Prp8 is an intein hot spot with diverse insertion sites

Recent data mining revealed over 100 inteins in the Prp8 protein present across assorted eukaryotic groups, some of which emerged as far back as approximately 1,100 million years ago (mya; Fig 1A, left) [27,31–33]. The vast majority of Prp8 inteins are found across different fungal species, particularly in Ascomycota, and the rest are dispersed in other eukaryotic phyla (Fig 1A, left). To characterize these Prp8 inteins, we performed comparative and phylogenetic analyses on a representative subset based on the splicing motifs (Fig 1; S1–S4 Figs) [15,34]. In total, there are 7 distinct intein insertion points, denoted Prp8-a through Prp8-g (Fig 1; S1–S4 Figs) [33,35,36]. With only a few exceptions, fungal Prp8 inteins occupy the same insertion site, Prp8-a (Fig 1A and 1B) [27,31,33]. The Prp8-g insertion is reported here for the first time (Fig 1B) and was found at the N-terminal end of Prp8 in the social amoeba Acytostelium subglobosum [37] (S3 Fig).

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Fig 1. Prp8 is an intein hot spot with multiple, independent insertion sites.

(A) Modified phylogenetic tree of eukaryotes (left) shows the phyla that contain Prp8 inteins, with representative genera listed. Evolutionary divergence times are denoted in mya. The number of Prp8 inteins in each phylum is shown in superscript, and insertion sites are shown on the branches (colored a–g). A phylogenetic intein tree (right) was reconstructed based on the amino acid sequences of intein splicing blocks for a subset of 50 Prp8 inteins. The radial tree shows numerous clusters, which correspond to grouping by insertion site. Abbreviated species names are shown (full names in S1 Fig). Shading (dark gray, light gray, or white) indicates phylogenetic distribution. The divergence of the inteins despite extein conservation (S4 Fig) suggests independent invasions. (B) A line diagram of the exteins (amino acid residues 127 to 2084) shows the domains of the Prp8 protein. The arrows below indicate the site of intein insertion (a–g) with the corresponding residue number based on Saccharomyces cerevisiae Prp8 (PDB 5GMK, chain A). Shapes represent how many inteins are found at each site (square = 10 inteins, triangle = 1 intein) and are shaded to denote phylogenetic origin as in Fig 1A. Prp8-a is the most common insertion site with approximately 100 inteins. (C) Multiple sequence alignment of the splicing blocks of Prp8 inteins from each insertion site. Comparative analysis of residues found in Blocks A, B, F, and G reveals that Prp8 inteins occupying other insertion sites are substantially different from one another, indicating independent acquisition. Identical residues are critical to self-splicing. Triangles indicate residues of general interest and those shaded blue are of specific interest. Numbers correspond to the Cne Prp8 intein. Shading is as follows: black, identical amino acid; dark gray, conserved amino acid; light gray, similar amino acid substitution. Cne, Cryptococcus neoformans; mya, millions of years ago; PDB, Protein Data Bank; Prp8, pre-mRNA processing factor 8.

https://doi.org/10.1371/journal.pbio.3000104.g001

The reconstructed phylogenetic tree reveals that Prp8 inteins group by insertion site (Fig 1A, right; S1 Fig). Although insertion sites b through g have limited representation, the observed clustering, as well as the level of sequence divergence between inteins from different insertion sites, suggest multiple independent intein invasion events throughout evolutionary history. Importantly, bifurcation of Prp8-a inteins into 2 well-supported clusters (a1 and a2, interior-branch test value of 92%) indicates recurrent invasion of inteins into site a across diverse fungi (S1A Fig). Furthermore, Prp8 extein phylogenetic analyses show clustering by host organism, adding support to independent intein acquisitions (S4 Fig). All 7 insertion sites were mapped to a simplified line diagram of Prp8 exteins and are peppered across the various domains (Fig 1B).

A multiple sequence alignment of the intein splicing motifs, referred to as Blocks A, B, F, and G, demonstrates the sequence divergence among Prp8 inteins (Fig 1C; S2 Fig). Other than identical residues located in Blocks A, B, and G (Fig 1C, black shading; S2 Fig), Prp8 inteins from different insertion sites share limited sequence homology. Block A contains the first residue of the intein, a highly conserved cysteine called C1, which performs the first nucleophilic attack of the protein splicing pathway. This amino acid is identical across the disparate Prp8 inteins (Fig 1C, Block A; S2 Fig). Block B usually carries a highly conserved motif known as TxxH [38]. Across the Prp8 inteins, Block B histidine of TxxH is present in all analyzed inteins, whereas the threonine is not as conserved (Fig 1C, Block B; S2 Fig). Also alike across all Prp8 inteins is a terminal asparagine at the C terminus of the intein in Block G, which also directly participates in splicing (Fig 1C, Block G; S2 Fig). The first amino acid of the C extein, known as the +1 residue, is usually a cysteine, serine, or threonine, and all Prp8 inteins use one of these as the +1 nucleophile. Block F shows little conservation across Prp8 inteins. The Saccharomyces cerevisiae (Sce) Vma1 intein, in the vacuolar ATPase, is as similar to Prp8 inteins as other Prp8 inteins are to each other (Fig 1C), indicating a close ancestral relationship. The poor sequence alignment among Prp8 inteins reinforces that distinct inteins recurrently invaded Prp8.

Cne Prp8 intein structure shows similarity to eukaryotic protein splicing elements

We next solved the crystal structure of the Cne Prp8 intein found at site a (Fig 2A; S4A Table). This intein was chosen because of its small size and because it is found in a significant human pathogen. The Cne Prp8 intein was solved to 1.75 Å resolution (Fig 2A). This novel structure helped us develop a sense of structural relatedness of the Cne Prp8 intein to other inteins and intein-like elements and to later model the intein into both the Prp8 protein and the spliceosome.

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Fig 2. Structure and features of the Cne Prp8 intein.

