skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era

Abstract

Zymomonas mobilis is a model bacterial ethanologen with many systems biology studies reported. Besides lignocellulosic ethanol production, Z. mobilis has been developed as a platform for biochemical production through metabolic engineering. However, identification and rigorous understanding of the genetic origins of cellular function, especially those based in non-coding region of DNA, such as promoters and ribosomal binding sites (RBSs), are still in its infancy. This knowledge is crucial for the effective application of Z. mobilis to new industrial applications of biotechnology for fuels and chemicals production. In this study, we explored the possibility to systematically predict the strength of promoters based on systems biology datasets. The promoter strength was clustered based on the expression values of downstream genes (or proteins) from systems biology studies including microarray, RNA-Seq and proteomics. Candidate promoters with different strengths were selected for further characterization, which include 19 strong, nine medium, and ten weak ones. A dual reporter-gene system was developed which included appropriate reporter genes. These are the opmCherry reporter gene driven by the constitutive PlacUV5 promoter for calibration, and EGFP reporter gene driven by candidate promoters for quantification. This dual reporter-gene system was confirmed using the inducible promoter, Ptet, which was used to determinemore » the strength of these predicted promoters with different strengths. In addition, the dual reporter-gene system was applied to determine four synthetic RBSs with different translation initiation rates based on the prediction from bioinformatics server RBS calculator. Our results showed that the correlations between the prediction and experimental results for the promoter and RBS strength are relatively high, with R2 values more than 0.7 and 0.9, respectively. This study not only identified and characterized 38 promoters and four RBSs with different strengths for future metabolic engineering in Z. mobilis, but also established a flow cytometry-based dual reporter-gene system to characterize genetic elements including, but not limited to the promoters and RBSs studied in this work. This study also suggested the feasibility of predicting and selecting candidate genetic elements based on omics datasets and bioinformatics tools. Moreover, the dual reporter-gene system developed in this study can be utilized to characterize other genetic elements of Z. mobilis, which can also be applied to other microorganisms.« less

Authors:
 [1];  [1];  [1];  [1];  [1]; ORCiD logo [2];  [2];  [2];  [2];  [1];  [1];  [1]; ORCiD logo [1]
  1. Hubei University, Wuhan (China)
  2. National Renewable Energy Laboratory (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Bioenergy Technologies Office (EE-3B)
OSTI Identifier:
1506610
Report Number(s):
NREL/JA-2700-73636
Journal ID: ISSN 1754-6834
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; Zymomonas mobilis; systems biology; promoter; ribosomal binding site; RBS; reporter genes; dual reporter-gene system

