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| Status |
Public on May 08, 2018 |
| Title |
Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032 |
| Organism |
Zymomonas mobilis subsp. mobilis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this study, we reported the updated chromosome and plasmid sequence of ZM4, and its two engineered xylose-utilizing strains derivatives (strains 2032 and 8b). The majority of plasmid genes have either homologs from other organisms or some conserved domains. Our bioinformatics analysis suggested that several plasmid genes may be essential genes of ZM4. To further validate the function of these plasmid genes, an RNA-Seq pipeline was developed for Z. mobilis and used to compare the gene expression under various conditions, including anaerobic and aerobic conditions, and in different biomass hydrolysates. Overall, these plasmids genes are more responsive to different concentrated hydrolysates than the different oxygen concentrations tested (such as anaerobic vs. aerobic conditions). Moreover, our results also indicate that the plasmid copy number is affected by growth conditions and foreign gene insertion while the chromosomal gene expression is relatively stable across different conditions in different strain backgrounds.
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| Overall design |
We combined and cross-compared the genome resequencing and RNA-Seq results of four independent research laboratories from three countries: USA, Greece, and China. This GEO submission contains 17 paired-end RNA-seq samples for Zymomonas mobilis subsp. mobilis strain 2032 with a minimum of two biological replicates per test condition. Cell samples were collected at different timepoints during batch fermentation culture.
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| Contributor(s) |
Yang S, Vera JM, Grass J, Savvakis G, Moskvin O, Yang Y, McIlwain SJ, Lyu Y, Zinonos I, Hebert AS, Coon JJ, Bates DM, Sato TK, Brown SD, Himmel ME, Zhang M, Landick R, Pappas K, Zhang Y |
| Citation(s) |
29743953 |
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| Submission date |
Jan 08, 2018 |
| Last update date |
Jun 06, 2018 |
| Contact name |
Robert Landick |
| E-mail(s) |
[email protected]
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| Organization name |
University of Wisconsin
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| Street address |
1550 Linden Dr
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platforms (1) |
| GPL24485 |
Illumina HiSeq 2000 (Zymomonas mobilis subsp. mobilis) |
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| Samples (17)
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| Relations |
| BioProject |
PRJNA429034 |
| SRA |
SRP128589 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108890_Plasmid_gene_counts.txt.gz |
5.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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