(A) A crystal structure of the Cne Prp8 intein from site a was solved to 1.75 Å resolution. This structure has the canonical horseshoe shape and resolution of the 4 splicing blocks, indicated in cyan (Block A), green (Block B), gray (Block F), and purple (Block G; Fig 1C). The NT and CT are annotated. Some regions of the structure are unresolved (dashed lines) and likely represent remnants of the original endonuclease domain or linker sequences. (B) Features of the active site. The catalytic center is shown, highlighting the first residue of the intein (C1), the penultimate histidine (H170), and the terminal asparagine (N171). The Block B TxxH motif is shown in green with T62 and H65 represented as sticks. These residues are critical to carrying out autocatalytic protein splicing. (C) Sequence of the Cne Prp8 intein (residues 1–171) overlaid with secondary structure features. Blocks distant in sequence fold close in 3D space to allow protein splicing to occur. Unresolved regions (dashed lines) are between Blocks B and F. Arrows represent β-strands, rectangles are α-helices. Residues noted in Fig 2B are highlighted. Cne, C. neoformans; CT, carboxy terminus; NT, amino terminus; Prp8, pre-mRNA processing factor 8.

https://doi.org/10.1371/journal.pbio.3000104.g002

The Cne Prp8 intein structure represents only the second known fungal nuclear intein structure. The first was of the Sce Vma1 intein, which was solved with its linker domain, a connector between the splicing blocks and the internal endonuclease domain [39,40]. As with all solved intein structures so far, the Cne Prp8 intein has the canonical horseshoe shape, created by pseudo–2-fold symmetry that positions the catalytic N- and C termini in close proximity (Fig 2A). Highlighting the splicing blocks (A, B, F, and G), we see the active core that carries out autocatalytic protein splicing (Fig 2A and 2B) [15,34]. This catalytic center contains the residues essential for splicing: the nucleophilic cysteine (C1) in Block A, and the terminal asparagine (N171) in Block G (Fig 2B and 2C; S5 Fig). The C1 and N171 are also positioned in the vicinity of the conserved Block B TxxH residues (T62 and H65), which are important for priming the intein for self-excision at its amino terminus (Fig 2B) [41]. All of these residues contribute critically to the protein splicing pathway, which involves a series of nucleophilic attacks, cyclization of the terminal asparagine, and reformation of a peptide bond between the exteins to form the functional protein [42]. Overlaying the Cne Prp8 intein primary sequence with its secondary structure shows the position of residues from each block within the context of the 3D architecture (Fig 2C). For example, Blocks A and B are far apart in sequence but fold proximally in 3D space to execute protein splicing (Fig 2). This representation also illustrates that the unresolved regions of the intein are between Block B and Block F and likely represent flexible linker sequences of a former endonuclease domain (Fig 2A and 2C).

We next performed a 3D BLAST to compare the Cne Prp8 intein structure to other solved structures (Fig 3). Unsurprisingly, the Cne Prp8 intein structure as the query returns the Sce Vma1 intein as the top hit (Fig 3A, PDB 1GPP) [39]. These are both fungal inteins encoded in nuclear genomes. An overlay of the Cne Prp8 intein (red) and the Sce Vma1 intein (splicing domain in cyan, linker/endonuclease domain in gray) displays high structural similarity in the splicing modules (Fig 3A, Root-mean-square deviation [RMSD] of 1.06 Å). The unstructured regions in the Cne Prp8 intein structure are where the Sce Vma1 intein encodes a linker domain (Fig 3, dashed red lines). A closer look at the active centers of the Cne Prp8 intein and the Sce Vma1 intein demonstrates unmistakable overlap of the catalytic residues (S5A Fig), further confirming the similarities.

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Fig 3. Similarity of the Cne Prp8 intein to eukaryotic protein splicing elements.

(A) Overlay of the Cne Prp8 intein (red) with the Sce Vma1 intein (cyan and gray, PDB 1GPP) with an RMSD of 1.06 Å. Structural similarities are most pronounced in the splicing domain (Blocks A, B, F, and G, cyan) of the Sce Vma1 intein, whereas the linker/endonuclease domain (gray) is where the Cne Prp8 intein did not resolve (dashed lines). The NT and CT are annotated. (B) Multiple sequence alignment of Cne Prp8 intein, Sce Vma1 intein, and Dme HHc. Sequence comparison (residues 1–193) reveals significant differences across the 3 proteins, which are only 22.6% identical. Overlaying secondary structure shows that, despite sequence divergence, the proteins have high structural similarity. Shading is as follows: black, identical amino acid; dark gray, conserved amino acid; light gray, similar amino acid substitution. Arrows represent β-strands, rectangles are α-helices. Unresolved regions shown as dashed lines. (C) Overlay of the Cne Prp8 intein (red) with Dme HHc (yellow, PDB 1AT0). Structural 3D BLAST shows parallels between the eukaryotic intein and the eukaryotic protein splicing Hedgehog domain, with an RMSD of 1.88 Å. The NT and CT are annotated. Cne, C. neoformans; CT, carboxy terminus; Dme, Drosophila melanogaster; HHc, Hedgehog C-terminal domain; NT, amino terminus; PDB, Protein Data Bank; Prp8, pre-mRNA processing factor 8; RMSD, Root-mean-square deviation; Sce, Saccharomyces cerevisiae.

https://doi.org/10.1371/journal.pbio.3000104.g003

Another top hit from the 3D BLAST is the 17 kDa fragment of the Drosophila melanogaster (Dme) Hedgehog C-terminal domain (HHc; Fig 3B and 3C) [43]. Hedgehog is an essential signaling molecule in higher eukaryotes with an analogous cleavage reaction performed by a highly conserved cysteine [44]. This allows the N-terminal domain of Hedgehog to ligate to a cholesterol molecule, which plays a critical role in metazoan development. There has been considerable speculation about the relatedness of Hedgehog and inteins [43,45]. It was recently proposed, based on sequence similarity, that the N-terminal portion of Hedgehog was acquired through horizontal gene transfer from a prokaryote [46]. However, a sequence alignment between the Cne Prp8 intein, the Sce Vma1 intein, and Dme HHc shows only an average of 22.6% sequence identity (Fig 3B, 26.4% identity Vma1 to Prp8, 19.2% HHc to Prp8, 22.2% Vma1 to HHc). One highly conserved residue across the 3 proteins is the initiating cysteine, shared by all the sequences, as well as a C-terminal valine (Fig 3B, black shading). Despite the sequence divergence, a secondary structure overlay demonstrates that these sequences all code for the same structural elements (Fig 3B). The Cne Prp8 intein and Dme HHc have an RMSD of 1.88 Å (Fig 3C, PDB 1AT0), sharing a similar degree of structural relatedness as a bacterial and a fungal intein (S5B Fig, RMSD 2.22 Å, PDB 2IMZ) [47]. These results reinforce the evolutionary connection between inteins and Hedgehog proteins.