Citation Formats

Yang, Yongfu, Shen, Wei, Huang, Ju, Li, Runxia, Xiao, Yubei, Wei, Hui, Chou, Yat-Chen, Zhang, Min, Himmel, Michael E., Chen, Shouwen, Yi, Li, Ma, Lixin, and Yang, Shihui. Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era. United States: N. p., 2019. Web. doi:10.1186/s13068-019-1399-6.
Yang, Yongfu, Shen, Wei, Huang, Ju, Li, Runxia, Xiao, Yubei, Wei, Hui, Chou, Yat-Chen, Zhang, Min, Himmel, Michael E., Chen, Shouwen, Yi, Li, Ma, Lixin, & Yang, Shihui. Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era. United States. doi:10.1186/s13068-019-1399-6.
Yang, Yongfu, Shen, Wei, Huang, Ju, Li, Runxia, Xiao, Yubei, Wei, Hui, Chou, Yat-Chen, Zhang, Min, Himmel, Michael E., Chen, Shouwen, Yi, Li, Ma, Lixin, and Yang, Shihui. Thu . "Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era". United States. doi:10.1186/s13068-019-1399-6. https://www.osti.gov/servlets/purl/1506610.
@article{osti_1506610,
title = {Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era},
author = {Yang, Yongfu and Shen, Wei and Huang, Ju and Li, Runxia and Xiao, Yubei and Wei, Hui and Chou, Yat-Chen and Zhang, Min and Himmel, Michael E. and Chen, Shouwen and Yi, Li and Ma, Lixin and Yang, Shihui},
abstractNote = {Zymomonas mobilis is a model bacterial ethanologen with many systems biology studies reported. Besides lignocellulosic ethanol production, Z. mobilis has been developed as a platform for biochemical production through metabolic engineering. However, identification and rigorous understanding of the genetic origins of cellular function, especially those based in non-coding region of DNA, such as promoters and ribosomal binding sites (RBSs), are still in its infancy. This knowledge is crucial for the effective application of Z. mobilis to new industrial applications of biotechnology for fuels and chemicals production. In this study, we explored the possibility to systematically predict the strength of promoters based on systems biology datasets. The promoter strength was clustered based on the expression values of downstream genes (or proteins) from systems biology studies including microarray, RNA-Seq and proteomics. Candidate promoters with different strengths were selected for further characterization, which include 19 strong, nine medium, and ten weak ones. A dual reporter-gene system was developed which included appropriate reporter genes. These are the opmCherry reporter gene driven by the constitutive PlacUV5 promoter for calibration, and EGFP reporter gene driven by candidate promoters for quantification. This dual reporter-gene system was confirmed using the inducible promoter, Ptet, which was used to determine the strength of these predicted promoters with different strengths. In addition, the dual reporter-gene system was applied to determine four synthetic RBSs with different translation initiation rates based on the prediction from bioinformatics server RBS calculator. Our results showed that the correlations between the prediction and experimental results for the promoter and RBS strength are relatively high, with R2 values more than 0.7 and 0.9, respectively. This study not only identified and characterized 38 promoters and four RBSs with different strengths for future metabolic engineering in Z. mobilis, but also established a flow cytometry-based dual reporter-gene system to characterize genetic elements including, but not limited to the promoters and RBSs studied in this work. This study also suggested the feasibility of predicting and selecting candidate genetic elements based on omics datasets and bioinformatics tools. Moreover, the dual reporter-gene system developed in this study can be utilized to characterize other genetic elements of Z. mobilis, which can also be applied to other microorganisms.},
doi = {10.1186/s13068-019-1399-6},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 12,
place = {United States},
year = {2019},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein
journal, November 2004

  • Shaner, Nathan C.; Campbell, Robert E.; Steinbach, Paul A.
  • Nature Biotechnology, Vol. 22, Issue 12
  • DOI: 10.1038/nbt1037

Towards an Informative Mutant Phenotype for Every Bacterial Gene
journal, August 2014

  • Deutschbauer, A.; Price, M. N.; Wetmore, K. M.
  • Journal of Bacteriology, Vol. 196, Issue 20
  • DOI: 10.1128/JB.01836-14

Flow cytometry of fluorescent proteins
journal, July 2012


Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations
journal, January 2009

  • Yang, Shihui; Tschaplinski, Timothy J.; Engle, Nancy L.
  • BMC Genomics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2164-10-34

Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects
journal, February 2009

  • Repoila, Francis; Darfeuille, Fabien
  • Biology of the Cell, Vol. 101, Issue 2
  • DOI: 10.1042/BC20070137

Characterization of Intrinsic Properties of Promoters
journal, January 2016


Expression of Zymomonas mobilis adhB (encoding alcohol dehydrogenase II) and adhB-lacZ operon fusions in recombinant Z. mobilis.
journal, September 1989


Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis
journal, January 2007

  • Tsantili, Ivi C.; Karim, M. Nazmul; Klapa, Maria I.
  • Microbial Cell Factories, Vol. 6, Issue 1
  • DOI: 10.1186/1475-2859-6-8

Glyceraldehyde-3-phosphate dehydrogenase gene from Zymomonas mobilis: cloning, sequencing, and identification of promoter region.
journal, December 1987


Engineered promoters enable constant gene expression at any copy number in bacteria
journal, March 2018

  • Segall-Shapiro, Thomas H.; Sontag, Eduardo D.; Voigt, Christopher A.
  • Nature Biotechnology, Vol. 36, Issue 4
  • DOI: 10.1038/nbt.4111

Cloning, sequencing, and characterization of the principal acid phosphatase, the phoC+ product, from Zymomonas mobilis.
journal, February 1989


