Enhanced pinocembrin production in Escherichia coli by regulating cinnamic acid metabolism
|
|
|
- Linette Clarke
- 5 years ago
- Views:
Transcription
1 1 Enhanced pinocembrin production in Escherichia coli by regulating cinnamic acid metabolism 2 Weijia Cao 1,2, Weichao Ma 1,2,3, Xin wang 1,2, Bowen Zhang 1,2, Xun Cao 1,2, Kequan Chen 1,2*, Yan Li 1,2 3 & Pingkai Ouyang 1, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing , P.R. China 6 2 College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing , 7 P.R. China 8 3 College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui , P.R. 9 China 10 *Correspondence and requests for materials should be addressed to K.C. (kqchen@njtech.edu.cn ) 11
2 12 Construction of plasmids. pet-yepal was constructed by amplifying Rhodotorula mucilaginosa 13 PAL (YEPAL) from pet28a-4gs [30] using primers YEPAL-F (BamHI) and YEPAL-R (SacI) and 14 cloning the resulting product into the BamHI/SacI sites of petduet-1. pet-yepal-se4cl was 15 constructed by amplifying Streptomyces. coelicolor A3 (2) 4CL (SE4CL) from pet28a-4gs using 16 primers SE4CL-F (NdeI) and SE4CL-R (XhoI) and cloning the resulting product into the NdeI/XhoI 17 sites of pet-yepal. pet-bopal was constructed by amplifying Bambusa oldhamii PAL (BOPAL) 18 from puc57-bopal (synthesized by GENEWIZ, Nanjing, China) using primers BOPAL-F (NcoI) and 19 BOPAL-R (HindIII) and cloning the resulting product into the NcoI/HindIII sites of petduet pet-bopal-se4cl was constructed by cloning the SE4CL product into the NdeI/XhoI sites of 21 pet-bopal. pet-yepal-pa4cl was constructed by amplifying Petroselinum crispum 4CL (PA4CL) 22 from puc57-pa4cl (synthesized by GENEWIZ, Nanjing, China) using primers PA4CL-F (NdeI) and 23 PA4CL-R (XhoI) and cloning the resulting product into the NdeI/XhoI sites of pet-yepal. 24 pet-bopal-pa4cl was constructed through the digestion of both pet-bopal-se4cl and 25 pet-yepal-pa4cl with NdeI and XhoI, followed by ligation of the appropriate fragments. 26 pet-chs was constructed by amplifying Glycyrrhiza uralensis CHS from pet28a-4gs [30] 27 using primers CHS-F (NcoI) and CHS-R (EcoRI) and cloning the resulting product into the NcoI/EcoRI 28 sites of petduet-1. puc-chs was constructed through the digestion of both pet-chs and puc19 29 with BamHI and EcoRI, followed by ligation of the appropriate fragments. pet-chs-chi was 30 constructed by amplifying Medicago sativa CHI from pet28a-4gs using primers CHI-F (NdeI) and 31 CHI-R (XhoI) and cloning the resulting product into the NdeI/XhoI sites of pet-chs. prsf-chs-chi 32 was constructed through the digestion of both pet-chs-chi and prsfduet-1 with NcoI and XhoI, 33 followed by ligation of the appropriate fragments.
3 34 ptrc-yepal was constructed by amplifying YEPAL from pet28a-4gs using primers YEPAL-F2 35 (SacI) and YEPAL-R2 (XbaI) and cloning the resulting product into the SacI/XbaI sites of ptrc99a. 36 ptrc-se4cl was constructed by amplifying SE4CL from pet28a-4gs using primers SE4CL-F2 37 (BamHI) and SE4CL-R2 (HindIII) and cloning the resulting product into the BamHI/HindIII sites of 38 ptrc99a. ptrc-bopal was constructed by amplifying BOPAL from puc57-bopal by using primers 39 BOPAL-F (NcoI) and BOPAL-R (HindIII) and cloning the resulting product into the NcoI/HindIII sites 40 of ptrc99a. ptrc-pa4cl was constructed by amplifying PA4CL from puc57-pa4cl by using primers 41 PA4CL-F2 (EcoRI) and PA4CL-R2 (PstI) and cloning the resulting product into the EcoRI/PstI sites of 42 ptrc99a. 43 YEPAL-rrnB fragment was amplified from YEPAL to rrnb T1 terminator by using YEPAL-F2 44 (SacI) and YEPAL-R3 (BglII). Trc-SE4CL-rrnB fragment was amplified from Trc promoter to rrnb T1 45 terminator by using SE4CL-F3 (BamHI) and SEPAL-R3 (XbaI). Trc-BOPAL-rrnB fragment was 46 amplified from BOPAL to rrnb T1 terminator using BOPAL-F (NcoI) and BOPAL-R2 (BglII). 47 Trc-PA4CL-rrnB fragment was amplified from Trc promoter to rrnb T1 terminator using SE4CL-F3 48 (BamHI) and SE4CL R3 (XbaI). ptrc-yepal-se4cl was constructed through the digestion of 49 ptrc99a, Trc-YEPAL-rrnB and Trc-SE4CL-rrnB with SacI/XbaI, SacI/BamHI, and BglII/XbaI, followed 50 by ligation of the appropriate fragments. ptrc-yepal-pa4cl, ptrc-bopal-se4cl and 51 ptrc-bopal-pa4cl were constructed as same as ptrc-yepal-se4cl. 52 pacyc-trc-bopal-trc-pa4cl was constructed by through the digestion of both 53 ptrc-bopal-pa4cl and pacycduet-1 with NcoI and XhoI, followed by ligation of the appropriate 54 fragments. Fused-CHS-CHI was amplified by using Fused-F (XbaI) and Fused-R (XbaI). 55 ptrc-bopal-pa4cl-chs-chi was constructed by in-fusion cloning of ptrc-bopal-pa4cl and