Cne Prp8 intein is responsive to stress

With the structure solved, we next sought to investigate Prp8 intein splicing and whether it is regulated in any way. For simplicity, the Cne Prp8 intein was studied in Escherichia coli. Given that full-length Prp8 contains approximately 2,500 amino acids, we cloned the Cne Prp8 intein into a reporter construct that uses maltose binding protein (MBP) and green fluorescent protein (GFP) as foreign N and C exteins, respectively [21,24] (Fig 4A). From this construct, termed MBP-Intein-GFP (MIG), which contains 5 native N- and C-extein residues, expression is induced and splicing products, such as ligated exteins (Fig 4A, LE), are visualized using nonreducing SDS-PAGE and scanning for GFP fluorescence (Fig 4A, left). Off-pathway cleavage (OPC) products, the result of either N-terminal or C-terminal cleavage, are also detectable in the gels. N-terminal cleavage occurs when the thioester bond generated by the first step of protein splicing is cleaved by an external nucleophile. C-terminal cleavage is caused when the terminal asparagine (N171) cyclizes prior to the first step of protein splicing (Fig 4A, right).

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Fig 4. MIG Prp8 A-1V is responsive to metal and RNS treatment.

(A) Schematic of the MIG reporter. The construct contains MIG and is expressed in E. coli. GFP allows monitoring of splicing using in-gel fluorescence. The P can undergo protein splicing (left), yielding LE and free INT (not seen on gels). OPC reactions (right), such as N- and C-terminal cleavage, can also occur. The catalytic cysteine, C1, is labeled. (B) MIG Prp8 WT splices rapidly. A fluorescent gel of a splicing time course shows that the WT Cne Prp8 intein in MIG is entirely spliced by the start of the assay (left, WT, 0 h). The A-1V mutant had precursor at the assay start and spliced over time (right, A-1V, 0 h). Quantitation is shown below in stacked plots. Data are representative of 3 biological replicates and mean standard deviations are shown. Data available in S1 Data. (C) MIG Prp8 A-1V accumulates precursor under RNS and metal treatment. After 5 h in vitro treatment with a panel of environmental stressors, there was an increase in P compared to the UT (red line) with the RNS compounds DEA at 1.2 mM and 12 mM and AS at 2 mM and 20 mM, and the metals Cu and Zn at 0.5 mM and 2 mM. H₂O₂ and Mg showed no effect at either concentration. Quantitation is shown below in a stacked plot. Data are representative of 3 biological replicates and mean standard deviations are shown. Data available in S1 Data. AS, Angeli’s salt; Cne, C. neoformans; DEA, DEA NONOate; GFP, green fluorescent protein; INT, intein; LE, ligated exteins; MBP, maltose-binding protein; MIG, MBP-Intein-GFP; OPC, off-pathway cleavage; P, precursor; Prp8, pre-mRNA processing factor 8; RNS, reactive nitrogen species; UT, untreated; WT, wild type.

https://doi.org/10.1371/journal.pbio.3000104.g004

First, we observed that the Cne Prp8 intein splices well in the foreign context to yield ligated exteins, as has been published previously by Pearl and colleagues [48]. However, splicing was so rapid that the amount of precursor remaining after induction (0 h) did not provide a suitable dynamic range for performing splicing assays (Fig 4B, WT). To slow down splicing and accumulate precursor, a mutation was made to the last residue of the N extein (referred to as -1), a site previously shown to affect splicing rates [49]. After random mutagenesis, a slower splicing mutant was isolated (Fig 4B, A-1V). The MIG Prp8 A-1V mutant has 40% precursor at 0 h and is splicing active over time (Fig 4B, A-1V). Interestingly, an A-1V mutant of the Cne Prp8 intein was previously shown to have attenuated splicing in other extein contexts [48], suggesting that splicing is somewhat dependent on both local flanking residues and distant extein context. It is worth noting that splicing rates are also intein-dependent, given that other Prp8-a inteins from fungal pathogens exhibit diverse splicing phenotypes when cloned into MIG (S6 Fig).

Next, using MIG Prp8 A-1V, we asked whether a condition exists in which intein splicing might be regulated. Treatments chosen were to mimic environmental stress that Cne experiences during infection, such as reactive oxygen species (ROS), reactive nitrogen species (RNS), and metals, all of which prevail during the intracellular respiratory burst (Fig 4C) [50,51]. From this initial panel, the RNS compounds DEA NONOate and Angeli’s salt showed significant precursor accumulation (Fig 4C, DEA and AS). It also appears that copper and zinc can cause splicing inhibition of MIG Prp8 A-1V (Fig 4C, Cu and Zn). Under these conditions, splicing was inhibited by approximately 50% (Fig 4C). This preliminary compound screen indicates that the Cne Prp8 intein may be subject to inhibition by specific conditions that occur during infection.

Splicing inhibition is mechanistically distinct under copper and zinc treatment

Metal binding has been reported for other inteins and often engages catalytic residues, which would stall protein splicing [47,52–57]. Therefore, we chose to follow up on the observed copper and zinc inhibition by running in vitro MIG Prp8 A-1V assays to further assess effects on protein splicing over time (Fig 5; S7 and S8 Figs). Because higher concentrations of copper can cause protein precipitation (Fig 4C), we decreased each metal to 1 mM.

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Fig 5. MIG Prp8 A-1V is differentially inhibited by copper and zinc.

