Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery

Reviewer #1 (Public Review):

In the manuscript there is not much comparison between the crystal and cryoEM structures provided, and on inspection they appear to be very similar. The crystal structures also reveal parts of the CC domains in Las1, which is not present in the cryoEM structures. It is interesting the CC domains in Sc and Cj are quite different as illustrated in Figure 4B. They also seem to be somewhat disconnected from the rest of the complex (more so for Cj), even though that's not apparent in Figures 2-4. Despite this, it would be very useful to show the cryoEM densities when describing the catalytic site and C-terminal domain interactions, for example, as this can be very useful to increase confidence in the model and proposed mechanisms.

The description of the complex as a butterfly is engaging, and from a certain angle it can be made to look as such; this was also described previously in (Pillon et al., 2019, NSMB) for the same complex from a different organism (Ct). However, it is a bit misleading, because the complex is actually C2 symmetric. Under this symmetry, the 'body' would consist of two 'heads' one pointing up, one down facing towards the back, and one wing would have its back toward the viewer, the other the front. The structures presented here in Sc and Cj seem quite similar to the previous structure of the same complex in Ct, though the latter was only solved with cryoEM, and was also lacking the structure of the CC domain in Las1.

For the model suggested in Figure 8, perhaps in the 'weak activity' state, the LCT in Las1 could still be connected to Grc3, via the LCT, rather than disconnected as shown. This could facilitate faster assembly of the 'high activity' state. The complex is described as 'compact and stable', but from the structure and this image, it appears more dynamic, which would serve its purpose and the illustrated model better. The two copies of HEPN appear to have more connective area, meaning they are indeed more likely to remain assembled in the 'weak activity' state. On the other hand, HEPN in one protein appears to have less binding surface with PNK in Grc3, and even less so with the CTD (both PNK and CTD being from the other associated protein), meaning these bindings could release easily to form the 'weak activity' state.

There is also the potential to speculate that the GCT is bound to HEPN near the catalytic area in the 'weak activity' state. The reduced activity when the GCT residues are replaced by Alanine could then be explained by the complex not being able to assemble as quickly upon binding of the substrate, as it could if the GCT remained bound, rather than by a conformational change that it induces upon binding. The conformational change is also likely to be influenced by the combined binding of PNK and CTD in the assembled state, which also contact HEPN, rather than by GCT alone.

When comparing the structure of the HEPN domain in the lone Las1 protein to the structure of Las1-HEPN in the Las1-Grc3 complex, it is mentioned that 'large conformational changes are observed'. These could be described a bit better. The conformational change is ~3-4Å C-alpha RMSD across all ~150 residues in the domain (~90 residues forming a stable core that only changes by ~1Å). There is also a shift in the associated HEPN domain in Las1B domain compared to the bound HEPN in the Las1-Grc3 complex, as shown in Figure 7D: ~1Å shift and ~12degrees rotation. This does point to the conformation of HEPN changing upon complex formation, as does the relative positions of the HEPN domains in Las1A and Las1B. The conformational change and relative shift could indeed by key for the catalysis of the substrate as mentioned.

Overall, the structures presented should be very useful in further study of this system, even though the exact dynamics and how the substrate is bound are aspects that are perhaps not fully clear yet. The addition of the structures of the CC domain in two different organisms and the Las1 HEPN domain (not in complex with Grc3) as new structural information should allow for increasing our understanding of the overall complex and its mechanism.

Reviewer #2 (Public Review):

In this manuscript, Chen et al. determined the structural basis for pre-RNA processing by Las1-Grc3 endoribonuclease and polynucleotide kinase complexes from S. cerevisiae (Sc) and C. jadinii (Cj). Using a robust set of biochemical assays, the authors identify that the sc- and CjLas1-Grc3 complexes can cleave the ITS2 sequence in two specific locations, including a novel C2' location. The authors then determined X-ray crystallography and cryo-EM structures of the ScLas1-Grc3 and CjLas1-Grc3 complexes, providing structural insight that is complimentary to previously reported Las1-Grc3 structures from C. thermophilum (Pillon et al., 2019, NSMB). The authors further explore the importance of multiple Las1 and Grc3 domains and interaction interfaces for RNA binding, RNA cleavage activity, and Las1-Grc3 complex formation. Finally, evidence is presented that suggests Las1 undergoes a conformational change upon Grc3 binding that stabilizes the Las1 HEPN active site, providing a possible rationale for the stimulation of Las1 cleavage by Grc3.

Several of the conclusions in this manuscript are supported by the data provided, particularly the identification and validation of the second cleavage site in the ITS2. However, several aspects of the structural analysis and complimentary biochemical assays would need to be addressed to fully support the conclusions drawn by the authors.

• There is a lack of clarity regarding the number of replicates performed for the biochemical experiments throughout the manuscript. This information is critical for establishing the rigor of these biochemical experiments.

• The authors conclude that Rat1-Rai1 can degrade the phosphorylated P1 and P2 products of ITS2 (lines 160-162, Figure 1H). However, the data in Fig. 1H shows complete degradation of 5'Phos-P2 and 5'Phos-P4 of ITS2, while the P1 and 5'Phos-P3 fragments remain in-tact. Additional clarification for this discrepancy should be provided.

• The authors determined X-ray crystal structures of the ScLas1-Grc3 (PDB:7Y18) and CjLas1-Grc3 (PDB:7Y17) complexes, which represents the bulk of the manuscript. However, there are major concerns with the structural models for ScLas1-Grc3 (PDB:7Y18) and CjLas1-Grc3 (PDB:7Y17). These structures have extremely high clashscores (>100) as well as a significant number of RSRZ outliers, sidechain rotamer outliers, bond angle outliers, and bond length outliers. Moreover, both structures have extensive regions that have been modeled without corresponding electron density, and other regions where the model clearly does not fit the experimental density. These concerns make it difficult to determine whether the structural data fully support several of the conclusions in the manuscript. A more careful and thorough reevaluation of the models is important for providing confidence in these structural conclusions.

• The presentation of the cryo-EM datasets is underdeveloped in the results section drawing and the contribution of these structures towards supporting the main conclusions of the manuscript are unclear. An in-depth comparison of the structures generated from X-ray crystallography and cryo-EM would have greatly strengthened the structural conclusions made for the ScLas1-Grc3 and CjLas1-Grc3 complexes.

• The authors conclude that truncation of the CC-domain contributes to Las1 IRS2 binding and cleavage (lines 220-222, Fig. 4C). However, these assays show that internal deletion of the CC-domain alone has minimal effect on cleavage (Fig 4C, sample 3). The loss in ITS2 cleavage activity is only seen when truncating the LCT and LCT+CC-domain (Fig 4C, sample 2 and 4, respectively). Consistently, the authors later show that Las1 is unable to interact with Grc3 when the LCT domain is deleted (Fig. 6 and Fig. 6-figure supplement 2). These data indicate the LCT plays a critical role in Las1-Grc3 complex formation and subsequent Las1 cleavage activity. However, it is unclear how this data supports the stated conclusion that the CC-domain is important for LasI cleavage.

• The authors conclude that the HEPN domains undergo a conformational change upon Grc3 binding, which is important for stabilization of the Las1 active site and Grc3-mediated activation of Las1. This conclusion is based on structural comparison of the HEPN domains from the CjLas1-Grc3 complex (PDB:7Y17) and the structure of the isolated HEPN domain dimer (PDB:7Y16). However, it is also possible that the conformational changes observed in the HEPN domain are due to truncation of the Las1 CC and CGT domains. A rationale for excluding this possibility would have strengthened this section of the manuscript.