4 56 Fused-CHS-CHI. 57 prsf-acc was constructed by amplifying accbc and dtsr1 from C. glutamicum using primers 58 accbc-f (EcoRV), accbc-f (KpnI), dtsr1-f (KpnI) and dtsr1-r (AvrII) and then cloning the resulting 59 product into the EcoRV/AvrII sites of prsfduet-1. prsf-acs-acc was constructed by amplifying acs 60 from E.coli using primers acs-f (BamHI) and acs-f (NotI) and cloning the resulting product into the 61 BamHI/NotI sites of prsf-acc. 62 prsf-acs-acc-chs(s165m)-chi was constructed by amplifying CHS(S165M)-CHI from 63 prsf-chs(s165m)-chi using primers Fused-F2 (AvrII) and Fused-R2 (AvrII) and cloning the 64 resulting product into the AvrII sites of prsf-acs-acc. 65
5 66 Supplementary Table 67 Table S1 Strains used in this study Strains Description Source or reference E. coli BL21(DE3) F ompt hsds B (r B m B ) gal (λ ci857 ind1 sam7 nin5 Transgen laci lacuv5-t7 gene1), dcm(de3) E. coli Trans-T1 F φ80 (lacz) M15 lacx 74 hsdr(r k m k ) reca Transgen 1398endA1 tona E.coli K-12 Wild-type strain, F + rpos (AM) rph-l CGSC 4401 Corynebacterium glutamicum Clone for ACC ATCC ATCC WT E. coli BL21(DE3) carrying prsfduet-1 Ser E. coli BL21(DE3) carrying ptrc-bopal-pa4cl and prsf-chs-chi ACC overexpression E. coli BL21(DE3) carrying prsf-acc acs and ACC overexpression E. coli BL21(DE3) carrying prsf-acs-acc FabF overexpression E. coli BL21(DE3) carrying pacyc-fabf [18] acs, ACC, and FabF E. coli BL21(DE3) carrying prsf-acs-acc and overexpression pacyc-fabf S165M, acs, ACC, FabF E. coli BL21(DE3) carrying ptrc-bopal-pa4cl, prsf-acs-acc-chs(s165m)-chi and pacyc-fabf
6 68 Table S2 Plasmids used in this study Plasmids Description Source or reference pet-28a T7 promoter, pbr322 ori,, Km R Novagen petduet-1 Double T7 promoters, pbr322 ori, Amp R Novagen pacycduet-1 Double T7 promoters, P15A ori, Cm R Novagen prsfduet-1 Double T7 promoters, RSF ori, Kn R Novagen puc19 pbr322 ori, Amp R Lab collection ptrc99a Trc promoter, pbr322 ori,, Amp R Lab collection pet28a-4gs pet-28a carrying pal from R. mucilaginosa, 4cl [30] from S. coelicolor, chs from G. uralensis and chi from M. sativa pet-yepal-se4cl petduet-1 carrying pal from R. mucilaginosa, 4cl from S. coelicolor pet-yepal-pa4cl petduet-1 carrying pal from R. mucilaginosa, 4cl from P. crispum pet-bopal-se4cl petduet-1 carrying pal from B. oldhamii, 4cl from S. coelicolor pet-bopal-pa4cl petduet-1 carrying pal from B. oldhamii, 4cl from P. crispum ptrc-yepal ptrc99a carrying pal from R. mucilaginosa ptrc-se4cl ptrc99a carrying 4cl from S. coelicolor ptrc-bopal ptrc99a carrying pal from B. oldhamii
7 ptrc-pa4cl ptrc99a carrying 4cl from P. crispum ptrc-yepal-se4cl ptrc99a carrying pal from R. mucilaginosa, 4cl from S. coelicolor ptrc-yepal-pa4cl ptrc99a carrying pal from R. mucilaginosa, 4cl from P. crispum ptrc-bopal-se4cl ptrc99a carrying pal from B. oldhamii, 4cl from S. coelicolor ptrc-bopal-pa4cl ptrc99a carrying pal from B. oldhamii, 4cl from P. crispum ptrc-bopal-pa4cl-chs-chi ptrc99a carrying pal from B. oldhamii, 4cl from P. crispum, chs from G. uralensis and chi from M. sativa pacyc-trc-bopal-trc-pa4cl pacycduet-1 carrying pal from B. oldhamii, 4cl from P. crispum under Trc promoter pet-chs petduet-1 carrying chs from G. uralensis puc-chs puc19 carrying chs from G. uralensis pet-chs-chi petduet-1 carrying chs from G. uralensis and chi from M. sativa prsf-chs-chi prsfduet-1 carrying chs from G. uralensis and chi from M. sativa prsf-acc prsfduet-1 carrying C. glutamicum accbc and dtsr1
8 prsf-acs-acc prsfduet-1 carrying E. coli acs and C. glutamicum accbc and dtsr1 prsf-acs-acc-chs(s165m)-chi prsfduet-1 carrying E. coli acs, C. glutamicum accbc and dtsr1, chs (S165M) from G. uralensis and chi from M. sativa 69 70