(A) Copper inhibition is alleviated by reducing agent only. MIG Prp8 A-1V splicing was completely inhibited by 1 mM copper treatment (Cu) over 22 h, given minimal loss in P or increase in LE occurred compared with the UT control. The inhibition was unaffected by treatment with metal chelator EDTA at 10 mM (Cu + EDTA). Upon adding copper for 2 h and then reducing agent TCEP at 40 mM (Cu + TCEP), splicing was restored and P converted into LE over time. Red arrows indicate splicing rescue. The splice products were quantitated, and the percent precursor is plotted as a proxy for splicing inhibition. Representative gels are shown. Data are representative of 3 biological replicates and mean standard deviations are shown. Data available in S1 Data. Lines through gels indicate where intervening lanes were cropped out of the image. (B) Zinc treatment is relieved by EDTA only. MIG Prp8 A-1V splicing was strongly inhibited by 1 mM zinc treatment (Zn) over 22 h compared with UT lysates. The zinc-based inhibition was relieved when treated with 10 mM EDTA (Zn + EDTA) after 2 h of zinc treatment, and splicing was observed at a rate comparable with the untreated samples. Red arrows indicate splicing rescue. When adding zinc for 2 h and then reducing agent TCEP at 40 mM (Zn + TCEP), splicing was unaffected. Representative gels are shown. Data are representative of 3 biological replicates and mean standard deviations are shown. Data available in S1 Data. Lines through gels indicate where intervening lanes were cropped out of the image. (C) Zinc binds to the Cne Prp8 intein tightly. Using ITC, 16 μM purified Cne Prp8 intein was titrated with 0.05 mM ZnSO₄ over 20 injections at 37°C and pH 7.0 on a Nano ITC. The binding isotherm (bottom) shows integrated heat per mole of ZnSO₄ as a function of the molar ratio of ZnSO₄ to the Cne Prp8 intein and a K_d of 1 ± 0.82 nM was calculated. The NanoAnalyze ITC software automatically discarded outlier data points. Experiment was performed in triplicate. (D) Two binding sites in the Cne Prp8 intein-Zn²⁺ crystal structure. A close-up view of the crystal structure of the Cne Prp8 intein soaked with zinc shows 2 densities, one surrounding the terminal asparagine (N171) at the C terminus and one around the catalytic cysteine (C1), at the N terminus. Electron density maps are shown for the bound Zn²⁺ with an omit Fo-Fc difference map (green mesh) contoured at 5δ level and for the alternative conformation of N171 with a 2Fo-Fc map (gray mesh) contoured at 1δ level. Atomic colors are as follows: oxygen, red; carbon, yellow; nitrogen, blue; Zn²⁺, gray. Zn²⁺ and water molecules are shown as spheres, and the Cne Prp8 intein residues at the binding site are represented as sticks. (E) Minor conformational changes in the zinc-bound Cne Prp8 intein. A structural superimposition is shown of the native Prp8 intein (red) and the Prp8-Zn²⁺ complex (yellow) at the Zn²⁺ binding sites. Atomic colors are as in panel D, except that the carbon atoms for residues C1, H65, H170, and N171 of the native structure are in cyan. Cne, C. neoformans; EDTA, ethylenediaminetetraacetic acid; ITC, isothermal titration calorimetry; LE, ligated exteins; MIG, MBP-Intein-GFP; P, precursor; Prp8, pre-mRNA processing factor 8; TCEP, tris-(2-carboxyethyl)phosphine; UT, untreated.

https://doi.org/10.1371/journal.pbio.3000104.g005

We found that 1 mM CuSO₄ caused strong splicing inhibition for up to 22 h compared with untreated controls (Fig 5A, Untreated and Cu; S7 Fig). This inhibition persisted up to 30 h (S7A Fig). To test a copper-binding hypothesis, the same assay was carried out, but after 2 h of incubation with copper, ethylenediaminetetraacetic acid (EDTA) was added in excess to the remaining copper-treated lysate. EDTA chelates copper and should strip bound copper from the Cne Prp8 intein so that splicing can occur. However, addition of EDTA did not rescue splicing, ruling out the possibility of inhibition purely by copper binding (Fig 5A, Cu + EDTA).

Copper is a redox active metal that can cause cysteine oxidation, either by promoting disulfide bond formation or by catalyzing reversible or irreversible oxidative modifications [58]. We next tested whether the Cne Prp8 intein cysteines are being reversibly modified by copper, which would prevent the C1 from performing the first nucleophilic attack, and has precedent in intein biology [21,25]. We added the reducing agent tris-(2-carboxyethyl)phosphine (TCEP) to copper-treated lysate after collecting a sample after 2 h incubation. Strikingly, TCEP completely relieved the splicing inhibition (Fig 5A, Cu + TCEP). After reduction, MIG Prp8 A-1V precursor conversion into ligated exteins occurred at a rate similar to that of no copper treatment (Fig 5A, bottom), indicating reversible cysteine oxidation. TCEP can reduce copper, which could also lead to the loss of inhibition.

The Cne Prp8 intein only has 2 cysteines: C1 in Block A, and C61 in Block B, immediately preceding the TxxH motif (see Fig 1C, blue arrowheads). The C1 to C61 distance is 8.9 Å (S7B Fig), generally too far to form a disulfide bond [21,59,60]. We also found that C61 is not conserved among known Prp8 inteins (Fig 1C; S2 and S7C Figs), and the most commonly used residue at this site is valine (S2 Fig). Therefore, to investigate if C1 modifications are sufficient to inhibit protein splicing, several mutants of C61 in MIG Prp8 A-1V were tested for splicing activity (S8A Fig) and treated with copper (S8B Fig). The C61 mutants also showed precursor accumulation with copper treatment (S8B Fig), suggesting that C1-C61 disulfide bonding is not the underlying inhibitory mechanism, and that copper induces at least C1 oxidation, which is enough to cause the nonsplicing phenotype.

We further confirmed cysteine modification by performing mass spectrometry on purified Cne Prp8 intein. This showed a peak shifted by 32 Da, consistent with an addition of 2 oxygen atoms (S9A Fig). Additional validation pinpointed reversible sulfenic acid modifications (-SOH) to C1 and C61 with copper treatment (S9B Fig), but these were also present in the untreated Cne Prp8 intein (S9A Fig). This indicates that the Cne Prp8 intein has highly reactive cysteines that can be modified by atmospheric oxygen alone. Such extreme sensitivity has been observed for other inteins that are regulated by cysteine modification [21]. At this time, it is unclear whether the modifications in this assay are the result of copper, oxygen in air, or both. Based on our MIG data, reversible, copper-induced cysteine modifications are the most likely explanation for the inhibition we observe (Fig 5A) and are mediated mainly through C1 (S8B Fig).

Next, zinc, a metal without redox activity, was added to MIG Prp8 A-1V lysates given that it too was inhibitory in preliminary treatments (Fig 4C). The addition of 1 mM ZnSO₄ also caused protein splicing inhibition and for similar time periods (Fig 5B, Untreated and Zn). To probe the mechanism of zinc inhibition, we followed up with the same EDTA chelation and TCEP reduction after taking samples treated with zinc for 2 h. In contrast to copper, EDTA alleviated protein splicing inhibition with zinc (Fig 5B, Zn + EDTA), but TCEP reduction did not (Fig 5B, Zn + TCEP). Thus, zinc likely causes inhibition by binding to the Cne Prp8 intein, because it is redox inactive and TCEP treatment yielded no change.