Translational control and target recognition by Escherichia coli small RNAs in vivo
journal, January 2007

  • Urban, Johannes H.; Vogel, Jörg
  • Nucleic Acids Research, Vol. 35, Issue 3
  • DOI: 10.1093/nar/gkl1040

High-level expression and characterization of a novel serine protease in Pichia pastoris by multi-copy integration
journal, October 2016


Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009

  • Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
  • Nature Methods, Vol. 6, Issue 5, p. 343-345
  • DOI: 10.1038/nmeth.1318

Transcriptional analysis of adaptation to high glucose concentrations in Zymomonas mobilis
journal, January 2015

  • Zhang, Kun; Shao, Huanhuan; Cao, Qinghua
  • Applied Microbiology and Biotechnology, Vol. 99, Issue 4
  • DOI: 10.1007/s00253-014-6342-y

Metabolic Engineering of a Pentose Metabolism Pathway in Ethanologenic Zymomonas mobilis
journal, January 1995


Insights into acetate toxicity in Zymomonas mobilis8b using different substrates
journal, September 2014

  • Yang, Shihui; Franden, Mary Ann; Brown, Steven D.
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/s13068-014-0140-8

Cloning and sequencing of the alcohol dehydrogenase II gene from Zymomonas mobilis.
journal, June 1987


Optimized Codon Usage and Chromophore Mutations Provide Enhanced Sensitivity with the Green Fluorescent Protein
journal, November 1996


The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4
journal, December 2004

  • Seo, Jeong-Sun; Chong, Hyonyong; Park, Hyun Seok
  • Nature Biotechnology, Vol. 23, Issue 1
  • DOI: 10.1038/nbt1045

Operon prediction using both genome-specific and general genomic information
journal, December 2006

  • Dam, Phuongan; Olman, Victor; Harris, Kyle
  • Nucleic Acids Research, Vol. 35, Issue 1
  • DOI: 10.1093/nar/gkl1018

Transcriptome profiling of Zymomonas mobilis under furfural stress
journal, May 2012

  • He, Ming-xiong; Wu, Bo; Shui, Zong-xia
  • Applied Microbiology and Biotechnology, Vol. 95, Issue 1
  • DOI: 10.1007/s00253-012-4155-4

Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis
journal, November 2010

  • Widiastuti, Hanifah; Kim, Jae Young; Selvarasu, Suresh
  • Biotechnology and Bioengineering, Vol. 108, Issue 3
  • DOI: 10.1002/bit.22965

Obtaining a Panel of Cascade Promoter-5′-UTR Complexes in Escherichia coli
journal, March 2017


Synthetic biology: applications come of age
journal, May 2010

  • Khalil, Ahmad S.; Collins, James J.
  • Nature Reviews Genetics, Vol. 11, Issue 5
  • DOI: 10.1038/nrg2775

Improving cellulosic ethanol fermentability of Zymomonas mobilis by overexpression of sodium ion tolerance gene ZMO0119
journal, September 2018


Characterization of Transcription from TATA-Less Promoters: Identification of a New Core Promoter Element XCPE2 and Analysis of Factor Requirements
journal, April 2009


Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system
journal, September 2009


Synthetic promoter libraries – tuning of gene expression
journal, February 2006


Functional characterization of a new promoter isolated from torque teno sus virus 1
journal, November 2015


Genome-wide transcriptomic analysis of a flocculent strain of Zymomonas mobilis
journal, February 2012

  • Jeon, Young Jae; Xun, Zhao; Su, Ping
  • Applied Microbiology and Biotechnology, Vol. 93, Issue 6
  • DOI: 10.1007/s00253-012-3948-9

Stochastic Gene Expression in a Single Cell
journal, August 2002


Improved genome annotation for Zymomonas mobilis
journal, October 2009

  • Yang, Shihui; Pappas, Katherine M.; Hauser, Loren J.
  • Nature Biotechnology, Vol. 27, Issue 10
  • DOI: 10.1038/nbt1009-893

Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis
journal, September 2018


Construction of expression vectors for the gram-negative bacterium Zymomonas mobilis
journal, September 1990

