Genetic Parts

1. Basic vectors

Plasmid name Properties Sequence files Reference Contact
pJFE1 S. cerevisiae/E. coli shuttle plasmid; yeast centomere plasmid (single copy); E. coli AmpR; S. cerevisiae URA3; containing a set of yeast promoter and terminator for 'constitutive' gene overexpression.
YCplac33; PTEF1-(BamHI-XbaI-PstI-SbfI)-TPGK1
  i-bio file Bingyin Peng Master's Thesis (Shandong University, China) Prof. Xiaoming Bao (Shandong University, China)
pJFE2 S. cerevisiae/E. coli shuttle plasmid; yeast centomere plasmid; E. coli AmpR; S. cerevisiae URA3; containing two sets of yeast promoter and terminator for 'constitutive' gene overexpression.
YCplac33; PTEF1-(BamHI-PstI-SbfI)-TPGK1, PTDH3-(XbaI-SphI-XhoI)-TCYC1
 i-bio file PubMed: 22178745 Prof. Xiaoming Bao (Shandong University, China)
pJFE3 S. cerevisiae/E. coli shuttle plasmid; yeast episomal plasmid (multiple copy); E. coli AmpR; S. cerevisiae URA3; containing a set of yeast promoter and terminator for 'constitutive' gene overexpression.
YCplac33; PTEF1-(BamHI-XbaI-PstI-SbfI)-TPGK1
 i-bio file PubMed: 23053078 Prof. Xiaoming Bao (Shandong University, China)
YEp-CH YEp; containing hygromycinB resistant gene and Cre gene under GAL2 regulative regulation promoter Not Available Unpublished A/Prof. Jin Hou (Shandong University, China)
         

2. Xylose-utilizing metabolic pathway modules

Plasmid name Properties Sequence files Reference (PubMed) Contact
pJX1 Overexpressing Pichia stipitis (aka Scheffersomyces stipitis) xylose reductase and xylitol dehydrogenase in S. cerevisiae using single-copy plasmid;
pJFE2; PTEF1-PsXYL1-TPGK1, PTDH3-PsXYL2-TCYC1
 i-bio file PubMed: 23053078 Prof. Xiaoming Bao (Shandong University, China)
pJX2 Overexpressing Pichia stipitis (aka Scheffersomyces stipitis) xylose reductase and NADP+-dependent xylitol dehydrogenase mutant ARS in S. cerevisiae using single-copy plasmid;
pJFE2; PTEF1-PsXYL1-TPGK1, PTDH3-PsXYL2ARS-TCYC1
i-bio file PubMed: 23053078 Prof. Xiaoming Bao (Shandong University, China)
pJX3 Overexpressing Pichia stipitis (aka Scheffersomyces stipitis) xylose reductase and NADP+-dependent xylitol dehydrogenase mutant ARSdR in S. cerevisiae using single-copy plasmid;
pJFE2; PTEF1-PsXYL1-TPGK1, PTDH3-PsXYL2ARSdR-TCYC1
i-bio file Unpublished Prof. Xiaoming Bao (Shandong University, China)

Figure. Coenzyme-binding domain of xylitol dehydrogenase (A), and binding sites of xylitol dehydrogenase from Pichia stipitis (B), sorbitol dehydrogenase from Bemisia argentifolii (C) and mutant ARSdR (D). Displayed by VMD: 1E3J (SDH from white fly with phosphate), IPL8 (SDH from human with NAD), PsXDH conenzyme-binding domain simulated by Swiss-model. Coordination was correlated with each other by Multiseq in VMD

pJX5 Overexpressing Piromyces sp. xylose isomerase in S. cerevisiae using multiple-copy plasmid;
pJFE3;
PTEF1-Piromyces XylA-TPGK1
i-bio file PubMed: 23053078 Prof. Xiaoming Bao (Shandong University, China)
pJFX11 Overexpressing Bacteroides vulgatus xylose isomerase in S. cerevisiae using multiple-copy plasmid;
pJFE11; PTEF1-BvuXylA-TCYC1
pDraw32 file:
i-bio file
PubMed: 25981595 Dr Anli Geng
(Ngee Ann Polytechnic, Singapore)

3. Non-oxidative pentose phosphate pathway modules

Plasmid name Properties Sequence files Reference (PubMed) Contact
pJPPP3 E. coli plasmid based on pUC19; Lineralized by SwaI digestion for genenomic integration to gre3 site in S. cerevisiae to give genotype:
gre3(-241, +338):: PTPI1-RKI1-TRKI1-PPGK1-TAL1-TTAL1-PFBA1-TKL1-TTKL1-PADH1-RPE1-TRPE1-loxP-KanMX4-loxP
 i-bio file PubMed: 23053078 Prof. Xiaoming Bao (Shandong University, China)
pJPPP4 E. coli plasmid based on pUC19; Lineralized by SwaI digestion for genenomic integration to gre3 site in S. cerevisiae to give genotype:
gre3(-241, +113):: PTPI1-RKI1-TRKI1-PPGK1-TAL1-TTAL1-PFBA1-TKL1-TTKL1-PADH1-RPE1-TRPE1-loxP-KanMX4-loxP
i-bio file Bingyin Peng Master's Thesis (Shandong University, China) Prof. Xiaoming Bao (Shandong University, China)
  For diploid industrial S. cerevisiae modification, SwaI-digested pJPPP3 is transformed firstly, KanMX4 is then removed by Cre-LoxP recombination (YEp-CH), and then SwaI-digested pJPPP4 is transformed.      
pJPPP-XK pUC19; Lineralized by SwaI; Genomic integrative plasmid used to overexpress S. cerevisiae endogenous genes RPE1RKI1TAL1TKL1 and XKS1 to generate genotype:
TKL1(-268, -1)::TRKI1-RKI1-PADH1-TRPE1-RPE1-PTPI1-LoxP-KanMX4-LoxP-TXKS1-XKS1-PPGK1-PPDC1-TAL1-TTAL1-PFBA1
pDraw32 file:
i-bio file
PubMed: 25981595 Dr Anli Geng
(Ngee Ann Polytechnic, Singapore)

