Structural Insights into the Rrp4 Subunit from the Crystal Structure of the Thermoplasma acidophilum Exosome

• Published in: Biomolecules (Basel, Switzerland) Vol. 14; no. 6; p. 621
• Main Authors: Park, Seonha, Kim, Hyun Sook, Bang, Kyuhyeon, Han, Ahreum, Shin, Byeongmin, Seo, Minjeong, Kim, Sulhee, Hwang, Kwang Yeon
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 24.05.2024; MDPI
• Subjects: Archaeal Proteins - chemistry; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Biodegradation; Chromatography; Crystal structure; Crystallography, X-Ray; Crystals; Cytoplasm; Data collection; exosome; Exosome Multienzyme Ribonuclease Complex - chemistry; Exosome Multienzyme Ribonuclease Complex - metabolism; Exosomes; Exosomes - chemistry; Exosomes - metabolism; Glycerol; Kinases; Labeling; Ligands; Messenger RNA; Models, Molecular; mRNA; PNPase; Polynucleotide phosphorylase; Protein Subunits - chemistry; Protein Subunits - metabolism; Proteins; Quality control; RNA processing; RNA Stability; RNase; Structure; Surface charge; Thermoplasma - metabolism; Thermoplasma acidophilum; South Korea; quality control; RNA processing; PNPase; exosome; RNase
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom14060621

The exosome multiprotein complex plays a critical role in RNA processing and degradation. This system governs the regulation of mRNA quality, degradation in the cytoplasm, the processing of short noncoding RNA, and the breakdown of RNA fragments. We determined two crystal structures of exosome components from ( ): one with a resolution of 2.3 Å that reveals the central components ( Rrp41 and Rrp42), and another with a resolution of 3.5 Å that displays the whole exosome ( Rrp41, Rrp42, and Rrp4). The fundamental exosome structure revealed the presence of a heterodimeric complex consisting of Rrp41 and Rrp42. The structure comprises nine subunits, with Rrp41 and Rrp42 arranged in a circular configuration, while Rrp4 is located at the apex. The RNA degradation capabilities of the Rrp4:41:42 complex were verified by RNA degradation assays, consistent with prior findings in other archaeal exosomes. The resemblance between archaeal exosomes and bacterial PNPase suggests a common mechanism for RNA degradation. Despite sharing comparable topologies, the surface charge distributions of Rrp4 and other archaea structures are surprisingly distinct. Different RNA breakdown substrates may be responsible for this variation. These newfound structural findings enhance our comprehension of RNA processing and degradation in biological systems.