9 71 Table S3 Primers used in this study Oligonucleotides Sequences, 5-3 * YEPAL-F (BamHI) CGCGGATCCGATGGCTCCGTCTGTTG YEPAL-R (SacI) CGAGCTCTTAAGCCATCATTTTAACCAGAACC SE4CL-F (NdeI) GGAATTCCATATGTTCCGTTCTGAATACGCTGAC SE4CL-R (XhoI) CCGCTCGAGTAACGCGGTTCACGCAGCTG BOPAL-F (NcoI) CATGCCATGGGCATGCCACGCGAGGATG BOPAL-R (HindIII) CCCAAGCTTTTAGCAAATCGGCAGCGG PA4CL-F (NdeI) GGAATTCCATATGGGTGACTGCGTTGCTCC PA4CL-R (XhoI) CCGCTCGAGTTATTTCGGCAGGTCACCAG CHS-F (NcoI) CATGCCATGGTTTCTGTTGCTGAAATCC CHS-R (EcoRI) CGGAATTCTTAGATAGCAACAGAGTGCAG CHI-F (NdeI) GGGAATTCCATATGGCTGCTTCTATCACCG CHI-R (XhoI) CCGCTCGAGTTAGTTACCGATTTTGAAAGCACC YEPAL-F2 (SacI) CGAGCTCATGGCTCCGTCTGTTGACTC YEPAL-R2 (XbaI) CTAGTCTAGATTAAGCCATCATTTTAACCAGAACCG SE4CL-F2 (BamHI) CGCGGATCCATGTTCCGTTCTGAATACGC SE4CL-R2 (HindIII) CCCAAGCTTTTAACGCGGTTCACGCAG PA4CL-F2 (EcoRI) CCGGAATTCATGGGTGACTGCGTTGCTCC PA4CL-R2 (PstI) AAAACTGCAGTTATTTCGGCAGGTCACCAGAAGC YEPAL-R3 (BglII) GGAAGATCTATTTGTCCTACTCAGGAGAGCGTTC SE4CL-F3 (BamHI) CGCGGATCCTTGACAATTAATCATCCGGCTCG
10 SEPAL-R3 (XbaI) CTAGTCTAGAATTTGTCCTACTCAGGAGAGCGTTC BOPAL-R2 (BglII) GGAAGATCTATTTGTCCTACTCAGGAGAGCGTTC Fused-F (XbaI) CTGAGTAGGACAAATTCTAGAGGATCTCGACGCTCTCCCTTATGC Fused-R (XbaI) TGCCTGCAGGTCGACTCTAGAGACCGTGTGCTTCTCAAATGCCTGAG accbc-f (EcoRV) GGCCGATATCGGTGTCAGTCGAGACTAGGAAGATCAC accbc-f (KpnI) CGGGGTACCCTTGATCTCGAGGAGAACAACG dtsr1-f (KpnI) CGGGGTACCATGACCATTTCCTCACCTTT dtsr1-r (AvrII) CGGCCTAGGTTACAGTGGCATGTTGCC acs-f (BamHI) CGGGATCCGATGAGCCAAATTCACAAACACAC acs-f (NotI) AAGGAAAAAAGCGGCCGCTTACGATGGCATCGCGATAG Fused-F2 (AvrII) CGGCAACATGCCACTGTAACCTAGGCGACTCCTGCATTAGG Fused-R2 (AvrII) CAGCGGTGGCAGCAGCCTAGGCAGCAGCGGTTTCTTTACCAG 72 *Bold and underlined letters are restriction enzyme cut sites. 73
11 74 Table S4 mutant-specific primers in this study Oligonucleotides Sequences, 5-3 Phe-F GAACGGTACCACCAGCGAAGCAACCCTGCTGGTAC Phe-R TCGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC Asp-F GAACGGTACCACCAGCATCGCAACCCTGCTGGTAC Asp-R GATGCTGGTGGTACCGTTCTGCGTCTGGCTAAAG Lys-F GAACGGTACCACCAGCTTTGCAACCCTGCTGGTAC Lys-R AAAGCTGGTGGTACCGTTCTGCGTCTGGCTAAAG Ala-F GAACGGTACCACCAGCTGCGCAACCCTGCTGGTAC Ala-R GCAGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC Val-F GAACGGTACCACCAGCAACGCAACCCTGCTGGTAC Val-R GTTGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC Leu-F GAACGGTACCACCAGCCAGGCAACCCTGCTGGTAC Leu-R CTGGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC Pro-F GAACGGTACCACCAGCCGGGCAACCCTGCTGGTAC Pro-R CCGGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC Trp-F GAACGGTACCACCAGCCCAGCAACCCTGCTGGTAC Trp-R TGGGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC Met-F GAACGGTACCACCAGCCATGCAACCCTGCTGGTAC Met-R ATGGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC Ile-F GAACGGTACCACCAGCAATGCAACCCTGCTGGTAC Ile-R ATTGCTGGTGGTACCGTTCTGCGTCTGGCTAAAGAC
12 75 Supplementary Figure Fig. S1 The sequence logo of chalcone and stilbene synthases by PROSITE. 9 th C: the active site 78 residue Fig. S2 A structure mode of G. uralensis CHS by SWISS-MODEL. S165: the mutation site 83 84
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature12536 Supplementary Discussion Fatty acyl-acp thioesterases for the production of FFAs There have been several reports on the production of FFAs, which are discussed
Improving fatty acids production by engineering dynamic pathway regulation and metabolic control
Supporting Information Appendix Improving fatty acids production by engineering dynamic pathway regulation and metabolic control Peng Xu 1, 2, Lingyun Li 2, 3, Fuming Zhang 1, 2, Gregory N. Stephanopoulos
Plant polyphenols are plant secondary metabolites which have
Metabolic Engineering of Escherichia coli for the Synthesis of the Plant Polyphenol Pinosylvin Philana Veronica van Summeren-Wesenhagen, Jan Marienhagen Institute of Bio- and Geosciences, IBG-1: Biotechnology,
Problem 2 (10 Points) The wild type sequence of the coding region of an mrna is shown below.
Problem 2 (10 Points) The wild type sequence of the coding region of an mrna is shown below. 5 AUG ACC UGG AAU AAA UGA 3 Use that sequence to answer each of the questions below. a) What is the sequence
Supporting Information
Supporting Information For Heterologous production of thiostrepton A and biosynthetic engineering of thiostrepton analogs Chaoxuan Li, Feifei Zhang, and Wendy L. Kelly* Table of Contents Figure S1. PCR
Supplementary Information
Supplementary Information Supplementary s Supplementary 1 All three types of foods suppress subsequent feeding in both sexes when the same food is used in the pre-feeding test feeding. (a) Adjusted pre-feeding
Supplementary Information
Supplementary Information Structural basis of improved second generation 3-nitro-tyrosine trna synthetases Richard B. Cooley, Jessica L. Feldman, Camden M. Driggers, Taylor Bundy, Audrey L. Stokes, P.
