In vitro RNA wrapping with I-Fv Cas proteins

38 To compare the structure of the type I-Fv complex to the published I-F “propeller” shaped complex, we initiated SAXS analysis to model the general shape of the structure. High amounts of sample were purified and scattering data was recorded but the obtained data did not provide the structure and these experiments need to be repeated. Structural analysis of the Cas1-2/3fv complex and comparison to the I-F system could be useful to understand the general interference mechanism of this system, in addition to solving the 3D structure of Cas3fv.

39

Figure 2.11: Schematic of the in vitro RNA wrapping process. Unbound RNA (extracted RNA or in vitro tra ns cri bed) i s mi xed a nd i ncuba ted wi th una s s embl ed a po -Ca s 7fv, formi ng a Ca s 7fv-RNA compl ex i n the proces s .

To obtain apo-Cas7fv, we used a variety of methods. First, we used the Cas5fv-Cas7fv dimer that is a consistent by-product during purifications because this dimerization stabilizes the otherwise insoluble proteins. We also theorized that the dimer form is required to deliver Cas7fv to the crRNA during natural Cascade assembly. To mimic this assembly process as closely as possible, we produced a target RNA with a handle sequencing by in vitro transcription and dephosphorylated it to create an OH-group at the 5′-end as is the case after processing by Cas6f. This was also considered to be potentially necessary, in case that assembly does require Cas5fv binding for initiation. In theory, the Cas5fv-Cas7fv dimer could also be used on a random RNA without repeat-tag for general RNA-binding without Cas5fv for target specificity but the properly processed repeat-tag should work for both eventualities if this process works in general. Fresh Cas5fv-Cas7fv dimer was taken from a I-Fv Cascade purification and mixed with the target RNA. After incubation for 1h at RT precipitation was noticeable. The supernatant was then loaded on an analytic size-exclusion column and separated to look for formed complexes. Unfortunately, no assembled complexes could be detected and the fractions corresponding to the only size -exclusion peak contains the Cas5fv-Cas7fv dimer as shown by SDS-PAGE (Figure 2.12).

40

Figure 2.12: In vitro RNA wrapping with the CasCas7fv dimer. (A) Schematic principle of the experiment. Puri fi ed Ca s 5fv-Ca s 7fv di mer i s incubated with in vitro tra nscribed sfgfp for 1h a t RT. Precipitated protein is removed a nd the s uperna ta nt i s then s eparated by a nalytic size-exclusion chromatography. (B) Gel electrophores i s of in vitro tra ns cri bed sfgfp RNA us ed a s template for RNA binding. (C) UV chromatogram of a nalytic size-exclusion chroma togra phy (l eft) a nd a na l ys i s by SDS-PAGE (ri ght) of RNA incubated with the dimer. Complex a ssembly was not detected, and only a pea k of the Ca s 5fv-Ca s 7fv di mer i s el uti ng.

A possible explanation for the inability of the dimer to form a complex on the provided RNA could be that the interaction of both proteins in the dimer is too strong. In addition, precipitation was noticeable after incubation, presumably of the entire Cas5fv-Cas7fv dimer. This is commonly observed for the Cas5fv-Cas7fv dimer and indicates it could not bind to RNA which would have stabilized the protein.

As an alternative, we decided to use Cas7fv alone for in vitro RNA wrapping instead of the Cas5fv-Cas7fv dimer. The first investigated way to produce Cas7fv was to repeat the crystallisation of I-Fv Cascade which has been shown to produce Cas7fv crystals as a by-product under some conditions. Crystals were created in drop format by addition of a screening solution and various concentrations of purified I-Fv Cascade. After overnight incubation at 18 °C, crystals were visible under light microscopy. To obtain sufficient amounts, we attempted to switch from the drop format for crystallization to crystallization in

41 a batch format (i.e. a micro-tube). Under all tested conditions, including those that worked for the drop format, protein precipitated overnight and no crystals were obtained.

