ArticleBiotechnology for biofuels2018
Complete genome sequence and the expression pattern of plasmids of the model ethanologen
Article in Biotechnology for biofuels, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Engineering ethanologenic bacteriumSynthetic and systems biotechnology · 2026Article
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- Higher Wood Density Lowers Feedstock Cost and Has Minimal Impact on Biomass Conversion to Biofuels.ACS sustainable chemistry & engineering · 2026Article
- Genetic tools for engineering Zymomonas mobilis, Cereibacter sphaeroides and Novosphingobium aromaticivorans to improve production of bioenergy compounds.Microbial cell factories · 2025Review
- AI-powered high-throughput digital colony picker platform for sorting microbial strains by multi-modal phenotypes.Nature communications · 2025Article
- Thermodynamics shapes themBio · 2025Article
- Integration of metabolic and evolutionary processes to construct efficient xylose-utilizing strain ofSynthetic and systems biotechnology · 2025Article
- pH adjustment increases biofuel production from inhibitory switchgrass hydrolysates.Bioresource technology · 2025Article
- Paradigm of engineering recalcitrant non-model microorganism with dominant metabolic pathway as a biorefinery chassis.Nature communications · 2024Article
- Biosensor-assisted CRISPRi high-throughput screening to identify genetic targets inSynthetic and systems biotechnology · 2024Article
- Metabolic engineering of an industrial bacteriumSynthetic and systems biotechnology · 2024Article
- Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis.Biotechnology for biofuels and bioproducts · 2024Article
- Systematic investigation of TetR-family transcriptional regulators and their roles on lignocellulosic inhibitor acetate tolerance inFrontiers in bioengineering and biotechnology · 2024Article
- Systematic metabolic engineering ofFrontiers in bioengineering and biotechnology · 2024Article
- Development of a counterselectable system for rapid and efficient CRISPR-based genome engineering in Zymomonas mobilis.Microbial cell factories · 2023Article
- Construction and application of high-quality genome-scale metabolic model ofSynthetic and systems biotechnology · 2023Article
- Non-canonical D-xylose and L-arabinose metabolism via D-arabitol in the oleaginous yeast Rhodosporidium toruloides.Microbial cell factories · 2023Article
- Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress.Microbial cell factories · 2023Article
- Regulation of biofilm formation inFrontiers in bioengineering and biotechnology · 2023Article
- Identification and Characterization of Genes Related to Ampicillin Antibiotic Resistance inAntibiotics (Basel, Switzerland) · 2022Article
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
background
resultsIn this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1-2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion.
conclusionsThe complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.
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