4. The mevalonate pathway modules

Plasmid name Properties Sequence files Reference (PubMed) Contact
pPMVAu5 S. cerevisiae/E. coli shuttle plasmid; yeast episomal plasmid (multiple copy); E. coli AmpR; S. cerevisiae HIS3; overexpressing yeast upper-part mevalonate pathway;
pRS423: PSSA1-ERG10-TNAT1-PRPL4A-ERG13-TEFM1-PRPL15A-tHMG1-TEBS1

pPMVAu5.gb

Pubmed:
27939849
Addgene:
98296
pPMVAu8 S. cerevisiae/E. coli shuttle plasmid; yeast episomal plasmid (multiple copy); E. coli AmpR; S. cerevisiae HIS3; overexpressing yeast upper-part mevalonate pathway;
pRS423: PRPL4A-EfmvaS-TEFM1-PRPL15A-EfmvaE-TEBS1

pPMVAu8.gb

Pubmed:
27939849
Addgene:
98297
pPMVAd3 S. cerevisiae/E. coli shuttle plasmid; yeast episomal plasmid (multiple copy); E. coli AmpR; S. cerevisiae TRP1; overexpressing yeast lower-part mevalonate pathway;
pRS424;PRPL8B-ERG12-TNAT5-PSSB1-ERG8-TIDP1-PRPL3-MVD1-TIDP1-PYEF3-IDI1-TRPL15A

pPMVAd3.gb

Pubmed:
27939849
Addgene:
98298
pPMVAugw S. cerevisiae/E. coli shuttle plasmid; yeast episomal plasmid (multiple copy); E. coli AmpR; S. cerevisiae HIS3;expressing yeast lower-part mevalonate pathway through copper-inducible promoter;
pRS423: TEFM1<EfmvaS<PCUP1–PCUP1>EfmvaE>TEBS1

pPMVAugw.gb

Pubmed:
28239415
Addgene:
98300
pPMVAd36 S. cerevisiae/E. coli shuttle plasmid; yeast episomal plasmid (multiple copy); E. coli AmpR; S. cerevisiae TRP1;overexpressing yeast lower-part mevalonate pathway with ERG12 controlled by copper-inducible promoter;
pRS424;PCUP1-ERG12-TNAT5-PSSB1-ERG8-TIDP1-PRPL3-MVD1-TIDP1-PYEF3-IDI1-TRPL15A

pPMVAd36.gb

Pubmed:
28239415
Addgene:
98302
pIMVAu1 Based on S. cerevisiae/E.coli shuttle plasmid pRS423; Enhancing the upper-part mevalonate pathway; overexpressing codon-optimized Enterococcus faecalis mevalonate pathway genes under the control of galactose-inducible promoters; overexpressing HMG2 K6R. Lineralized by SwaI digestion for genomic integration to HMG2 in S. cerevisiae to give genotype:
HMG2K6R(−152 ,−1)::HIS3-TEFM1<EfmvaS<PGAL1PGAL10>ACS2>TACS2PGAL2>EfmvaE>TEBS1–PGAL7

pIMVAu1.gb

Pubmed:
28239415
Addgene:
98301
pIMVAd39T Based on E.coli plasmid pUC19; Enhancing the lower-part mevalonate pathway; overexpressing yeast mevalonate pathway genes under the control of consitutive promoters or GAL2 promoter; Lineralized by PmeI digestion for genomic integration into pdc5 locus in S. cerevisiae to give genotype:
pdc5(−31, 94)::PGAL2>ERG12>TNAT5–PTEF2>ERG8>TIDP1–TPRM9<MVD1<PADH2−TRPL15A<IDI1<PTEF1-TRP1

pIMVAd39T.gb

Pubmed:
28239415
Addgene:
98303
   
   
   
 
 

5. Specific terpene synthetic pathway modules

Plasmid name Properties Sequence files Reference (PubMed) Contact
pJT1 S. cerevisiae/E. coli shuttle plasmid; based on yeast episomal plasmid pRS425; E. coli AmpR; S. cerevisiae LEU2; overexpressing yeast farnesyl pyrophosphate synthase Erg20p and Actinidia chinensis nerolidol/linalool synhtase AcNES1 under the control of TEF1/TEF2 promoter:
PTEF2-ERG20-TRPL3-PTEF1-AcNES1-TRPL41B

pJT1.gb

Pubmed:
27939849
Addgene:
98299
pJT3 S. cerevisiae/E. coli shuttle plasmid; based on yeast episomal plasmid pRS425; E. coli AmpR; S. cerevisiae LEU2; overexpressing yeast farnesyl pyrophosphate synthase Erg20p and Actinidia chinensis nerolidol/linalool synhtase AcNES1 under the control of CUP1 promoter:
TRPL3<ScERG20<PCUP1-PCUP1>AcNES1>TRPL41B

pJT3.gb

Pubmed:
28239415
Addgene:
98304
pJT9R S. cerevisiae/E. coli shuttle plasmid; based on yeast episomal plasmid pRS425; E. coli AmpR; S. cerevisiae LEU2; overexpressing yeast farnesyl pyrophosphate synthase Erg20p and Actinidia chinensis nerolidol/linalool synhtase AcNES1 under the control of GAL1/GAL2 promoter:
TRPL3<ScERG20<PGAL1-PGAL2>AcNES1>TRPL41B

pJT9R.gb

Pubmed:
28239415
Addgene:
98305