  • Reynen, Michael; Reipen, Ina; Sahm, Hermann
  • MGG Molecular & General Genetics, Vol. 223, Issue 2
  • DOI: 10.1007/BF00265073

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates
journal, January 2013

  • Skerker, Jeffrey M.; Leon, Dacia; Price, Morgan N.
  • Molecular Systems Biology, Vol. 9, Issue 1
  • DOI: 10.1038/msb.2013.30

Macromolecular Mimicry in Translation Initiation: A Model for the Initiation Factor IF2 on the Ribosome
journal, December 2000

  • Moreno, Juan Manuel Palacios; SØrensen, Hans Peter; Mortensen, Kim Kusk
  • IUBMB Life, Vol. 50, Issue 6
  • DOI: 10.1080/713803743

Single-cell quantification of molecules and rates using open-source microscope-based cytometry
journal, January 2007

  • Gordon, Andrew; Colman-Lerner, Alejandro; Chin, Tina E.
  • Nature Methods, Vol. 4, Issue 2
  • DOI: 10.1038/nmeth1008

Phosphoglycerate kinase gene from Zymomonas mobilis: cloning, sequencing, and localization within the gap operon.
journal, April 1988


Zymomonas mobilis as a model system for production of biofuels and biochemicals
journal, September 2016


Fluorescent proteins at a glance
journal, December 2010

  • Kremers, G. -J.; Gilbert, S. G.; Cranfill, P. J.
  • Journal of Cell Science, Vol. 124, Issue 2
  • DOI: 10.1242/jcs.072744

Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses
journal, July 2013


Identification and Characterization of 5′ Untranslated Regions (5′UTRs) in Zymomonas mobilis as Regulatory Biological Parts
journal, December 2017


DOOR: a database for prokaryotic operons
journal, November 2008

  • Mao, Fenglou; Dam, Phuongan; Chou, Jacky
  • Nucleic Acids Research, Vol. 37, Issue suppl_1
  • DOI: 10.1093/nar/gkn757

Fluorescent Reporter Libraries as Useful Tools for Optimizing Microbial Cell Factories: A Review of the Current Methods and Applications
journal, September 2015

  • Delvigne, Frank; Pêcheux, Hélène; Tarayre, Cédric
  • Frontiers in Bioengineering and Biotechnology, Vol. 3
  • DOI: 10.3389/fbioe.2015.00147

Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae
journal, May 2010

  • Yang, S.; Land, M. L.; Klingeman, D. M.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 23
  • DOI: 10.1073/pnas.0914506107

Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars
journal, September 2016

  • Yang, Shihui; Mohagheghi, Ali; Franden, Mary Ann
  • Biotechnology for Biofuels, Vol. 9, Issue 1
  • DOI: 10.1186/s13068-016-0606-y

A High-Throughput Approach to Promoter Study Using Green Fluorescent Protein
journal, December 2004

  • Lu, C.; Bentley, W. E.; Rao, G.
  • Biotechnology Progress, Vol. 20, Issue 6
  • DOI: 10.1021/bp049751l

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues
journal, July 2010

  • Chudakov, Dmitriy M.; Matz, Mikhail V.; Lukyanov, Sergey
  • Physiological Reviews, Vol. 90, Issue 3
  • DOI: 10.1152/physrev.00038.2009

Investigation of specific interactions between T7 promoter and T7 RNA polymerase by force spectroscopy using atomic force microscope
journal, January 2018

  • Zhang, Xiaojuan; Yao, Zhixuan; Duan, Yanting
  • Biochemical Journal, Vol. 475, Issue 1
  • DOI: 10.1042/BCJ20170616

Advances and prospects in metabolic engineering of Zymomonas mobilis
journal, November 2018


Quantitative analysis of transient gene expression in mammalian cells using the green fluorescent protein
journal, August 1996


Cloning and sequencing of the sacA gene: characterization of a sucrase from Zymomonas mobilis.
journal, December 1990


Monitoring promoter activity in a single bacterial cell by using green and red fluorescent proteins
journal, July 2003


Discovery of Ethanol-Responsive Small RNAs in Zymomonas mobilis
journal, May 2014