Unraveling and engineering the production of 23,24-bisnorcholenic steroids in sterol metabolism
Unraveling and engineering the production of 23,24-bisnorcholenic steroids in sterol metabolism Li-Qin Xu, Yong-Jun Liu, Kang Yao, Hao-Hao Liu, Xin-Yi Tao, Feng-Qing Wang*, Dong-Zhi Wei* State Key Laboratory
reads observed in trnas from the analysis of RNAs carrying a 5 -OH ends isolated from cells induced to express
Supplementary Figure 1. VapC-mt4 cleaves trna Ala2 in E. coli. Histograms representing the fold change in reads observed in trnas from the analysis of RNAs carrying a 5 -OH ends isolated from cells induced
JBC Papers in Press. Published on January 14, 2002 as Manuscript M
JBC Papers in Press. Published on January 14, 2002 as Manuscript M109976200 Pig Liver Carnitine Palmitoyltransferase: Chimera Studies Show That Both the N- and C-Terminal Regions of the Enzyme Are Important
Amino acids-incorporated nanoflowers with an
Amino acids-incorporated nanoflowers with an intrinsic peroxidase-like activity Zhuo-Fu Wu 1,2,+, Zhi Wang 1,+, Ye Zhang 3, Ya-Li Ma 3, Cheng-Yan He 4, Heng Li 1, Lei Chen 1, Qi-Sheng Huo 3, Lei Wang 1,*
Supplementary Figure-1. SDS PAGE analysis of purified designed carbonic anhydrase enzymes. M1-M4 shown in lanes 1-4, respectively, with molecular
Supplementary Figure-1. SDS PAGE analysis of purified designed carbonic anhydrase enzymes. M1-M4 shown in lanes 1-4, respectively, with molecular weight markers (M). Supplementary Figure-2. Overlay of
Strain Improvement of Recombinant Escherichia coli for Efficient Production of Plant Flavonoids
Strain Improvement of Recombinant Escherichia coli for Efficient Production of Plant Flavonoids Effendi Leonard, Yajun Yan, Zachary L. Fowler, Zhen Li, Chin-Giaw Lim, Kok-Hong Lim, and Mattheos A. G. Koffas*
Supplementary Figure 1. Amino acid sequences of GodA and GodA*. Inserted. residues are colored red. Numbers indicate the position of each residue.
Supplementary Figure 1. Amino acid sequences of GodA and GodA*. Inserted residues are colored red. Numbers indicate the position of each residue. Supplementary Figure 2. SDS-PAGE analysis of purified recombinant
Nature Methods: doi: /nmeth Supplementary Figure 1
Supplementary Figure 1 Subtiligase-catalyzed ligations with ubiquitin thioesters and 10-mer biotinylated peptides. (a) General scheme for ligations between ubiquitin thioesters and 10-mer, biotinylated
Synthesis of Unnatural Flavonoids and Stilbenes by Exploiting the Plant Biosynthetic Pathway in Escherichia coli
Article Synthesis of Unnatural Flavonoids and Stilbenes by Exploiting the Plant Biosynthetic Pathway in Escherichia coli Yohei Katsuyama, 1 Nobutaka Funa, 1 Ikuo Miyahisa, 1 and Sueharu Horinouchi 1, *
BIOCHEMISTRY REVIEW. Overview of Biomolecules. Chapter 4 Protein Sequence
BIOCHEMISTRY REVIEW Overview of Biomolecules Chapter 4 Protein Sequence 2 3 4 Are You Getting It?? A molecule of hemoglobin is compared with a molecule of lysozyme. Which characteristics do they share?
This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth 2 points.
MBB 407/511 Molecular Biology and Biochemistry First Examination - October 1, 2002 Name Social Security Number This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is
Luminescent platforms for monitoring changes in the solubility of amylin and huntingtin in living cells
Electronic Supplementary Material (ESI) for Molecular BioSystems. This journal is The Royal Society of Chemistry 2016 Contents Supporting Information Luminescent platforms for monitoring changes in the
Construction of a hepatocellular carcinoma cell line that stably expresses stathmin with a Ser25 phosphorylation site mutation
Construction of a hepatocellular carcinoma cell line that stably expresses stathmin with a Ser25 phosphorylation site mutation J. Du 1, Z.H. Tao 2, J. Li 2, Y.K. Liu 3 and L. Gan 2 1 Department of Chemistry,
Supplementary Information. Amino group carrier protein-mediated secondary metabolite biosynthesis in Streptomyces
Supplementary Information Amino group carrier protein-mediated secondary metabolite biosynthesis in Streptomyces Fumihito Hasebe 1, Kenichi Matsuda 1, Taro Shiraishi 1, Yushi Futamura 2, Takeshi Nakano
Supplemental Data Functional characterization of core components of the Bacillus subtilis c- di-
Supplemental Data Functional characterization of core components of the Bacillus subtilis c- di- GMP signaling pathway Xiaohui Gao 1,3, Sampriti Mukherjee 2, Paige M. Matthews 1, Loubna A. Hammad 1, Daniel
Table S1. Strains, Plasmids and Phage
Table S1. Strains, Plasmids and Phage Strain, Plasmid, Phage Genotype or Description Reference S. enterica 14028 wild type ATCC strain (1) HK132 yfin; 14028 with deletion of yfin This study QW262 yhjh
Supporting Information
Supporting Information Nothaft et al. 10.1073/pnas.0903078106 Fig. S1. N-linked protein glycosylation in C. jejuni 11168. Genes with known function in the C. jejuni pgl pathway are depicted in black: Gne,
Proteolytic processing at a novel cleavage site in the N-terminal region of the tomato ringspot nepovirus RNA-1-encoded polyprotein in vitro
Journal of General Virology (2000), 81, 2771 2781. Printed in Great Britain... Proteolytic processing at a novel cleavage site in the N-terminal region of the tomato ringspot nepovirus RNA-1-encoded polyprotein
Biosynthesis of 5-deoxyflavanones in microorganisms
