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| Status |
Public on Jun 28, 2022 |
| Title |
Expression profiling of Cellvibrio japonicus using starch |
| Organism |
Cellvibrio japonicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Recent interest in rare α-diglucosides such as kojibiose (α-1,2), nigerose (α-1,3), and isomaltose (α-1,6) reflects developments in pharmaceutical, biotechnological, and culinary industries that value these sugars as prebiotics, carrier molecules, and low glycemic index sweeteners. There have been only a few enzymes capable of degrading these substrates characterized, largely due in part to difficulties in identifying potential targets based solely on bioinformatic predictions. Previous genome sequencing of three Cellvibrio japonicus strains adapted to utilize rare α-diglucosides identified multiple, but thus far uncharacterized, mutations in each strain. In this report we analyzed the 36, 44, and 60 mutations that were in the kojibiose, nigerose, and isomaltose-adapted strains, respectively. The majority of mutations were unique to a specific adapted strain, which included indels that resulted a truncated protein, and single nucleotide variations within complete proteins. A single nucleotide variation in the C-terminus cyclomaltodextrin domain of the amy13E gene product (P606S) was observed in several adapted strains. RNAseq data identified amy13E as highly expressed in starch media, which suggested a key role for this gene in the metabolism of sugars with α-glycosidic bonds. Mutational analysis of amy13E found that this gene was essential for rare α-diglucoside metabolism and critical for the maintenance of adaptation phenotypes. Bioinformatic analysis coupled with biochemical assays using cell-free extracts indicated that the amy13E gene product is located in the periplasm and directly cleaves α-diglucosides into glucose. Our revised model of α-diglucoside degradation by C. japonicus is likely to be useful for making functional enzyme predictions in related bacteria.
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| Overall design |
One carbon condition (starch); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 6 samples; Data from GSE90955 (glucose) was used in data analysis
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| Contributor(s) |
Gardner JG |
| Citation(s) |
37800973 |
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| Submission date |
Jun 24, 2022 |
| Last update date |
Jan 02, 2024 |
| Contact name |
Jeffrey G. Gardner |
| Organization name |
University of Maryland - Baltimore County
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| Department |
Department of Biological Sciences
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| Street address |
1000 Hilltop Circle
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21250 |
| Country |
USA |
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| Platforms (2) |
| GPL22758 |
Illumina HiSeq 2000 (Cellvibrio japonicus) |
| GPL28467 |
Illumina HiSeq 2500 (Cellvibrio japonicus) |
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| Samples (12)
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| GSM6266232 |
STAR, STA, REP1 |
| GSM6266233 |
STAR, STA, REP2 |
| GSM6266234 |
STAR, STA, REP3 |
| GSM6266235 |
GLU, EXP, REP1 (control for STAR samples) |
| GSM6266236 |
GLU, EXP, REP2 (control for STAR samples) |
| GSM6266237 |
GLU, EXP, REP3 (control for STAR samples) |
| GSM6266238 |
GLU, STA, REP1 (control for STAR samples) |
| GSM6266239 |
GLU, STA, REP2 (control for STAR samples) |
| GSM6266240 |
GLU, STA, REP3 (control for STAR samples) |
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| Relations |
| BioProject |
PRJNA852536 |
| SRA |
SRP383457 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE206866_STAR_EXP_vs_STAR_STA.xlsx |
3.0 Mb |
(ftp)(http) |
XLSX |
| GSE206866_STAR_vs_GLU_EXP.xlsx |
2.7 Mb |
(ftp)(http) |
XLSX |
| GSE206866_STAR_vs_GLU_STA.xlsx |
2.6 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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