Nature of filaments and rRNA contamination

94 To confirm the maximum length of RNA in the synthetic Cascade -like complexes, it will be necessary to purify full Cascade complexes with Cas6f at the 3′-end that include crRNAs with a spacer length close to the observed ~ 100 nt limit. By step-wise increasing the spacer length by 6 nt for one Cas7fv subunit, it would be possible to confirm the maximum number of Cas7fv subunits in the Cascade backbone (Figure 3.3). The addition of Cas6f at the 3′-end would guarantee a defined end of the complex, ensure stability and also allow for purification with a second affinity tag.

Figure 3.3: Schematic representation of step-wise crRNA spacer extension. Sta rti ng from a n ensured poss i bl e s pa cer l ength s uch a s 80 nt (a pproximately the position of the highest count of mapped reads during RNA-seq a nalysis a nd s ize of a defi ned ba nd during small RNA Urea-PAGE), the crRNA l ength is i ncreas ed i n s teps of 6 nt for 1 Ca s 7fv s ubuni t a t a ti me. Mul ti pl e cons tructs with va rying l ength a re created and used for Ca scade assembly. Purification is then performed to i denti fy formed Ca s ca de complexes. The fi rst construct that does not form a Ca s ca de compl ex m a rks the defi ni te end of pos s i bl e s pa cer extension. A 3′-repeat sequence for Cas6f binding a nd full Cascade assembly is i ncluded to ensure stability of these complexes .

95 they are starting with a Cas5fv subunit. Cas5fv was never really detected on SDS-PAGE though, which we thought to be due to overlapping bands or due to the overrepresentation of Cas7fv in these structures.

The 3D structure of a small Cas7fv helix obtained during crystallization of I-Fv Cascade Cas7fv matched the purified filamentous structures observed on TEM and the later created model by 2D class averaging.

This crystallized helix also does not contain RNA and while it is possible that RNA was pulled out during crystallization, it is also possible that the purified filaments are empty and simply oligomers caused by overproduction of Cas7fv. Recombinant overexpression in E. coli compared to minimal wild-type expression in S. putrefaciens CN-32 might have also increased the amount of unspecific interaction and by-product formation.

A recent crystallographic study elucidated the 3D structure of the Cas7f protein from Zymomonas mobilis (ZmCsy3), forming a molecular helix and filamentous structure in the crystalline state (Gu et al., 2019). The model of this helix looks generally similar to the Cas7fv helix provided in this work, exhibiting a hollow cleft through the structure by the concave palms and with a positively charged cleft to the solvent by the extended regions (here “extended web” instead of wrist-loops). In contrast to the Cas7fv helix in this work, the ZmCsy3 helix requires seven instead of eight subunits for one full rotation and is thus slightly shorter in comparison (Figure 3.4). In addition, the ZmCsy3 helix also appears moderately compressed with a distance of 82 Å between coils in comparison to  130 Å. However, this might also be due to the packing in the crystal form.

Figure 3.4: Comparison of filament structures. (A) Crys ta l s tructure of ZmCs y3 (Cas7f from Zymomonas mobilis). Left: s ide vi ew of the molecular helix formed by s even Cs y3 molecul es i n the a s ymmetri c uni t of the crys ta l l i ne s ta te . Ea ch mol ecul e i s di fferentiated by colors a nd l abeled from 3.1 to 3.7 to i ndicate the first to 7th Cs y3 molecules. Right: The filamentous structures formed by Cs y3 molecules. The symmetry-related molecules a re displayed wi th coi l s . Fi gure from Gu et al., 2019. (B) Crys ta l Structure of Ca s 7fv hel i x from thi s work (s ee 2.2.2.3 a nd Fi gure 2.19).