DOI 10.1002/biot.200700119 Biotechnol. J. 2007, 2, 1250 1262 Research Article Biosynthesis of 5-deoxyflavanones in microorganisms Yajun Yan 1, Lixuan Huang 2 and Mattheos A. G. Koffas 1 1 Department of
Increased Unsaturated Fatty Acid Production Associated with a Suppressor of the faba6(ts) Mutation in Escherichia coli
JOURNAL OF BACTERIOLOGY, Sept. 1996, p. 5382 5387 Vol. 178, No. 18 0021-9193/96/$04.00 0 Copyright 1996, American Society for Microbiology Increased Unsaturated Fatty Acid Production Associated with a
LAB#23: Biochemical Evidence of Evolution Name: Period Date :
LAB#23: Biochemical Evidence of Name: Period Date : Laboratory Experience #23 Bridge Worth 80 Lab Minutes If two organisms have similar portions of DNA (genes), these organisms will probably make similar
Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR-1 gene
Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR-1 gene YUELIN ZHANG, WEIHUA FAN, MARK KINKEMA, XIN LI, AND
Author(s) Sugihara, Shinji; Orikasa, Yoshitak. Citation Biotechnology Letters, 30(3): 411-4
An EntD-like phosphopantetheinyl tr Title Photobacterium profundum SS9 comple Moritella marina strain MP-1 involv docosahexaenoic acid Author(s) Sugihara, Shinji; Orikasa, Yoshitak Citation Biotechnology
SUPPLEMENTARY INFORMATION Glucosylceramide synthase (GlcT-1) in the fat body controls energy metabolism in Drosophila
SUPPLEMENTARY INFORMATION Glucosylceramide synthase (GlcT-1) in the fat body controls energy metabolism in Drosophila Ayako Kohyama-Koganeya, 1,2 Takuji Nabetani, 1 Masayuki Miura, 2,3 Yoshio Hirabayashi
Supplemental Table 1. Plasmid Construct backbone. Restriction sites. PCR template. HLA DRα pcdna3.1 Zeo+
SupplementalTable1 Plasmid Construct backbone HLA DRα Zeo+ Restriction sites PCR template PCRCloningstrategy Primerpairs(F/R)andpairsofprimersforchimericconstructs(N terminalandc terminal codingregion)weregiven
Post-PKS tailoring steps of the spiramycin. macrolactone ring in Streptomyces ambofaciens
Post-PKS tailoring steps of the spiramycin macrolactone ring in Streptomyces ambofaciens Hoang-Chuong NGUYEN, Emmanuelle DARBN, Robert THAI, Jean-Luc PERNDET, Sylvie LAUTRU SUPPLEMENTARY DATA 1 Figure
Microbial Cell Factories. Open Access RESEARCH. Xiaomeng Tong, Eun Kyoung Oh, Byeong ha Lee and Jeong K. Lee *
https://doi.org/.86/s2934-9-7-8 Microbial Cell Factories RESEARCH Open Access Production of long chain free fatty acids from metabolically engineered Rhodobacter sphaeroides heterologously producing periplasmic
Cloning and Expression of a Subfamily 1.4 Lipase from Bacillus licheniformis IBRL-CHS2
Tropical Life Sciences Research, 27(Supp. 1), 145 150, 2016 Cloning and Expression of a Subfamily 1.4 Lipase from Bacillus licheniformis IBRL-CHS2 1 Nidyaletchmy Subba Reddy, 1 Rashidah Abdul Rahim *,
SUPPLEMENTARY INFORMATION. Supplementary Figures S1-S9. Supplementary Methods
SUPPLEMENTARY INFORMATION SUMO1 modification of PTEN regulates tumorigenesis by controlling its association with the plasma membrane Jian Huang 1,2#, Jie Yan 1,2#, Jian Zhang 3#, Shiguo Zhu 1, Yanli Wang
AA s are the building blocks of proteins
Chamras Chemistry 106 Lecture otes Chapter 24: Amino Acids, Peptides, and Proteins General Formula: () n (') α-amino Acids: (n = 1) Example: Amino Acids and Proteins: Glycine Alanine Valine AA s are the
CS612 - Algorithms in Bioinformatics
Spring 2016 Protein Structure February 7, 2016 Introduction to Protein Structure A protein is a linear chain of organic molecular building blocks called amino acids. Introduction to Protein Structure Amine
Title: Authors: Affiliation(s): * Correspondence:
Title: Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-ntetraose and lacto-n-neo-tetraose through overlapping, yet distinct pathways. Authors: Kieran James 1,2, Mary O Connell
Development of safe and immunogenic reassortant viruses with 5:3 genotype for live attenuated influenza vaccine
Development of safe and immunogenic reassortant viruses with 5:3 genotype for live attenuated influenza vaccine Irina Isakova-Sivak, PhD Institute of Experimental Medicine, Saint Petersburg, Russia The
Expression of a soluble flavone synthase allows the biosynthesis of phytoestrogen derivatives in Escherichia coli
Appl Microbiol Biotechnol (2006) 70: 85 91 DOI 10.1007/s00253-005-0059-x APPLIED GENETICS AND MOLECULAR BIOTECHNOLOGY Effendi Leonard. Joseph Chemler. Kok Hong Lim. Mattheos A. G. Koffas Expression of
Identification of Mutation(s) in. Associated with Neutralization Resistance. Miah Blomquist
Identification of Mutation(s) in the HIV 1 gp41 Subunit Associated with Neutralization Resistance Miah Blomquist What is HIV 1? HIV-1 is an epidemic that affects over 34 million people worldwide. HIV-1
EGFR shrna A: CCGGCGCAAGTGTAAGAAGTGCGAACTCGAGTTCGCACTTCTTACACTTGCG TTTTTG. EGFR shrna B: CCGGAGAATGTGGAATACCTAAGGCTCGAGCCTTAGGTATTCCACATTCTCTT TTTG
Supplementary Methods Sequence of oligonucleotides used for shrna targeting EGFR EGFR shrna were obtained from the Harvard RNAi consortium. The following oligonucleotides (forward primer) were used to
1. Describe the relationship of dietary protein and the health of major body systems.
Food Explorations Lab I: The Building Blocks STUDENT LAB INVESTIGATIONS Name: Lab Overview In this investigation, you will be constructing animal and plant proteins using beads to represent the amino acids.