Because high-yield crystallization proved to be problematic and beyond the scope of this work, we purified monomeric RNA-free Cas7fv fused to a SUMO-tag for solubility following a previously established protocol that includes a high salt wash step to remove all bound RNA during Ni-NTA.

Afterwards, monomeric Cas7fv was separated by size-exclusion chromatography and incubated with RNA to form complexes (Figure 2.13 A). SUMO protease was added in the mixture to remove the SUMO-tag and to exclude possible steric clashes during complex formation. We performed this experiment with both small RNAs and in vitro transcribed full length sfgfp RNA (Figure 2.13 B). Unfortunately, a second size-exclusion chromatography purification after incubation with RNA did not result in an additional peak at an earlier elution volume (Figure 2.13 D).

42

Figure 2.13: In vitro RNA wrapping with tagged Cas7fv. (A) Schema ti c pri nci pl e of the experi ment. Puri fi ed SUMO-Ca s 7fv i s i ncubated with either small RNA or in vitro tra ns cri bed sfgfp a s wel l a s SUMO protea s e for 1h a t RT fol l owed by overni ght at 4°C. The s ample i s then separated by analytic s ize-exclusion chromatography. (B) Gel electrophores i s of ei ther in vitro produced RNA or extra cted s ma l l RNA us ed for experi ments . (C) Puri fi ca ti on of SUMO-Ca s 7fv by s i ze-excl us i on chroma tography (left) and analysis by SDS-PAGE (ri ght). SUMO-Cas7fv was eluted at the corres pondi ng el uti on vol ume a nd s howed a matching signal on SDS-PAGE, although s ome partially degraded SUMO-Cas7fv is pres ent. (D) UV chroma togra m of a na lytic size-exclusion chromatography (l eft) a nd a nalysis by SDS-PAGE (right) of incuba ted protei n a nd the extra cted s ma l l RNA. Compl ex a s s embl y wa s not detected, cons i deri ng the s a me pea ks of SUMO-Ca s 7fv a re pres ent.

Some aggregated SUMO-Cas7fv, presumably still bound to nucleic acids, elutes in the void volume of the first size-exclusion chromatography step. This is supported by the high 260 nm UV absorbance in this peak and a faint signal matching the size of Cas7fv during SDS-PAGE. Monomeric SUMO-Cas7fv elutes

43 either intact in peak 2 or mostly degraded in peak 3. The bands of these smaller products are also visible in the sample from the Ni-NTA step before size-exclusion chromatography and could be due to either unspecific interactions or by fragments created by the 1M NaCl wash step. The UV absorbance ratio of 280 nm compared to 260 nm indicates that mostly protein is eluted in this peak and RNA was indeed removed. In accordance with this, no RNA was detected by Urea-PAGE. All fractions of peak 2 and 3 with a signal of SUMO-Cas7fv were concentrated and mixed with the small RNA (3.5 µg of small RNA and 1 mg of SUMO-Cas7fv corresponding to a 160x molar excess of protein).

In vitro assembly and RNA wrapping by this method was apparently not successful and thus the same peaks are present in the UV chromatogram of the second size-exclusion purification step. SUMO protease treatment was partially effective considering that the intensity of the band of SUMO-Cas7fv was drastically reduced and a band at the size of monomeric Cas7fv was present instead. Due to the small size of the SUMO-tag, a shifted elution volume in this size-range is not distinguishable. The same result was obtained with the in vitro transcribed sfgfp RNA.

Overall, no method proved successful for in vitro RNA wrapping. The most promising method seems to be the purification of SUMO-tagged Cas7fv. While good amounts of monomeric Cas7fv were produced via SUMO-tag and the high salt wash removed all bound RNA, in vitro RNA binding was not observed.

Complex formation might need to occur much faster as is the case for in vivo conditions. It could also be possible that still not enough RNA was provided (even though multiple µg should be in the detectable range).