To corroborate zinc binding, purified Cne Prp8 intein was titrated with zinc in an isothermal titration calorimetry (ITC) experiment. This revealed tight binding of zinc to the intein, with a K_d in the 1 nM range (Fig 5C). To further understand the mode of zinc binding, we turned to crystal soaking in zinc acetate (S4B Table). We determined the crystal structure of the Cne Prp8 intein in complex with Zn²⁺ at 1.85 Å resolution (Fig 5D and 5E). Compared with the native form, the complex does not show significant conformational changes, as is reflected by a small overall RMSD (0.17 Å) between the 2 structures (Fig 5E). There are 6 molecules per asymmetric unit cell. All 6 molecules bind 1 Zn²⁺ at their C terminus with the terminal asparagine (N171), and 3 molecules bind an additional Zn²⁺ at their N terminal C1 (Fig 5D). It is currently unclear why all 6 molecules do not bind a second Zn²⁺ at C1. It is possible that the second zinc site, coordinated by the C1 side chain and main chain amide, has a lower affinity, and the high concentration of Zn²⁺ (4 mM) used for soaking allowed partial binding. Interestingly, a dissociated platinum atom binds to the C1 in a similar fashion in the mycobacterial RecA intein [52]. The Zn²⁺ at the C terminus is coordinated by the main chain carboxyl oxygen of the N171 and 2 water molecules. Binding at this site induces an alternative conformation for the main chain peptide carboxyl group to provide a ligand for Zn²⁺. This alternative conformation is not seen in the native structure (Fig 5D and 5E). Zn²⁺ binding to either of these 2 catalytic residues prevents Prp8 protein splicing.

Protein splicing in Cne is inhibited by copper

To investigate whether metal stress affects protein splicing in vivo, in Cne, Western blotting was employed to probe for intein using a Prp8 intein antibody (Fig 6). The level of excised intein is a read-out for inhibition, because protein splicing is the most plausible pathway to yield free intein. We first determined that the intein antibody can detect the Prp8 intein, because it reacts with overexpressed Cne Prp8 intein at the expected size of approximately 20 kDa (Fig 6A and 6B, [+] lane). Moreover, the intein antibody does not detect any bands close to 20 kDa in an inteinless strain of Cne that we constructed (Fig 6A and 6B, Prp8ΔIn). Upon metal treatment, blots consistently revealed that incubation with CuSO₄ (1 mM) caused a marked decrease in the amount of free intein (Figs 4C, 5A and 6A, Cu). Compared with unsupplemented media, copper treatment showed up to 50% reduction of free intein in Cne, correlating with the expected protein splicing inhibition. Importantly, this inhibition was relieved in vitro by addition of reducing agent β-mercaptoethanol to the treated lysate (Fig 6B), agreeing well with our MIG data that showed reversible cysteine modifications after copper incubation (Fig 5A). The ZnSO₄ treated cultures show only a minimal decrease in free intein, possibly because the zinc, which we showed to be reversibly bound (Fig 5B), dissociates from the intein during lysate preparation. The intein antibody was unable to detect Prp8 precursor, perhaps because at a size of >290 kDa, the protein transfers poorly to the membrane. Regardless, these results indicate that Prp8 intein splicing is regulated in vivo, with implications for biological relevance to intron splicing.

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Fig 6. Native protein splicing in Cne is inhibited by copper.

(A) Copper treatment shows decreased intein (In) levels under nonreducing conditions. Cne (WT) and an inteinless strain (Prp8ΔIn) were grown in defined media supplemented with 1 mM CuSO₄ or 1 mM ZnSO₄ for 3 h. Top blot is probed with Prp8 intein antibody, and the bottom blot is probed with Cdc2 antibody as a loading control. Intein bands at approximately 20 kDa often appear as doublets because of different oxidation states of cysteines. Bands migrating around 150 kDa that appear in the Prp8ΔIn and WT strain have not been identified, whereas bands from Sce lysate may be related to the Vma1 intein. Lanes are as follows: (+), 2.5 ng of overexpressed pET47b Cne Prp8 intein in E. coli lysate; Sce, 10 μg of soluble S. cerevisiae extract; UT, unsupplemented SC media; Cu, SC media + 1 mM CuSO₄; Zn, SC media + 1 mM ZnSO₄. All Cne lysates contain 20 μg of soluble protein. (B) Reducing conditions alleviate splicing inhibition in vitro. Blots are as in panel A but treated with βME in the loading dye. The reducing conditions in the lysate are sufficient to cause splicing in vitro and the intein band reappears. βME, β-mercaptoethanol; Cdc2, cyclin-dependent kinase 1; Cne, C. neoformans; Prp8, pre-mRNA processing factor 8; SC, synthetic complete; Sce, Saccharomyces cerevisiae; UT, untreated; WT, wild type.

https://doi.org/10.1371/journal.pbio.3000104.g006

A precursor model of Prp8 relates intein retention to spliceosome function

Finally, we wished to ask how protein splicing inhibition might affect both Prp8 and the spliceosome. Therefore, we docked the intein into a known Prp8 structure and generated a precursor model, in which the intein is still covalently connected to the exteins. In this model, the bonds flanking the intein were broken at site a in Prp8 from the spliceosomal U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) solved from Sce (Fig 7A, PDB 5GAN, chain A) [12,61]. The Cne Prp8 intein structure was computationally inserted using an energy optimization protocol, allowing insight into how intein presence might affect Prp8 and spliceosome assembly or activation.

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Fig 7. Modeling the Cne Prp8 intein into Prp8 and docking into the spliceosomal U4/U6.U5 tri-snRNP reveals unfavorable interactions.

