RRM domain of human RBM7: purification, crystallization and structure determination

Sofos, N.; Winkler, Mikael B L; Brodersen, D.E.

doi:10.1107/s2053230x16006129

Cited by 6 publications

(8 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…X-ray crystallographic and solution state NMR structures of the human RBM7 RRM have been previously determined using constructs with varying C-terminal boundaries [58, 59, 80]. For all solved structures, the RRM contains the canonical 1-α1-β2-β3-α2-β4 topology between amino acid (aa) residues T11-Q83; however, X-ray crystal structures report an additional β4’ strand in the α2-β4 loop and extended β4 strand.…”

Section: Resultsmentioning

confidence: 99%

“…In vitro , the RBM7 RRM preferentially interacts with polypyrimidine repeat sequences with micromolar binding affinity [56]. Four high-resolution structures have been determined of the RBM7 RRM by solution NMR spectroscopy or X-ray crystallography, with varying N- and C-terminal ends and observed structural features [56, 58, 59]. Here, we recombinantly expressed and purified RBM7 RRM constructs with various N-terminal fusion tags and C-terminal ends.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition

Sobeh

Eichhorn

2022

Preprint

View full text Add to dashboard Cite

The 7SK ribonucleoprotein (RNP) is a critical regulator of eukaryotic transcription. Recently, RNA binding motif 7 (RBM7), which contains an RNA recognition motif (RRM), was reported to associate with 7SK RNA and core 7SK RNP protein components in response to DNA damage. However, little is known about the mode of RBM7-7SK RNA recognition. Here, we recombinantly expressed and purified RBM7 RRM constructs and found that constructs containing extended C-termini have increased solubility and stability compared to shorter constructs. To identify potential RBM7-7SK RNA binding sites, we analyzed deposited data from in cellulo crosslinking experiments and found that RBM7 crosslinks specifically to the distal region of 7SK stem-loop 3 (SL3). Electrophoretic mobility shift assays and NMR chemical shift perturbation experiments showed weak binding to 7SK SL3 constructs in vitro. Together, these results provide new insights into RBM7 RRM folding and recognition of 7SK RNA.Graphical abstractHighlightsExtending the RBM7 RRM C-terminus improves protein expression and solubilityThe RBM7 RRM interacts weakly with 7SK stem-loop 3 single-stranded RNASolution state NMR dynamics measurements support presence of additional β4’ strand

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition

Sobeh

Eichhorn

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…How this complex mediates precise processing of some RNA targets and complete destruction of other RNAs is still poorly understood. Moreover, the mutations in these RNA exosome genes have been reported to different tissue-specific diseases 41 , 42 . Major challenges in understanding the function of the RNA exosome still remain.…”

Section: Discussionmentioning

confidence: 99%

Oncogenic action of the exosome cofactor RBM7 by stabilization of CDK1 mRNA in breast cancer

Zhang

Zhu

et al. 2020

npj Breast Cancer

View full text Add to dashboard Cite

RNA exosome can target the specific RNAs for their processing/degradation by distinct exosome cofactors. As a key component in exosome cofactors, RNA binding motif protein 7 (RBM7) shows the binding specificity for uridine-rich sequences in mRNAs via its RNA recognition motifs. However, the specific function of RBM7 in human breast cancer remains unclear. In vitro, experiments revealed that knockdown of RBM7 dramatically inhibited breast cancer cell proliferation, while inducing G1 cell cycle arrest; the opposite was true when RBM7 was overexpressed. Meanwhile, experiments in vivo confirmed the oncogenic function of RBM7 in breast cancer. RNA sequencing and the following pathway analysis found that cyclin-dependent kinase1 (CDK1) was one of the main gene regulated by RBM7. Overexpression of RBM7 increased CDK1 expression, while RBM7 knockdown decreased it. RIP assays additionally found that RBM7 bound directly to CDK1 mRNA. It was also showed that RBM7 could directly bind to the AU-rich elements (AREs) in 3′-UTR of CDK1 mRNA, which contributed to the stability of CDK1 mRNA by lengthening its half-life. More importantly, the oncogenic activity reduced by knockdown of RBM7 could be rescued by overexpression of CDK1 both in vitro and in vivo, but mutant CDK1 failed. All the evidences implied RBM7 promoted breast cancer cell proliferation by stabilizing CDK1 mRNA via binding to AREs in its 3′-UTR. As we knew, it was the first attempt to connect the RNA exosome to the tumor development, providing new insights into the mechanisms of RNA exosome-linked diseases.

show abstract

“…Of note, we found that repression of RBM7 alone in the fibrotic phase results in reduced fibrosis, suggesting that RBM7 in the fibrotic phase is critical for fibrosis development in the lung. RBM7 was shown to regulate the target RNA specificity of the NEXT complex and bind to U-rich stretches in RNAs, requiring a minimum of four pyrimidine nucleotides [27]. Previous studies revealed a role of the NEXT complex in the decay of long noncoding RNAs (lncRNAs) [28,29].…”

Section: Cell Death In Structured Cells Initiates Fibrosis Developmentmentioning

confidence: 99%

Revisiting Cell Death Responses in Fibrotic Lung Disease: Crosstalk between Structured and Non-Structured Cells

et al. 2020

View full text Add to dashboard Cite

Fibrosis is a life-threatening disorder caused by excessive formation of connective tissue that can affect several critical organs. Innate immune cells are involved in the development of various disorders, including lung fibrosis. To date, several hematopoietic cell types have been implicated in fibrosis, including pro-fibrotic monocytes like fibrocytes and segregated-nucleus-containing atypical monocytes (SatMs), but the precise cellular and molecular mechanisms underlying its development remain unclear. Repetitive injury and subsequent cell death response are triggering events for lung fibrosis development. Crosstalk between lung structured and non-structured cells is known to regulate the key molecular event. We recently reported that RNA-binding motif protein 7 (RBM7) expression is highly upregulated in the fibrotic lung and plays fundamental roles in fibrosis development. RBM7 regulates nuclear degradation of NEAT1 non-coding RNA, resulting in sustained apoptosis in the lung epithelium and fibrosis. Apoptotic epithelial cells produce CXCL12, which leads to the recruitment of pro-fibrotic monocytes. Apoptosis is also the main source of autoantigens. Recent studies have revealed important functions for natural autoantibodies that react with specific sets of self-antigens and are unique to individual diseases. Here, we review recent insights into lung fibrosis development in association with crosstalk between structured cells like lung epithelial cells and non-structured cells like migrating immune cells, and discuss their relevance to acquired immunity through natural autoantibody production.

show abstract

RRM domain of human RBM7: purification, crystallization and structure determination

Cited by 6 publications

References 32 publications

C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition

C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition

Oncogenic action of the exosome cofactor RBM7 by stabilization of CDK1 mRNA in breast cancer

Revisiting Cell Death Responses in Fibrotic Lung Disease: Crosstalk between Structured and Non-Structured Cells

Contact Info

Product

Resources

About