Biomolecules: amino acids
Biomolecules: amino acids Amino acids Amino acids are the building blocks of proteins They are also part of hormones, neurotransmitters and metabolic intermediates There are 20 different amino acids in
Chemical Mechanism of Enzymes
Chemical Mechanism of Enzymes Enzyme Engineering 5.2 Definition of the mechanism 1. The sequence from substrate(s) to product(s) : Reaction steps 2. The rates at which the complex are interconverted 3.
Supplementary Figure 1
Supplementary Figure 1 Asymmetrical function of 5p and 3p arms of mir-181 and mir-30 families and mir-142 and mir-154. (a) Control experiments using mirna sensor vector and empty pri-mirna overexpression
Four melanocyte-stimulating hormones have the following amino acid sequences:
Assignment 14: Melanocyte-stimulating hormone belongs to a group called the melanocortins. This group includes ACTH, alpha-msh, beta-msh and gamma-msh; these peptides are all cleavage products of a large
TetR repressor-based bioreporters for the detection of doxycycline using Escherichia
Supplementary materials TetR repressor-based bioreporters for the detection of doxycycline using Escherichia coli and Acinetobacter oleivorans Hyerim Hong and Woojun Park * Department of Environmental
Supplementary Information
Supplementary Information J. Braz. Chem. Soc., Vol. 24, No. 12, S1-S21, 2013. Printed in Brazil - 2013 Sociedade Brasileira de Química 0103-5053 $6.00+0.00 SI Rui He, a,b,c Bochu Wang,*,b Toshiyuki Wakimoto,
Beta Amyloid Peptides
Beta Amyloid Peptides The Most Comprehensive Collection for Alzheimer s Disease Academic Services Pharmaceutical Services Beta Amyloid Peptides The Most Comprehensive Collection for Alzheimer s Disease
Figure S1. Molecular confirmation of the precise insertion of the AsMCRkh2 cargo into the kh w locus.
Supporting Information Appendix Table S1. Larval and adult phenotypes of G 2 progeny of lines 10.1 and 10.2 G 1 outcrosses to wild-type mosquitoes. Table S2. List of oligonucleotide primers. Table S3.
Algal Biofuels Research: Using basic science to maximize fuel output. Jacob Dums, PhD candidate, Heike Sederoff Lab March 9, 2015
Algal Biofuels Research: Using basic science to maximize fuel output Jacob Dums, PhD candidate, jtdums@ncsu.edu Heike Sederoff Lab March 9, 2015 Outline Research Approach Dunaliella Increase Oil Content
Construction of a Doxycycline-Dependent Simian Immunodeficiency Virus Reveals a Nontranscriptional Function of Tat in Viral Replication
JOURNAL OF VIROLOGY, Oct. 2007, p. 11159 11169 Vol. 81, No. 20 0022-538X/07/$08.00 0 doi:10.1128/jvi.01354-07 Copyright 2007, American Society for Microbiology. All Rights Reserved. Construction of a Doxycycline-Dependent
Introduction to Peptide Sequencing
Introduction to Peptide equencing Quadrupole Ion Traps tructural Biophysics Course December 3, 2014 12/8/14 Introduction to Peptide equencing - athan Yates 1 Why are ion traps used to sequence peptides?
Supporting Information
Supporting Information Keller et al. 10.1073/pnas.1222607110 MB1 Ori puc18 Ori AscI (8713) pdad downstream flank pdad PpdaD SphI (6970) Msed1993 ApaI (10721) Apr ApaLI (9115) NcoI (8) PmeI (8796) PvuI
The Sex-lethal Early Splicing Pattern Uses a Default Mechanism Dependent on the Alternative 5 Splice Sites
MOLECULAR AND CELLULAR BIOLOGY, Mar. 1997, p. 1674 1681 Vol. 17, No. 3 0270-7306/97/$04.00 0 Copyright 1997, American Society for Microbiology The Sex-lethal Early Splicing Pattern Uses a Default Mechanism
Supplementary Figure 1
Supplementary Figure 1 Isolation of mt-trnas and RNA-MS analysis of mt-trna Asn from M. nudus (a)m. nudus mt-trnas were isolated by RCC and resolved by 10% denaturing PAGE. The gel was stained with SYBR
Nature Biotechnology: doi: /nbt Supplementary Figure 1. Folate stability in GA9.15
Supplementary Figure 1 Folate stability in GA9.15 Total folate levels in GA9.15 until 7 months of storage at 28 C. Seeds of the sixth (T5) generation (upon harvest stored at -80 C) were used to confirm
Available online at ScienceDirect. Procedia Chemistry 14 (2015 )
Available online at www.sciencedirect.com ScienceDirect Procedia Chemistry 14 (2015 ) 117 121 2nd Humboldt Kolleg in conjunction with International Conference on Natural Sciences, HK-ICONS 2014 Design
Figure C5.1 H. pylori cells (
CHAPTER 5 Propionibacterium acnes and Helicobacter pylori lipases: isolation, characterization and inhibition by natural substances Figure C5.1 H. pylori cells (http://www.helico.com). Chapter 5: Propionibacterium
Electronic Supplementary Information. Table of Contents
Electronic Supplementary Information Examination of native chemical ligation using peptidyl prolyl thioester Takahiro Nakamura, Akira Shigenaga, Kohei Sato, Yusuke Tsuda, Ken Sakamoto, and Akira Otaka*
jmb Synthesis of Chlorogenic Acid and p-coumaroyl Shikimates from Glucose Using Engineered Escherichia coli Research Article Review
J. Microbiol. Biotechnol. (2014), 24(8), 1109 1117 http://dx.doi.org/10.4014/jmb.1403.03033 Review Research Article jmb Synthesis of Chlorogenic Acid and p-coumaroyl Shikimates from Glucose Using Engineered
Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of proteins
SUPPLEMENTARY INFORMATION Structural insights into the potential of 4-fluoroproline to modulate biophysical properties of proteins Bastian Holzberger, Samra Obeid, Wolfram Welte, Kay Diederichs, and Andreas
Amino Acids. Amino Acids. Fundamentals. While their name implies that amino acids are compounds that contain an NH. 3 and CO NH 3
Fundamentals While their name implies that amino acids are compounds that contain an 2 group and a 2 group, these groups are actually present as 3 and 2 respectively. They are classified as α, β, γ, etc..
