Crystal structure and biochemical analysis of the heptameric Lsm1-7 complex

Zhou, Lijun; Zhou, Yulin; Hang, Jing; Wan, Ruixue; Lu, Gongxun; Yan, Chuangye; Shi, Yigong

doi:10.1038/cr.2014.18

Cited by 21 publications

(35 citation statements)

References 14 publications

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“…1) and determination of the tryptic peptide sequences (data not shown) by mass spectrometry analysis of the proteins present in the complex purified from pat1Δ cells revealed that all the seven Lsm proteins (Lsm1 through Lsm7) are present in the complex purified from pat1Δ cells, indicating that Pat1 is not required for the assembly of the Lsm1-7 heptamer. These results are consistent with the observation that the human and yeast Lsm1-7 complexes can be reconstituted in vitro in the absence of Pat1 (Zaric et al 2005;Zhou et al 2014). The complex purified from pat1Δ cells will be referred to as Lsm1-7 complex hereafter.…”

Section: Lsm1-7 Complex Assembles In Pat1δ Cellssupporting

confidence: 79%

“…Thus Lsm1 is a key distinguishing subunit of this complex. The Lsm1-7, Lsm2-8, and Sm complexes have a very similar doughnut-shaped quaternary structure wherein the individual Lsm/Sm subunits are organized relative to each other in an analogous fashion (Kambach et al 1999;Zhou et al 2013Zhou et al , 2014. A unique feature of the Lsm1-7 complex is that the extended C-terminal domain of Lsm1 forms a long α-helix that crosses the entire diameter of the doughnut and partially blocks the central hole Zhou et al 2014).…”

Section: Introductionmentioning

confidence: 99%

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Pat1 contributes to the RNA binding activity of the Lsm1-7–Pat1 complex

Chowdhury

Kalurupalle

Tharun

2014

RNA

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A major mRNA decay pathway in eukaryotes is initiated by deadenylation followed by decapping of the oligoadenylated mRNAs and subsequent 5 ′ -to-3 ′ exonucleolytic degradation of the capless mRNA. In this pathway, decapping is a rate-limiting step that requires the hetero-octameric Lsm1-7-Pat1 complex to occur at normal rates in vivo. This complex is made up of the seven Sm-like proteins, Lsm1 through Lsm7, and the Pat1 protein. It binds RNA and has a unique binding preference for oligoadenylated RNAs over polyadenylated RNAs. Such binding ability is crucial for its mRNA decay function in vivo. In order to determine the contribution of Pat1 to the function of the Lsm1-7-Pat1 complex, we compared the RNA binding properties of the Lsm1-7 complex purified from pat1Δ cells and purified Pat1 fragments with that of the wild-type Lsm1-7-Pat1 complex. Our studies revealed that both the Lsm1-7 complex and purified Pat1 fragments have very low RNA binding activity and are impaired in the ability to recognize the oligo(A) tail on the RNA. However, reconstitution of the Lsm1-7-Pat1 complex from these components restored these abilities. We also observed that Pat1 directly contacts RNA in the context of the Lsm1-7-Pat1 complex. These studies suggest that the unique RNA binding properties and the mRNA decay function of the Lsm1-7-Pat1 complex involve cooperation of residues from both Pat1 and the Lsm1-7 ring. Finally our studies also revealed that the middle domain of Pat1 is essential for the interaction of Pat1 with the Lsm1-7 complex in vivo.

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Section: Lsm1-7 Complex Assembles In Pat1δ Cellssupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Pat1 contributes to the RNA binding activity of the Lsm1-7–Pat1 complex

Chowdhury

Kalurupalle

Tharun

2014

RNA

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“…This result is consistent with a model that deadenylated, uridylated mRNAs are normally degraded rapidly by the 5′–3′ decay factors while poly(A) + mRNAs without U-tails are relatively stable. The LSM1–7 complex is known to preferentially bind to RNAs with 3′ terminal uridyl residues (Chowdhury et al, 2007; Sharif and Conti, 2013; Song and Kiledjian, 2007; Zhou et al, 2014) and facilitate decapping through PATL1 (Pat1p in yeast) (Marnef and Standart, 2010; Wilusz and Wilusz, 2013). Thus, a short U-tail may first be recognized by the LSM1–7 complex which in turn facilitates decapping (by the DCP1/2 complex) and subsequent 5′–3′ degradation (by XRN1).…”

Section: Resultsmentioning

confidence: 99%

Uridylation by TUT4 and TUT7 Marks mRNA for Degradation

Lim

Chang

et al. 2014

Cell

257

320

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Summary Uridylation occurs pervasively on mRNAs, yet its mechanism and significance remain unknown. By applying TAIL-seq, we identify TUT4 and TUT7 (TUT4/7), also known as ZCCHC11 and ZCCHC6, respectively, as mRNA uridylation enzymes. Uridylation readily occurs on deadenylated mRNAs in cells. Consistently, purified TUT4/7 selectively recognize and uridylate RNAs with short A-tails (less than ∼25 nt) in vitro. PABPC1 antagonizes uridylation of polyadenylated mRNAs, contributing to the specificity for short A-tails. In cells depleted of TUT4/7, the vast majority of mRNAs lose the oligo-U-tails, and their half-lives are extended. Suppression of mRNA decay factors leads to the accumulation of oligo-uridylated mRNAs. In line with this, microRNA induces uridylation of its targets, and TUT4/7 are required for enhanced decay of microRNA targets. Our study explains the mechanism underlying selective uridylation of deadenylated mRNAs and demonstrates a fundamental role of oligo-U-tail as a molecular mark for global mRNA decay.

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“…The described scenario therefore would not only account for the lower affinity of the LSm1–7 ring for uridine-rich RNA 3′-ends, 85 but it also suggests how the LSm1–7 ring could recognize 3′-ends on oligoadenylated mRNA 106 . In this case, the ring would simultaneously bind two or three upstream uridines, as are frequently found near the end of mRNA 3′-UTRs, 108 and one to three 3′-terminal adenines that could fit the nucleotide binding pockets reasonably well.…”

Section: The Lsm1–7 Ringmentioning

confidence: 99%

RNA binding by Hfq and ring-forming (L)Sm proteins

Weichenrieder¹

2014

RNA Biology

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The eukaryotic Sm and the Sm-like (LSm) proteins form a large family that includes LSm proteins in archaea and the Hfq proteins in bacteria. Commonly referred to as the (L)Sm protein family, the various members play important roles in RNA processing, decay, and riboregulation. Particularly interesting from a structural point of view is their ability to assemble into doughnut-shaped rings, which allows them to bind preferentially the uridine-rich 3′-end of RNA oligonucleotides. With an emphasis on Hfq, this review compares the RNA-binding properties of the various (L)Sm rings that were recently co-crystallized with RNA substrates, and it discusses how these properties relate to physiological function.

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Crystal structure and biochemical analysis of the heptameric Lsm1-7 complex

Cited by 21 publications

References 14 publications

Pat1 contributes to the RNA binding activity of the Lsm1-7–Pat1 complex

Pat1 contributes to the RNA binding activity of the Lsm1-7–Pat1 complex

Uridylation by TUT4 and TUT7 Marks mRNA for Degradation

RNA binding by Hfq and ring-forming (L)Sm proteins

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