  • Cho, Seung Hee; Lei, Roy; Henninger, Trey D.
  • Applied and Environmental Microbiology, Vol. 80, Issue 14
  • DOI: 10.1128/AEM.00429-14

Thermotolerant genes essential for survival at a critical high temperature in thermotolerant ethanologenic Zymomonas mobilis TISTR 548
journal, August 2017

  • Charoensuk, Kannikar; Sakurada, Tomoko; Tokiyama, Amina
  • Biotechnology for Biofuels, Vol. 10, Issue 1
  • DOI: 10.1186/s13068-017-0891-0

Structural Studies of lac UV5-RNA Polymerase Interactions in Vitro : ETHYLATION INTERFERENCE AND MISSING NUCLEOSIDE ANALYSIS
journal, March 2000

  • Noel, Richard J.; Reznikoff, William S.
  • Journal of Biological Chemistry, Vol. 275, Issue 11
  • DOI: 10.1074/jbc.275.11.7708

Predictive and Interpretive Simulation of Green Fluorescent Protein Expression in Reporter Bacteria
journal, December 2001


Transcriptome profiling of Zymomonas mobilis under ethanol stress
journal, January 2012

  • He, Ming-xiong; Wu, Bo; Shui, Zong-xia
  • Biotechnology for Biofuels, Vol. 5, Issue 1
  • DOI: 10.1186/1754-6834-5-75

Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis
journal, February 2018


    Works referencing / citing this record:

    Cloning and sequencing of the sacA gene: characterization of a sucrase from Zymomonas mobilis.
    journal, December 1990


    Cloning and sequencing of the alcohol dehydrogenase II gene from Zymomonas mobilis.
    journal, June 1987


    Macromolecular Mimicry in Translation Initiation: A Model for the Initiation Factor IF2 on the Ribosome
    journal, December 2000

    • Moreno, Juan Manuel Palacios; SØrensen, Hans Peter; Mortensen, Kim Kusk
    • IUBMB Life, Vol. 50, Issue 6
    • DOI: 10.1080/713803743

    Synthetic promoter libraries – tuning of gene expression
    journal, February 2006


    Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates
    journal, January 2013

    • Skerker, Jeffrey M.; Leon, Dacia; Price, Morgan N.
    • Molecular Systems Biology, Vol. 9, Issue 1
    • DOI: 10.1038/msb.2013.30

    Improving cellulosic ethanol fermentability of Zymomonas mobilis by overexpression of sodium ion tolerance gene ZMO0119
    journal, September 2018


    Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars
    journal, September 2016

    • Yang, Shihui; Mohagheghi, Ali; Franden, Mary Ann
    • Biotechnology for Biofuels, Vol. 9, Issue 1
    • DOI: 10.1186/s13068-016-0606-y

    Operon prediction using both genome-specific and general genomic information
    journal, December 2006

    • Dam, Phuongan; Olman, Victor; Harris, Kyle
    • Nucleic Acids Research, Vol. 35, Issue 1
    • DOI: 10.1093/nar/gkl1018

    A High-Throughput Approach to Promoter Study Using Green Fluorescent Protein
    journal, December 2004

    • Lu, C.; Bentley, W. E.; Rao, G.
    • Biotechnology Progress, Vol. 20, Issue 6
    • DOI: 10.1021/bp049751l

    DOOR: a database for prokaryotic operons
    journal, November 2008

    • Mao, Fenglou; Dam, Phuongan; Chou, Jacky
    • Nucleic Acids Research, Vol. 37, Issue suppl_1
    • DOI: 10.1093/nar/gkn757

    Zymomonas mobilis as a model system for production of biofuels and biochemicals
    journal, September 2016


    Metabolic Engineering of a Pentose Metabolism Pathway in Ethanologenic Zymomonas mobilis
    journal, January 1995


    Advances and prospects in metabolic engineering of Zymomonas mobilis
    journal, November 2018


    Identification and Characterization of 5′ Untranslated Regions (5′UTRs) in Zymomonas mobilis as Regulatory Biological Parts
    journal, December 2017


    Fluorescent Reporter Libraries as Useful Tools for Optimizing Microbial Cell Factories: A Review of the Current Methods and Applications
    journal, September 2015

