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| Status |
Public on Dec 31, 2023 |
| Title |
Functional exploration of novel glycoside hydrolases in Fervidibacter sacchari PD1T |
| Organism |
Candidatus Fervidibacter sacchari |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Few aerobic hyperthermophiles degrade polysaccharides. We describe the genome-enabled enrichment and isolation of an aerobic hyperthermophile, Fervidibacter sacchari, which was originally ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides as sole carbon sources from 65-87.5 °C, and its genome encodes 117 glycoside hydrolases (GHs) spanning 49 GH families, including 31 homologs of understudied GH109, GH177, and GH179 domains. Here, we analyzed the transcriptomes of F. sacchari cells grown on eight different sole carbon and energy sources (beta-glucan, chondroitin sulfate, corn stover, gellan gum, locust bean gum, starch, xanthan gum, and xyloglucan) to link glycoside hydrolase substrate to function, as well as identify potential regulatory mechanisms. These data will provide preliminary characterization of novel carbohydrate-active enzymes at high temperatures.
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| Overall design |
To investigate differential expression of F. sacchari glycoside hydrolases, we grew, in triplicate, cells in media each containing one of eight different carbon sources (beta-glucan, chondroitin sulfate, corn stover, gellan gum, locust bean gum, starch, xanthan gum, and xyloglucan) to mid-exponential phase. Using RNA-seq, we identify highest expressed transcripts as well as most distinct transcriptomes based on carbon source during growth.
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| Contributor(s) |
Nou N, Seymour CO, Hedlund BP, Harmon-Smith ML |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 11, 2023 |
| Last update date |
Dec 31, 2023 |
| Contact name |
Nancy Nou |
| Organization name |
University of Nevada, Las Vegas
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| Department |
School of Life Sciences
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| Lab |
Hedlund Lab
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| Street address |
4505 S Maryland Parkway
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| City |
Las Vegas |
| State/province |
NV |
| ZIP/Postal code |
89154 |
| Country |
USA |
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| Platforms (1) |
| GPL34001 |
Illumina NovaSeq 6000 (Candidatus Fervidibacter sacchari) |
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| Samples (23)
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| GSM7967883 |
Fervidibacter sacchari, beta-glucan, biol 1 |
| GSM7967884 |
Fervidibacter sacchari, beta-glucan, biol 2 |
| GSM7967885 |
Fervidibacter sacchari, beta-glucan, biol 3 |
| GSM7967886 |
Fervidibacter sacchari, chondroitin sulfate, biol 1 |
| GSM7967887 |
Fervidibacter sacchari, chondroitin sulfate, biol 2 |
| GSM7967888 |
Fervidibacter sacchari, chondroitin sulfate, biol 3 |
| GSM7967889 |
Fervidibacter sacchari, corn stover, biol 1 |
| GSM7967890 |
Fervidibacter sacchari, corn stover, biol 2 |
| GSM7967891 |
Fervidibacter sacchari, gellan gum, biol 1 |
| GSM7967892 |
Fervidibacter sacchari, gellan gum, biol 2 |
| GSM7967893 |
Fervidibacter sacchari, gellan gum, biol 3 |
| GSM7967894 |
Fervidibacter sacchari, locust bean gum, biol 1 |
| GSM7967895 |
Fervidibacter sacchari, locust bean gum, biol 2 |
| GSM7967896 |
Fervidibacter sacchari, locust bean gum, biol 3 |
| GSM7967897 |
Fervidibacter sacchari, starch, biol 1 |
| GSM7967898 |
Fervidibacter sacchari, starch, biol 2 |
| GSM7967899 |
Fervidibacter sacchari, starch, biol 3 |
| GSM7967900 |
Fervidibacter sacchari, xanthan gum, biol 1 |
| GSM7967901 |
Fervidibacter sacchari, xanthan gum, biol 2 |
| GSM7967902 |
Fervidibacter sacchari, xanthan gum, biol 3 |
| GSM7967903 |
Fervidibacter sacchari, xyloglucan, biol 1 |
| GSM7967904 |
Fervidibacter sacchari, xyloglucan, biol 2 |
| GSM7967905 |
Fervidibacter sacchari, xyloglucan, biol 3 |
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| Relations |
| BioProject |
PRJNA1051158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE249938_feature-counts.tsv.xls.gz |
199.6 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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