(A) Cne Prp8 intein in Prp8 exteins. The Cne Prp8 intein structure (red) was modeled into a structure of S. cerevisiae (PDB 5GAN, chain A) Prp8 exteins (lavender). The S+1 is shown as blue spheres to indicate the site where a peptide bond was broken to insert the intein. The C1 is shown as yellow spheres and specifies start of the intein. The Prp8 intein localizes to a crowded site of the Prp8 structure, in a region that is highly conserved and functionally important. (B) The Cne Prp8 intein in the spliceosomal U4/U6.U5 tri-snRNP. The intein-containing Prp8 was overlaid into the tri-snRNP subunit structure (PDB 5GAN). This revealed a clash of the intein with spliceosomal protein Dib1 (top panel, orange). There are also possible clashes with the intein and U4 snRNA and U6 snRNA (bottom panel, teal and pink, respectively). Cne, C. neoformans; PDB, Protein Data Bank; Prp8, pre-mRNA processing factor 8; snRNA, small nuclear RNA; tri-snRNP, triple small nuclear ribonucleoprotein.

https://doi.org/10.1371/journal.pbio.3000104.g007

Upon docking, it appears that the Cne Prp8 intein is accommodated in the Prp8 protein, albeit in a crowded area that would otherwise be occupied by helical folds (Fig 7A). The insertion site is in the 1585 loop, 1 of 3 structural motifs responsible for directly facilitating both steps of intron splicing [62]. Presence of the intein likely interrupts Prp8 function; given the importance of this location, the supporting contacts Prp8 makes within the spliceosome, and the RNA splicing defects in Prp8 mutants [1,2] (see Discussion). Mapping the other insertion sites onto another Prp8 structure from Sce also reveals that their presence would presumably disrupt Prp8 function, because they too cluster around the active site (S10 Fig, PDB 5GMK, chain A) [10].

We next overlaid the Prp8 intein-containing precursor in the tri-snRNP from Sce (Fig 7B, PDB 5GAN) [61]. It appears that the intein now occupies a cramped area of the spliceosome (S11 Fig). There are a few crucial components, both protein and RNA, in the vicinity of the intein. For example, one essential splicing protein, the U5 component Dib1, is located in the same 3D space as the intein (Fig 7B, top) [63]. Furthermore, there are important RNAs in the area of the intein (Fig 7B, bottom). These include the U4 and U6 snRNAs, which are central to spliceosome activation and RNA splicing catalysis [62]. Generally, the information gleaned from our precursor model suggests that the tri-snRNP subunit of the spliceosome would be disturbed by intein retention before spliceosomes are even fully formed, which would lead to inhibition of RNA splicing.

Prp8 is an intein sink with functional implications

We demonstrated a broad distribution of Prp8 inteins with multiple insertion sites (Fig 1A and 1B), a pattern noted by others as well [27,31,33]. Our data support the notion that Prp8 was invaded repeatedly, including at least twice at site a (Fig 1A, a1 and a2; S1A Fig). Previously, a limited number of site a inteins was analyzed and shown to be highly similar to each other [35]. We further discovered a novel insertion in a social amoeba, site g, bringing the total number of known insertion sites in Prp8 to 7 (Fig 1C; S3 Fig). This preponderance suggests Prp8 inteins have been retained over evolutionary time with functional implications. Similar trends were formerly reported with the mycobacterial iron-sulfur cluster assembly protein SufB, which has 3 distinct insertion sites, and the mycobacteriophage terminase TerL, which has at least 5 intein insertion sites [20,21,26]. Such bioinformatics observations have led to fruitful research on intein function, which is now beginning to show that inteins can be tuned to respond to environmental cues [19,21,23,24]. A striking example is a mycobacterial intein in DnaB helicase, located in the P loop of the ATPase domain [64], which is sensitive to ROS both in vitro and in vivo [59].

Structural insights into the Prp8 intein

Here, we present the second structure of a eukaryotic intein, and the sole structure of a eukaryotic intein in an essential protein (Fig 2A). The Cne Prp8 intein structure provides insight into the similarity of inteins in eukaryotes (Fig 3A), suggesting that they likely evolved from a common ancestor. The Cne Prp8 intein also has a comparable structure to the C terminus of a Hedgehog protein (Fig 3C), which executes a cleavage and ligation reaction to cholesterol also by utilizing a cysteine [44]. These results suggest that eukaryotic inteins and Hedgehog proteins might be ancestrally related, but why inteins do not exist in metazoan genomes is a puzzle yet to be explained.

Around a dozen intein structures have been solved so far, comprising of mainly bacterial and archaeal inteins [65]. These have proven useful for studying inteins as novel drug targets [52]. As inteins often invade essential proteins in pathogens, inhibiting them from splicing out is an attractive option for developing new antimicrobials [52,66,67]. Progress toward this goal has been made in prokaryotes using the mycobacterial RecA recombinase intein. A co-crystal of the RecA intein and the antineoplastic compound, cisplatin, helped resolve the mechanism of protein splicing inhibition [52]. This showed that the platinum ions of cisplatin bind to the RecA intein at its 2 catalytic cysteines, C1 and C+1. Concurrent work studying cisplatin and the Prp8 intein also demonstrated effective splicing inhibition, both in vitro and in a mouse model, although the mechanism is different than the RecA intein [68]. Solving the Cne Prp8 intein structure, along with the observed metal inhibition, provides impetus for advancing these studies in an essential protein in a eukaryote, at an opportune time given that the antifungal pipeline is drying up [69].

Cne Prp8 intein is responsive to metals in vitro and in vivo with biological ramifications

The Cne Prp8 intein was studied here using MIG, a GFP splicing reporter, given that full-length Prp8 could not be expressed well in E. coli. Studies have shown that intein splicing with surrogate exteins can be less effective than with native exteins [70,71]. However, we found that the wild-type Cne Prp8 intein spliced well in the MIG reporter. This illuminates how important extein context is in either constraining or allowing splicing of the Cne Prp8 intein. Previous studies placed the Cne Prp8 intein into non-native contexts and showed splicing, but contrary to our work, there was almost complete inactivation by the A-1V mutation [48]. This earlier work only used 1 to 2 flanking extein residues, whereas MIG contains 5, suggesting that more native context allows greater tolerance to sequence variation. Such discrepancies do raise the important point that the extein context of an intein is extremely important when asking questions about splicing.

Here, MIG Prp8 was useful in a screen for identifying the divalent metals copper and zinc as potential regulatory signals for protein splicing. Given that the intein-containing organism is the pathogenic fungus Cne, we wondered whether metal-based inhibition contributes to a stress response during infection. Pathogenic microbes occupy niches that expose them to the opposing toxicities of metal ion excess and deprivation [72]. Cne employs extensive strategies to control metal ion concentrations, including responsive transcription factors, transporters, importers, and exporters [73]. Many of these are utilized during the oxidative burst of the phagolysosome when the fungus is exposed to acute metal stress [73]. Levels of copper can reach up to several hundred micromolar, while zinc concentrations are initially high, but drop with ongoing infection [72,74,75].

We speculate that the Cne Prp8 intein might provide cryptococci an additional means to sense metals during infection. The sensing “machinery” of the Cne Prp8 intein is its catalytic C1 and N171 (Fig 5). Cysteines are reactive amino acids that endow proteins with catalytic activity, redox chemistry, and metal binding capacity, whereas asparagines can be both catalytic and metal-coordinating residues [58]. A pause in protein splicing may be useful for overcoming toxic levels of copper or zinc (Figs 4C, 5 and 6). Copper generates destructive ROS intermediates and can displace iron from iron-sulfur clusters [74], whereas both copper and zinc can dislodge divalent metals from other metalloprotein complexes. Like other stressors known to inhibit RNA splicing, copper and zinc would act post-translationally to block Prp8 intein splicing and inhibit spliceosome function until levels of the metals are diminished by scavenger proteins or metal transporters [73]. Indeed, we provide the first evidence here that Prp8 intein splicing in Cne can be modulated under metal stress (Fig 6).

Post-translational programs that regulate expression of intron-containing transcripts in response to environmental cues have been described in the budding yeast, Sce [76] and in Cne [77]. Work done on alternative splicing in Cne supports pausing of spliceosome function [77]. This fungus is intron dense, with over 40,000 introns in its genome, and abundant alternative splicing has been observed [29]. Intriguingly, the most common type of aberrant splicing is intron retention [77]. Intron retention has even been shown to play a role in virulence and is regulated by environmental conditions [77]. If intron retention is an adaptive mechanism for Cne to finely tune expression levels in adverse environments, then inhibiting Prp8 intein splicing is a possible means of controlling that intron retention.

Protein splicing inhibition and its implications for RNA splicing

We turned to molecular modeling of structures to help predict in vivo effects of intein splicing inhibition. The intein-containing Prp8 precursor model generated from a solved Sce U4/U6.U5 tri-snRNP revealed a snug accommodation of the intein in a highly conserved region of Prp8 (Fig 7A, PDB 5GAN, chain A) [61]. This insertion (site a) is in a linker located between the thumb domain and the endonuclease-like domain of the reverse transcriptase (Fig 1B; S10 Fig). This highly conserved region of Prp8 (55%–87% identity over 113 residues) contains the 1585 loop and its longer version, the α-finger [62]. These structural motifs are involved in coordinating the RNA-mediated catalysis that leads to eventual intron removal [1,62], at the core of the protein and at the catalytic center of the spliceosome.

Although Prp8 likely cannot perform its critical functions with the intein present, the structural tolerance of a flexible linker domain may allow for proper folding of the intein, as well as that of Prp8. In the longer term, this flexibility gives the intein freedom to adapt to its surroundings, supporting some degree of Prp8 function in a precursor state. Mini-inteins, such as the one present in Cne Prp8, are not mobile and may therefore be under more selective pressure to adapt to their exteins. This is in line with work that shows partial activity of the RadA precursor with its mini-intein intact [19].

If the Cne Prp8 intein remains unspliced in the tri-snRNP, perhaps because of metal sensing and inhibition, it would almost certainly be disruptive. In the subunit modeled here, the intein would overlap with the Dib1 protein (Fig 7B, top) [61], which is an essential spliceosome component. Dib1 is a small, 16.8 kDa protein well-conserved from yeast to humans and is postulated to play a central role in preventing premature spliceosome activation [63]. If Dib1 is unable to localize to its cognate site, this would likely be detrimental to spliceosomal function [63]. Furthermore, certain RNAs, such as U4 and U6, thread close to the intein (Fig 7B, bottom). Dislodging these critical snRNAs would almost certainly disrupt intron splicing.

If the Cne Prp8 intein were to sense a stressor, such as metals, and stay lodged in Prp8, then Prp8 precursor would undoubtedly affect spliceosome assembly and possibly activation (Fig 7; S11 Fig). Such spliceosome assembly defects may lead to pre-mRNA accumulation, as even point mutations in Prp8 are known to do [2]. Thus, this work proposes that the Cne Prp8 intein is subject to modifications that influence protein splicing and thereby Prp8 function, with implications for spliceosome activity.

Bioinformatic and phylogenetic analyses

The Prp8 intein sequences used to build the phylogenetic trees in Fig 1A and S1 Fig and the Prp8 extein sequences used to build the phylogenetic trees in S4 Fig were accessed from Green and colleagues, 2018 [27]. For comparative and phylogenetic analyses, amino acid sequences of inteins were manually trimmed to the splicing blocks (A, B, F, and G). All multiple sequence alignments of the amino acid sequences were performed using ClustalOmega with default parameters [78] and edited manually (Fig 1; S1, S2 and S4 Figs). Where alignments are shown shaded, black represents an identical amino acid, dark gray is a conserved amino acid, whereby the same amino acid is at the same position in a majority of the sequences, and light gray is a similar amino acid, defined as a semiconserved amino acid substitution from the same class. Phylogenetic analysis was performed using the neighbor-joining (NJ) method in the MEGA7 program [79]. Statistical support for the NJ tree was evaluated by interior-branch test (number of replications, 1,000) [80]. The sequence logo for Block B was generated based on the multiple sequence alignment using WebLogo3 [81] (http://weblogo.threeplusone.com). The 7 Prp8 intein insertions were mapped onto a model of a Sce Prp8 (S10 Fig, PDB 5GMK). All intein, Prp8, and spliceosome structures were viewed, edited, or aligned using PyMol 1.3 (http://pymol.org). The 3D BLAST protein structure search was performed by BioXGEM with default parameters (http://3d-blast.life.nctu.edu.tw).

Bacterial strains and growth conditions

All strains used in the present study can be found in S1 Table. E. coli DH5α, MG1655(DE3), and BL21(DE3) were grown in Luria Broth (LB), unless otherwise indicated, with aeration at 250 rpm. Media contained kanamycin (50 μg/mL) or chloramphenicol (25 μg/mL) where appropriate. Plasmids were transformed into cells by electroporation using a Bio-Rad Gene Pulser (Hercules, CA) and recovered for 1 h at 37°C in SOC medium (0.5% yeast extract, 2% tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgCl₂, 10 mM MgSO₄, and 20 mM glucose). Transformants were selected by plating on LB agar with the appropriate antibiotic and incubated at 37°C overnight.