96 Gu et al. also claim that the molecular helix is formed in the absence of crRNA in the crystalline state and suggest the possibility for ZmCsy3 to aggregate at high concentrations to form a molecular backbone without crRNA. In turn, this might be an indication for the backbone to self-assemble before binding crRNA and other subunits. This research further indicates that the filament structures we always observed do not contain the specifically wrapped RNA and they are only an unspecific product of the purification. In the first performed RNA wrapping experiments, filaments would only be formed in case of low amounts of available repeat-tagged targets compared to massive overproduction of Cas7fv, which is not a native condition. In this case, instead of forming a Cascade-like complex, Cas7fv would aggregate to the long helical filament structures.

Besides the RNA-free helices from type I-F and type I-Fv, the length of all filaments visualized with TEM was mostly consistent and did not match the length of any repeat-tagged RNA construct potentially inside RNA. Specifically, filaments purified from cultures expressing the sfgfp-half construct looked identical to filaments obtained when full repeat-tagged sfgfp was expressed. The few observed filaments with a longer length could be overlapping structures. Small repeat-tagged RNA was only extracted from Cascade-like structures. Identical looking filament structures with the same lengths were also co-purified during recombinant production of type IV crRNP complex in E. coli (Ozcan et al., 2019).

All this combined, highly suggests that filaments are not formed on RNA.

Another direct comparison can be made with somewhat filamentous structures of Cas7 from the type I -C system (Hochstrasser et al., 2016). These structures also appear to be filamentous, with a similar size compared to the Cas7fv filaments in this work. However, they feature a much more open and less compressed configuration (Figure 3.5). Filaments of Cas7fc are stated to be formed on a 44 nt RNA after incubation and presumably by bridging adjacent RNA molecules together which would explain their large size compared to a type I-C Cascade. Either these structures are also a product of oligomerization of Cas7 without RNA or they are more similar to the synthetic Cascade assemblies produced in this work, perhaps presenting something closer to the larger complexes we couldn’t visualize yet.

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Figure 3.5: Comparison of filament structures from type I-Fv and type I-C visualized with TEM. (A) Fi l a mentous s tructures from the voi d vol ume of Ca s protein puri fi ca ti ons i n thi s work (s ee s ecti on 2.2.2.3 a nd Fi gure 2.18). (B) TEM a na l ys i s of s tructures from oligomerized type I-C Ca s7 protein, obtained after i ncubation of monomeric protein with RNA. Figure modifi ed from Hochs tra s s er et al., 2016.

Because RNA was always co-purified with these proteins, we were previously unable to locate the position of this RNA, specifically if it is bound by the central RRM of Cas7fv or sticking on the outside.

Only when rRNA (and other additional co-purified RNA) was removed, we were able to separate small RNA containing complexes and full-length transcript.

Ribosomal RNA was commonly purified before we removed MgCl2 from the purification buffer which indicates that this component was essential for rRNA contamination. Mg²⁺ ions are essential co-factors for ribosomes and an increased MgCl2 concentration can lead to their stabilization and co-purification (Nierhaus, 2014). While Mg²⁺ is naturally occurring in the cell, their addition to the wash buffer could have pulled out rRNA or entire ribosomes. However, ribosomal proteins were not detected on SDS-PAGE arguing that only rRNA was co-purified. Otherwise, it might have been possible that ribosome binding to the repeat-tagged transcript might be the reason for co-purification.

Ribosomal RNA proved difficult to remove and no method (RNase I treatment, size -exclusion, strep-affinity or salt-wash) showed any noticeable effect which speaks for a strong interaction between rRNA and Cas proteins. We also hypothesized that rRNA was in the filament structures due to the unique positively charges wrist loops of Cas7fv. However, the co-purification of repeat-tagged RNA and Cas proteins with mutated and neutralized amino acids still contained rRNA. It is still unclear, why rRNA was not detected by Illumina RNA-seq and only by Nanopore sequencing. It is likely that this was a problem with fragmentation, which is circumvented by Nanopore sequencing. These results are intriguing because rRNA usually is a common contaminant during RNA-seq with Illumina.

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