Supplemental Material for. Figure S1. Identification of TetR responsive promoters in F. novicida and E. coli.
Supplemental Material for Synthetic promoters functional in Francisella novicida and Escherichia coli Ralph L. McWhinnie and Francis E. Nano Department of Biochemistry and Microbiology, University of Victoria,
Functional expression of a P450 flavonoid hydroxylase for the biosynthesis of plant-specific hydroxylated flavonols in Escherichia coli
Metabolic Engineering 8 (2006) 172 181 www.elsevier.com/locate/ymben Functional expression of a P450 flavonoid hydroxylase for the biosynthesis of plant-specific hydroxylated flavonols in Escherichia coli
BCH 4054 December 13, 1999
BH 4054 December 13, 1999 FINL EXM This exam consists of six pages. Make sure you have one of each. For questions indicating a choice, answer only one of the choices. (If you answer both, you need to indicate
Midterm 2 Results. Standard Deviation:
Midterm 2 Results High: Low: Mean: Standard Deviation: 97.5% 16% 58% 16.3 Lecture 17 Amino Acid Metabolism Urea Cycle N and S assimilation Last cofactors: THF and SAM Dietary (Exogenous) Proteins Hydrolyzed
Introduction 1/3. The protagonist of our story: the prokaryotic ribosome
Introduction 1/3 The protagonist of our story: the prokaryotic ribosome Introduction 2/3 The core functional domains of the ribosome (the peptidyl trasferase center and the decoding center) are composed
Structure of the measles virus hemagglutinin bound to the CD46 receptor. César Santiago, María L. Celma, Thilo Stehle and José M.
Supporting Figures and Table for Structure of the measles virus hemagglutinin bound to the CD46 receptor César Santiago, María L. Celma, Thilo Stehle and José M. Casasnovas This PDF file includes: Supplementary
Amino acids. Side chain. -Carbon atom. Carboxyl group. Amino group
PROTEINS Amino acids Side chain -Carbon atom Amino group Carboxyl group Amino acids Primary structure Amino acid monomers Peptide bond Peptide bond Amino group Carboxyl group Peptide bond N-terminal (
Supplementary Table 1. List of primers used in this study
Supplementary Table 1. List of primers used in this study Gene Forward primer Reverse primer Rat Met 5 -aggtcgcttcatgcaggt-3 5 -tccggagacacaggatgg-3 Rat Runx1 5 -cctccttgaaccactccact-3 5 -ctggatctgcctggcatc-3
Proximate composition, amino acid and fatty acid composition of fish maws. Department of Biology, Lingnan Normal University, Zhanjiang, , China
SUPPLEMENTARY MATERIAL Proximate composition, amino acid and fatty acid composition of fish maws Jing Wen a, Ling Zeng b *, Youhou Xu c, Yulin Sun a, Ziming Chen b and Sigang Fan d a Department of Biology,
Controlling Macromolecular Topology with Genetically Encoded. SpyTag-SpyCatcher Chemistry
Electronic Supporting Information for Controlling Macromolecular Topology with Genetically Encoded SpyTag-SpyCatcher Chemistry Wen-Bin Zhang, Fei Sun, David A. Tirrell,* and Frances H. Arnold* Division
A Mechanism of Gene Amplification Driven by Small DNA Fragments
A Mechanism of Gene Amplification Driven by Small DNA Fragments Kuntal Mukherjee, Francesca Storici* School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America Abstract
Interlab Study - Cloning and measuring of GFP and RFP
Interlab Study - Cloning and measuring of GFP and RFP The following constructs are build for further GFP and RFP measurement: I2020 GFP construct 0 K823005 + E0240 GFP construct I K823012 + E0240 GFP construct
Flavonoids are the most ubiquitous polyphenolic secondary
Production of 7-O-Methyl Aromadendrin, a Medicinally Valuable Flavonoid, in Escherichia coli Sailesh Malla, a Mattheos A. G. Koffas, b Romas J. Kazlauskas, c and Byung-Gee Kim a Laboratory of Molecular
Late assembly of the Vibrio cholerae cell division machinery postpones
2 Late assembly of the Vibrio cholerae cell division machinery postpones septation to the last % of the cell cycle 3 4 Elisa Galli, Evelyne Paly and François-Xavier Barre,# 5 6 7 Institute for Integrative
Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products)
Page 8/6: The cell Where to start: Proteins (control a cell) (start/end products) Page 11/10: Structural hierarchy Proteins Phenotype of organism 3 Dimensional structure Function by interaction THE PROTEIN
Supplementary Materials and Methods
Supplementary Materials and Methods Reagents and antibodies was purchased from iaffin GmbH & Co KG. Cisplatin (ristol-myers Squibb Co.) and etoposide (Sandoz Pharma Ltd.) were used. Antibodies recognizing
Figure S1! CrFK! DNA Synthesis! Copies viral DNA/ 100 ng DNA (Log 10 ) % Infected (GFP+) cells! 100! 80! 60! 40! 20! 0! 1! 10! 100! 1000!
Figure S1! A! B! % Infected (GFP+) cells! 100! 80! 60! 40! 20! 0! 1! 10! 100! 1000! Dose μl! CrFK! B-MLV! N-MLV! Template:! Water! Ube2V2! Ube2V1! Primers:! V2! V1! V2! V1! V2! V1! bp! 500! 300! 200! 150!
