The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.
Pascal Donsbach, Brian A Yee, Dione Sanchez-Hevia, José Berenguer, Stefan Aigner, Gene W Yeo, Dagmar Klostermeier
RNA (New York, N.Y.) · 2020 · Vol. 26 (11) · pp. 1557-1574
Abstract
RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate specificity and guide the helicase to a specific RNA. However, the in vivo RNA substrates of most helicases are currently not defined. The DEAD-box helicase Hera from <i>Thermus thermophilus</i> contains a helicase core, followed by a dimerization domain and an RNA binding domain that folds into an RNA recognition motif (RRM). The RRM mediates high affinity binding to an RNA hairpin, and an adjacent duplex is then unwound by the helicase core. Hera is a cold-shock protein, and has been suggested to act as an RNA chaperone under cold-shock conditions. Using crosslinking immunoprecipitation of Hera/RNA complexes and sequencing, we show that Hera binds to a large fraction of <i>T. thermophilus</i> RNAs under normal-growth and cold-shock conditions without a strong sequence preference, in agreement with a structure-specific recognition of RNAs and a general function in RNA metabolism. Under cold-shock conditions, Hera is recruited to RNAs with high propensities to form stable secondary structures. We show that selected RNAs identified, including a set of tRNAs, bind to Hera in vitro, and activate the Hera helicase core. Gene ontology analysis reveals an enrichment of genes related to translation, including mRNAs of ribosomal proteins, tRNAs, tRNA ligases, and tRNA-modifying enzymes, consistent with a key role of Hera in ribosome and tRNA metabolism.
Linked datasets 1
The Thermus thermophilus DEAD-box protein Hera is a general RNA chaperone and plays a key role in tRNA metabolism
Thermus thermophilus HB27
16 data files
| File | Type | Size |
|---|---|---|
| DK_Hera_1_Hera_S59_L004_R1_001.fastq.gz | RIP-Seq | 67.1 MB |
| DK_Hera_1_Input_S57_L004_R1_001.fastq.gz | RIP-Seq | 104.6 MB |
| DK_Hera_2_Hera_S62_L004_R1_001.fastq.gz | RIP-Seq | 57.8 MB |
| DK_Hera_2_Input_S60_L004_R1_001.fastq.gz | RIP-Seq | 103.1 MB |
| DK_Hera_3_Hera_S65_L004_R1_001.fastq.gz | RIP-Seq | 49.4 MB |
| DK_Hera_3_Input_S63_L004_R1_001.fastq.gz | RIP-Seq | 125.7 MB |
| DK_Hera_4_Hera_S40_L003_R1_001.fastq.gz | RIP-Seq | 51.3 MB |
| DK_Hera_4_Input_S38_L003_R1_001.fastq.gz | RIP-Seq | 102.0 MB |
| SRR9909221_GSM4008944 | RIP-Seq | 67.0 MB |
| SRR9909222_GSM4008945 | RIP-Seq | 57.0 MB |
| SRR9909223_GSM4008946 | RIP-Seq | 49.0 MB |
| SRR9909224_GSM4008947 | RIP-Seq | 51.0 MB |
| SRR9909225_GSM4008948 | RIP-Seq | 104.0 MB |
| SRR9909226_GSM4008949 | RIP-Seq | 103.0 MB |
| SRR9909227_GSM4008950 | RIP-Seq | 125.0 MB |
| SRR9909228_GSM4008951 | RIP-Seq | 101.0 MB |
Potentially related datasets 1
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
Analysis pipelines 1
| Pipeline | Assay | Steps | Dataset |
|---|---|---|---|
| GSE135435 eCLIP Data Processing geo_data_processing | eCLIP | 29 | GSE135435 |
Funding 3 grants
| Grant | Funder |
|---|---|
| U24 HG009889 | NHGRI NIH HHS (United States) |
| R01 HG004659 | NHGRI NIH HHS (United States) |
| U41 HG009889 | NHGRI NIH HHS (United States) |