    • Delvigne, Frank; Pêcheux, Hélène; Tarayre, Cédric
    • Frontiers in Bioengineering and Biotechnology, Vol. 3
    • DOI: 10.3389/fbioe.2015.00147

    Thermotolerant genes essential for survival at a critical high temperature in thermotolerant ethanologenic Zymomonas mobilis TISTR 548
    journal, August 2017

    • Charoensuk, Kannikar; Sakurada, Tomoko; Tokiyama, Amina
    • Biotechnology for Biofuels, Vol. 10, Issue 1
    • DOI: 10.1186/s13068-017-0891-0

    Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations
    journal, January 2009

    • Yang, Shihui; Tschaplinski, Timothy J.; Engle, Nancy L.
    • BMC Genomics, Vol. 10, Issue 1
    • DOI: 10.1186/1471-2164-10-34

    Phosphoglycerate kinase gene from Zymomonas mobilis: cloning, sequencing, and localization within the gap operon.
    journal, April 1988


    Establishment and application of a CRISPR–Cas12a assisted genome-editing system in Zymomonas mobilis
    journal, October 2019


    Single-cell quantification of molecules and rates using open-source microscope-based cytometry
    journal, January 2007

    • Gordon, Andrew; Colman-Lerner, Alejandro; Chin, Tina E.
    • Nature Methods, Vol. 4, Issue 2
    • DOI: 10.1038/nmeth1008

    High-level expression and characterization of a novel serine protease in Pichia pastoris by multi-copy integration
    journal, October 2016


    Stochastic Gene Expression in a Single Cell
    journal, August 2002


    Transcriptome profiling of Zymomonas mobilis under ethanol stress
    journal, January 2012

    • He, Ming-xiong; Wu, Bo; Shui, Zong-xia
    • Biotechnology for Biofuels, Vol. 5, Issue 1
    • DOI: 10.1186/1754-6834-5-75

    Fluorescent proteins at a glance
    journal, December 2010

    • Kremers, G. -J.; Gilbert, S. G.; Cranfill, P. J.
    • Journal of Cell Science, Vol. 124, Issue 2
    • DOI: 10.1242/jcs.072744

    Establishment and application of a CRISPR–Cas12a assisted genome-editing system in Zymomonas mobilis
    journal, October 2019


    Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis
    journal, September 2018


    Translational control and target recognition by Escherichia coli small RNAs in vivo
    journal, January 2007

    • Urban, Johannes H.; Vogel, Jörg
    • Nucleic Acids Research, Vol. 35, Issue 3
    • DOI: 10.1093/nar/gkl1040

    Engineered promoters enable constant gene expression at any copy number in bacteria
    journal, March 2018

    • Segall-Shapiro, Thomas H.; Sontag, Eduardo D.; Voigt, Christopher A.
    • Nature Biotechnology, Vol. 36, Issue 4
    • DOI: 10.1038/nbt.4111

    The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4
    journal, December 2004

    • Seo, Jeong-Sun; Chong, Hyonyong; Park, Hyun Seok
    • Nature Biotechnology, Vol. 23, Issue 1
    • DOI: 10.1038/nbt1045

    Progress and perspective on lignocellulosic hydrolysate inhibitor tolerance improvement in Zymomonas mobilis
    journal, February 2018


    Enzymatic assembly of DNA molecules up to several hundred kilobases
    journal, April 2009

    • Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
    • Nature Methods, Vol. 6, Issue 5, p. 343-345
    • DOI: 10.1038/nmeth.1318

    Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues
    journal, July 2010

    • Chudakov, Dmitriy M.; Matz, Mikhail V.; Lukyanov, Sergey
    • Physiological Reviews, Vol. 90, Issue 3
    • DOI: 10.1152/physrev.00038.2009

    Structural Studies of lac UV5-RNA Polymerase Interactions in Vitro : ETHYLATION INTERFERENCE AND MISSING NUCLEOSIDE ANALYSIS
    journal, March 2000

    • Noel, Richard J.; Reznikoff, William S.
    • Journal of Biological Chemistry, Vol. 275, Issue 11
    • DOI: 10.1074/jbc.275.11.7708

    Flow cytometry of fluorescent proteins
    journal, July 2012


    Quantitative analysis of transient gene expression in mammalian cells using the green fluorescent protein
    journal, August 1996


    Characterization of Transcription from TATA-Less Promoters: Identification of a New Core Promoter Element XCPE2 and Analysis of Factor Requirements
    journal, April 2009


    Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis
    journal, November 2010

    • Widiastuti, Hanifah; Kim, Jae Young; Selvarasu, Suresh
    • Biotechnology and Bioengineering, Vol. 108, Issue 3
    • DOI: 10.1002/bit.22965

    Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae
    journal, May 2010

    • Yang, S.; Land, M. L.; Klingeman, D. M.
    • Proceedings of the National Academy of Sciences, Vol. 107, Issue 23
    • DOI: 10.1073/pnas.0914506107

    Characterization of Intrinsic Properties of Promoters
    journal, January 2016


    Obtaining a Panel of Cascade Promoter-5′-UTR Complexes in Escherichia coli
    journal, March 2017


    Optimized Codon Usage and Chromophore Mutations Provide Enhanced Sensitivity with the Green Fluorescent Protein
    journal, November 1996


    Transcriptome profiling of Zymomonas mobilis under furfural stress
    journal, May 2012

    • He, Ming-xiong; Wu, Bo; Shui, Zong-xia
    • Applied Microbiology and Biotechnology, Vol. 95, Issue 1
    • DOI: 10.1007/s00253-012-4155-4

    Synthetic biology: applications come of age
    journal, May 2010

    • Khalil, Ahmad S.; Collins, James J.
    • Nature Reviews Genetics, Vol. 11, Issue 5
    • DOI: 10.1038/nrg2775

    Glyceraldehyde-3-phosphate dehydrogenase gene from Zymomonas mobilis: cloning, sequencing, and identification of promoter region.
    journal, December 1987


    Analysis of stochasticity in promoter activation by using a dual-fluorescence reporter system
    journal, September 2009


    Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses
    journal, July 2013


    Genome-wide transcriptomic analysis of a flocculent strain of Zymomonas mobilis
    journal, February 2012

    • Jeon, Young Jae; Xun, Zhao; Su, Ping
    • Applied Microbiology and Biotechnology, Vol. 93, Issue 6
    • DOI: 10.1007/s00253-012-3948-9

    Cloning, sequencing, and characterization of the principal acid phosphatase, the phoC+ product, from Zymomonas mobilis.
    journal, February 1989


    Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein
    journal, November 2004

    • Shaner, Nathan C.; Campbell, Robert E.; Steinbach, Paul A.
    • Nature Biotechnology, Vol. 22, Issue 12
    • DOI: 10.1038/nbt1037

    Improved genome annotation for Zymomonas mobilis
    journal, October 2009

    • Yang, Shihui; Pappas, Katherine M.; Hauser, Loren J.
    • Nature Biotechnology, Vol. 27, Issue 10
    • DOI: 10.1038/nbt1009-893

    Expression of Zymomonas mobilis adhB (encoding alcohol dehydrogenase II) and adhB-lacZ operon fusions in recombinant Z. mobilis.
    journal, September 1989


    Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis
    journal, January 2007

    • Tsantili, Ivi C.; Karim, M. Nazmul; Klapa, Maria I.
    • Microbial Cell Factories, Vol. 6, Issue 1
    • DOI: 10.1186/1475-2859-6-8

    Insights into acetate toxicity in Zymomonas mobilis8b using different substrates
    journal, September 2014

    • Yang, Shihui; Franden, Mary Ann; Brown, Steven D.
    • Biotechnology for Biofuels, Vol. 7, Issue 1
    • DOI: 10.1186/s13068-014-0140-8

    Transcriptional analysis of adaptation to high glucose concentrations in Zymomonas mobilis
    journal, January 2015

    • Zhang, Kun; Shao, Huanhuan; Cao, Qinghua
    • Applied Microbiology and Biotechnology, Vol. 99, Issue 4
    • DOI: 10.1007/s00253-014-6342-y

    Functional characterization of a new promoter isolated from torque teno sus virus 1
    journal, November 2015