The composition of macromolecular cellular composition of mouse cell lines can be found
Supplementary 2: Cell biomass composition The composition of macromolecular cellular composition of mouse cell lines can be found elsewhere. 1-5 Following table shows the percentage composition of important
In Vivo Action of the HRD Ubiquitin Ligase Complex: Mechanisms of Endoplasmic Reticulum Quality Control and Sterol Regulation
MOLECULAR AND CELLULAR BIOLOGY, July 2001, p. 4276 4291 Vol. 21, No. 13 0270-7306/01/$04.00 0 DOI: 10.1128/MCB.21.13.4276 4291.2001 Copyright 2001, American Society for Microbiology. All Rights Reserved.
Inverted Terminal Repeat Sequences Are Important for Intermolecular Recombination and Circularization of Adeno-Associated Virus Genomes
JOURNAL OF VIROLOGY, Jan. 2005, p. 364 379 Vol. 79, No. 1 0022-538X/05/$08.00 0 doi:10.1128/jvi.79.1.364 379.2005 Copyright 2005, American Society for Microbiology. All Rights Reserved. Inverted Terminal
Characterization of Methionine Export in Corynebacterium glutamicum
JOURNAL OF BACTERIOLOGY, June 2005, p. 3786 3794 Vol. 187, No. 11 0021-9193/05/$08.00 0 doi:10.1128/jb.187.11.3786 3794.2005 Copyright 2005, American Society for Microbiology. All Rights Reserved. Characterization
SIMPLE BASIC METABOLISM
SIMPLE BASIC METABOLISM When we eat food such as a tuna fish sandwich, the polysaccharides, lipids, and proteins are digested to smaller molecules that are absorbed into the cells of our body. As these
Biosynthesis of β-carotene in engineered E. coli using the MEP and MVA pathways
Yang and Guo Microbial Cell Factories 2014, 13:160 RESEARCH Open Access Biosynthesis of β-carotene in engineered E. coli using the MEP and MVA pathways Jianming Yang * and Lizhong Guo Abstract Background:
Supporting Information
Supporting Information Discovery of linear low-cationic peptides to target methicillin-resistant Staphylococcus aureus in vivo Yuan Liu, Meirong Song, Shuangyang Ding,, Kui Zhu*,,, Beijing Advanced Innovation
SUPPLEMENTARY MATERIAL
SYPPLEMENTARY FIGURE LEGENDS SUPPLEMENTARY MATERIAL Figure S1. Phylogenic studies of the mir-183/96/182 cluster and 3 -UTR of Casp2. (A) Genomic arrangement of the mir-183/96/182 cluster in vertebrates.
SUPPORTING INFORMATION FOR. A Computational Approach to Enzyme Design: Using Docking and MM- GBSA Scoring
SUPPRTING INFRMATIN FR A Computational Approach to Enzyme Design: Predicting ω- Aminotransferase Catalytic Activity Using Docking and MM- GBSA Scoring Sarah Sirin, 1 Rajesh Kumar, 2 Carlos Martinez, 2
Supplemental Information
Cell Host & Microbe, Volume 14 Supplemental Information HIV-1 Induces the Formation of Stable Microtubules to Enhance Early Infection Yosef Sabo, Derek Walsh, Denis S. Barry, Sedef Tinaztepe, Kenia de
Properties of amino acids in proteins
Properties of amino acids in proteins one of the primary roles of DNA (but far from the only one!!!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids
W I S S E N T E C H N I K L E I D E N S C H A F T MOL.911. Cell Engineering. u
1 W I S S E N T E C H N I K L E I D E N S C H A F T MOL.911 Cell Engineering u www.tugraz.at MOL.911 Molecular Biotechnology I 2 Cell Engineering General strategies: Knock out of specific genes - Gene
The C-Terminal Region but Not the Arg-X-Pro Repeat of Epstein-Barr Virus Protein EB2 Is Required for Its Effect on RNA Splicing and Transport
JOURNAL OF VIROLOGY, May 1999, p. 4090 4100 Vol. 73, No. 5 0022-538X/99/$04.00 0 Copyright 1999, American Society for Microbiology. All Rights Reserved. The C-Terminal Region but Not the Arg-X-Pro Repeat
Molecular Biology. general transfer: occurs normally in cells. special transfer: occurs only in the laboratory in specific conditions.
Chapter 9: Proteins Molecular Biology replication general transfer: occurs normally in cells transcription special transfer: occurs only in the laboratory in specific conditions translation unknown transfer:
The Basics: A general review of molecular biology:
The Basics: A general review of molecular biology: DNA Transcription RNA Translation Proteins DNA (deoxy-ribonucleic acid) is the genetic material It is an informational super polymer -think of it as the
SYNTHESIS OF L-[ 15 N]-ISOLEUCINE, L-[ 15 N]-NORLEUCINE AND L-[ 15 N]-NORVALINE BY ENZYMATIC METHOD
![SYNTHESIS OF L-[ 15 N]-ISOLEUCINE, L-[ 15 N]-NORLEUCINE AND L-[ 15 N]-NORVALINE BY ENZYMATIC METHOD](/thumbs/72/67383139.jpg "SYNTHESIS OF L-[ 15 N]-ISOLEUCINE, L-[ 15 N]-NORLEUCINE AND L-[ 15 N]-NORVALINE BY ENZYMATIC METHOD")
SYNTHESIS OF L-[ 15 N]-ISOLEUCINE, L-[ 15 N]-NORLEUCINE AND L-[ 15 N]-NORVALINE BY ENZYMATIC METHOD IULIA LUPAN 1, BEATRIX FERENCZ 1, MARIA CHIRIAC 2, NADIA BUCURENCI 3, OCTAVIAN POPESCU 1 1 Molecular
Midterm 2. Low: 14 Mean: 61.3 High: 98. Standard Deviation: 17.7
Midterm 2 Low: 14 Mean: 61.3 High: 98 Standard Deviation: 17.7 Lecture 17 Amino Acid Metabolism Review of Urea Cycle N and S assimilation Last cofactors: THF and SAM Synthesis of few amino acids Dietary