NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE163955 Query DataSets for GSE163955
Status Public on Dec 31, 2020
Title Global transcriptional response of Methylorubrum extorquens to formaldehyde stress includes both overlapping and unique gene sets in comparison to antibiotic translational inhibition and expands the role of EfgA
Organism Methylorubrum extorquens
Experiment type Expression profiling by high throughput sequencing
Summary The potency and indiscriminate nature of formaldehyde reactivity upon biological molecules make it a universal stressor. However, some organisms such as Methylorubrum extorquens possess means to rapidly and effectively mitigate formaldehyde-induced damage. EfgA is a recently identified formaldehyde sensor predicted to halt translation in response to elevated formaldehyde as a means to protect cells. Herein, we investigate growth, formaldehyde consumption, and changes in gene expression to better understand how M. extorquens responds to formaldehyde with and without the EfgA-formaldehyde-mediated translational response, and how this mechanism compares to other forms of translation inhibition. These distinct mechanisms of translation inhibition have notable differences: they each involve different specific players and in addition, formaldehyde also acts as a general, multi-target stressor and a potential carbon source. Here, we present findings demonstrating that in addition to its characterized impact on translation, functional EfgA also allows for a rapid and robust transcriptional response to formaldehyde and that removal of efgA leads to heightened proteotoxic and genotoxic stress in the presence of increased formaldehyde levels. As our previous work suggested that formaldehyde is proteotoxic in M. extorquens, we accurately predicted that strains lacking efgA would experience increased protein damage. We also found that many downstream consequences of translation inhibition were shared by EfgA-formaldehyde- and kanamycin-mediated translation inhibition. Our work to modularize the transcriptional response uncovered additional layers of regulatory control enacted by functional EfgA upon experiencing formaldehyde stress, and further demonstrate the importance this protein plays at both transcriptional and translational levels in this model methylotroph.
 
Overall design Time courses of gene expression after treatment with two different translational inhibitors (kanamycin and formaldehyde). The responses of wild type and an ΔefgA mutant of Methylorubrum extorquens were compared.
 
Contributor(s) Bazurto JV, Riazi S, D’Alton S, Deatherage DE, Barrick JE, Marx CJ
Citation(s) 33578755
Submission date Dec 28, 2020
Last update date Mar 10, 2021
Contact name Jeffrey E. Barrick
Organization name The University of Texas at Austin
Department Molecular Biosciences
Street address 2500 Speedway, Stop A4800
City Austin
State/province TX
ZIP/Postal code 78712-1639
Country USA
 
Platforms (2)
GPL25388 Illumina HiSeq 4000 (Methylorubrum extorquens)
GPL29545 Illumina NextSeq 500 (Methylorubrum extorquens)
Samples (81)
GSM4991148 13E efgA mutant, pretreatment
GSM4991149 13W Wild type, pretreatment
GSM4991150 142W Wild type, 720 min after formaldehyde treatment
Relations
BioProject PRJNA688312
SRA SRP299540

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE163955_counts.txt.gz 614.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap