Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, 7 University of Copenhagen, 1871 Frederiksberg, Denmark 8 2The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 9 2800 Kongens Lyngby, Denmark 10 3 Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland 11 12 *Corresponding author: Hussam H. Nour-Eldin ([email protected]) 13 14 15 16 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.248047; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 18 Abstract 19 Bioengineering aimed at producing complex and valuable plant specialized metabolites in microbial hosts 20 requires efficient uptake of precursor molecules and export of final products to alleviate toxicity and 21 feedback inhibition. Plant genomes encode a vast repository of transporters of specialized metabolites that— 22 due to lack of molecular knowledge—remains largely unexplored in bioengineering. Using phlorizin as a case 23 study—an anti-diabetic and anti-cancerous flavonoid from apple—we demonstrate that brute-force 24 functional screening of plant transporter libraries in Xenopus oocytes is a viable approach to identify 25 transporters for bioengineering. By screening 600 Arabidopsis transporters, we identified and characterized 26 purine permease 8 (AtPUP8) as a bidirectional phlorizin transporter. Functional expression in the plasma 27 membrane of a phlorizin-producing yeast strain increased phlorizin titer by more than 80 %. This study 28 provides a generic approach for identifying plant exporters of specialized metabolites and demonstrates the 29 potential of transport-engineering for improving yield in bioengineering approaches. 30 31 32 33 34 35 36 Keywords 37 Phlorizin transporter, transport-engineering, Saccharomyces cerevisiae, purine permease family (PUP), 38 Xenopus laevis oocytes 39 40 Abbreviations 41 UGT, UDP-dependent-glycosyltransferase; HRT, homologous recombination tag; OD600, optical density at 600 42 nm; LC-MS, liquid chromatography mass spectrometry 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.248047; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 43 1. Introduction 44 Plants synthesize a vast number of specialized small molecules that have pharmaceutical and nutraceutical 45 values. These molecules are usually produced in minute amounts in the natural plant host, wherefrom 46 extraction may be costly, insufficient and time-consuming (Liu et al., 2017; Lv et al., 2016). As a promising 47 alternative, bioengineering in microorganisms such as Saccharomyces cerevisiae and Escherichia coli has 48 emerged as a sustainable and cost-effective means for large-scale production of high-value plant natural 49 products (Keasling, 2012; Krivoruchko and Nielsen, 2015; Suzuki et al., 2014). 50 For any bioengineering approach, transport proteins play critical roles in uptake of nutrients, cofactors and 51 precursors and also for secretion of final products to alleviate toxicity and feedback inhibition that may 52 hamper yield (Jones et al., 2015; Lee et al., 2012; Liu et al., 2017; Shu and Liao, 2002). 53 Transporters native to the producing microbial cell factory (endogenous transporters) or heterologous 54 transporters obtained from other organisms can be utilized in transport-engineering approaches aimed at 55 improving these transport processes. Most studies implementing transport-engineering have so far targeted 56 microbial transporters. For example, tolerance of E. coli was improved by applying directed evolution to 57 enhance the export efficiency of AcrB towards toxic biofuels and plastic precursors (Fisher et al., 2014; Foo 58 and Leong, 2013). In other examples, overexpression of YddG, MsbA and YadH improved secretion and 59 thereby production of various amino acids, biofuels and plant natural products such as anthocyanins in E. coli 60 (Doroshenko et al., 2007; Doshi et al., 2013; Lim et al., 2015). 61 Given the enormous diversity of chemical structures in plant specialized metabolism, the field of transport- 62 engineering will require access to a large repository of transporters. The general participation of separate 63 organs and/or cells in the synthesis and accumulation of plant specialized metabolites indicates that plant 64 genomes encode a plethora of specialized metabolite transporters (Shitan, 2016; Yazaki, 2005). However, in 65 the context of bioengineering, plant transporters remain largely unexplored. 66 In this study, we seek to address two challenges; i) how to identify plant transporters relevant for a given 67 bioengineering approach and ii) demonstrating the potential of using plant transporters to improve 68 production in a given bioengineering approach. 69 As a case study, we focus on phlorizin, a dihydrochalcone O-glucoside predominantly found in apple (Malus 70 sp.), which is comprised of a glucose moiety and two aromatic rings joined by an alkyl spacer. Phlorizin is 71 medicinally important as it decreases blood glucose levels, has been used as both a remedy and a tool to 72 study renal physiology for nearly two centuries and has been used as a blueprint to develop several 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.248047; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 73 commercialized anti-diabetic drugs (Ehrenkranz et al., 2005; Kramer and Zinman, 2019; Meng et al., 2008; 74 Nomura et al., 2010; Scheen, 2015). 75 Recently, a pathway consisting of seven enzymes was engineered into S. cerevisiae for de novo production of 76 phlorizin (Eichenberger et al., 2017). The titer is low for industrial production indicating that optimization of 77 the biosynthesis pathway is possible, for example by increasing cytoplasmic malonyl-CoA, altering gene copy 78 number, enzyme origins, and culture conditions (Galanie and Smolke, 2015; Li et al., 2015; Rodriguez et al., 79 2015). Although precursor supply (such as malonyl-CoA, a ) is a major bottleneck for microbial production of 80 flavonoids in general and phlorizin in particular (Delmulle et al., 2018; Eichenberger et al., 2017), product 81 toxicity, negative feedback inhibition by intermediates (such as cinnamic acid and p-coumaric acid) on early 82 biosynthetic enzymes (Blount et al., 2000; Lam et al., 2008; Sarma and Sharma, 1999) and by-product UDP 83 inhibition on the last biosynthetic enzyme UGT (Zhang et al., 2016) could hamper overall flux into the 84 phlorizin pathway. 85 Phlorizin is a polar compound that requires a membrane-bound transporter protein to traverse membranes. 86 In this study, we explore whether titer can be increased by expressing an efficient phlorizin exporter to 87 improve product secretion from the phlorizin producing yeast strain. To test this hypothesis, we faced a 88 typical knowledge gap in plant specialized metabolism, which is that as of date, no phlorizin transporters 89 have been identified. 90 We have developed a functional genomics approach wherein we build and functionally screen sequence- 91 indexed full-length transporter cDNA libraries in Xenopus oocytes for activity towards target compounds 92 (Nour-Eldin et al., 2006). Here, we screen a library consisting of 600 transporters from Arabidopsis and 93 identify the first reported phlorizin transporter. Extensive biophysical characterization in Xenopus oocytes 94 reveals a passive, medium-affinity, proton gradient-independent, bidirectional transport activity, which 95 when introduced into a phlorizin producing yeast strain increased titer significantly. The transporter belongs 96 to the purine permease family (PUP) present in all plants, which here has its substrate spectrum expanded 97 to include a novel class of specialized metabolites. This study provides a generic approach for identifying 98 plant exporters of specialized metabolites and demonstrates the potential of transport-engineering for 99 improving yield in bioengineering of plant specialized metabolites. 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.14.248047; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is