Construction of plasmids

All plasmids used in the present study can be found in S2 Table and all oligonucleotides, synthesized by Integrated DNA Technologies (IDT, Coralville, IA), are in S3 Table. Plasmid DNA was prepared using EZNA Plasmid Mini Kit (Omega, Norcross, GA). DNA was visualized in 1% agarose gels using EZ-Vision DNA Dye (Amresco, Radnor, PA). PCR fragments were amplified using CloneAmp HiFi PCR Premix (Clontech, Mountain View, CA) from genomic DNA of Cne var. grubii H99 or C. gattii NIH444 (Dr. Sudha Chaturvedi, New York State Department of Health), A. fumigatus AF293 (Dr. Robert J. Cramer, Darmouth College), B. dendrobatitidis JEL423 (Dr. Timothy James, University of Michigan), or H. capsulatum G186A (Dr. Chad Rappleye, Ohio State University). For insertion into the MIG construct, the inserts included 5 native N- and C-extein residues flanking the intein. For insertion into the overexpression vector, pET47b, the intein alone with 3 native N exteins was PCR amplified. Digested backbone was gel purified using Zymoclean Gel DNA Recovery Kit (Zymo Research, Irvine, CA). Restriction enzymes (NEB, Ipswitch, MA), T4 ligase (NEB, Ipswitch, MA), and In-Fusion HD Cloning Plus Kit (Clontech, Mountain View, CA) were all used per manufacturer protocol. Mutagenesis was performed using the QuikChange Lightning Site-Directed Mutagenesis Kit (Agilent, Santa Clara, CA) for single amino acid mutations or the QuikChange Lightning Multi Site-Directed Mutagenesis Kit (Agilent, Santa Clara, CA) for multiple amino acid mutations. For the A-1V mutation, primers were designed to randomly mutate the A-1 to all other possible codons using a degenerate primer with NNS at the mutated location. All clones were verified by sequencing (EtonBio, Union, NJ).

MIG splicing assays

MIG Prp8 (WT, A-1V, and derived C61 mutants) was transformed by electroporation into MG1655(DE3). The cells were subcultured 1:100 from an overnight culture into fresh LB medium and grown at 37°C with 250 rpm shaking to an OD₆₀₀ of 0.5. Cells were induced with 0.5 mM IPTG for 1 h at 30°C and pelleted by spinning for 10 min at 4,000 rpm. The pellets were lysed immediately using tip sonication (20 s on/30 s off at 30% amplitude for 1 min total) in 50 mM Tris (pH 8.0) and 10% glycerol or stored at −80°C until lysis. For any ROS/RNS or metal treatment, the indicated compound was added to cells at the desired concentration prior to incubation at 30°C for the specified time. For the assays to determine mechanism of inhibition, MIG Prp8 A-1V lysate was split, and half was left untreated, whereas the other was preincubated with 1 mM CuSO₄ or ZnSO₄. After 2 h, each lysate (with metal or untreated) was split in half and either treated with EDTA to a final concentration of 10 mM or with TCEP to a final concentration of 40 mM. Aliquots of the EDTA/TCEP-treated lysates were then collected immediately at t0, 2 h, and 22 h postincubation with EDTA/TCEP. Because EDTA/TCEP is added after an initial 2 h incubation, these new t0, 2 h, and 22 h samples actually represent 2 h, 4 h, and 24 h since start of the assay. Upon completion of the assay or time point, the lysate was frozen at −80°C. To visualize MIG splicing assay results, samples were separated under nonreducing conditions on Novex WedgeWell 12% Tris-Glycine gels (Invitrogen, Carlsbad, CA) using loading dye lacking β-mercaptoethanol and visualized using a Typhoon 9400 scanner (GE Healthcare, Chicago, IL) with excitation at 488 nm and emission at 526 nm. Quantitation and analysis were done using ImageJ and GraphPad Prism (version 7.02).

Prp8 intein purification

For isothermal titration calorimetry and mass spectrometry, the Cne Prp8 intein from Cne var. grubii H99 was amplified with 3 native N-extein residues (EKA) and cloned into pET47b in front of an N-terminal His₆-tag and an HRV 3C protease site. For crystallization, the Cne Prp8 intein with 2 native N-extein residues (KA), and the native C-extein S+1 was amplified and cloned into pET28a with a C-terminal His₆-tag using a megaprimer approach as described previously by Li and colleagues [82].

The pET47b (or pET28a) Cne Prp8 intein construct was transformed by electroporation into BL21(DE3) cells. The cells were subcultured 1:100 from an overnight culture into fresh LB medium and grown to an OD₆₀₀ of 0.6. Cells were induced with 0.5 mM IPTG and grown with shaking at 250 rpm overnight at 16°C. The following morning, cells were harvested by centrifugation at 4,000 rpm for 10 min. Pellets were frozen at −80°C until ready for lysis. Tip sonication was performed (30 s on/59 s off at 30% amplitude for 4 min total) in buffer containing 20 mM Tris (pH 7.8), 500 mM NaCl, 25 mM imidazole, and 5% glycerol. Whole cell lysate was centrifuged at 20,000g for 20 min to separate the soluble fraction, which was loaded onto a nickel affinity column equilibrated with the lysis buffer. Washes were carried out using buffer containing 20 mM Tris (pH 7.8), 500 mM NaCl, 75 mM imidazole, and 5% glycerol and elution buffer with 20 mM Tris (pH 7.8), 500 mM NaCl, 250 mM imidazole, and 5% glycerol. Purified fractions of the Cne Prp8 intein were checked by separation on SDS-PAGE, and the cleanest elution samples were pooled. For the pET47b construct, the His₆-tag on the Cne Prp8 intein was removed through digestion with HRV 3C protease according to the manufacturer’s protocol (Thermo Fisher, Waltham, MA). The cleaved Cne Prp8 intein reaction was passed back over a nickel affinity column, and the flow-through was collected to ensure no His₆-tagged Cne Prp8 intein or HRV 3C protease was in the sample. For analysis by ITC, the flow-through intein was exchanged into 50 mM sodium acetate (pH 7.0), 100 mM NaCl using a HiPrep 26/10 desalting column or a dialysis cassette. For mass spectrometry, the flow-through intein was used directly for metal treatments and then further purified by liquid chromatography (LC) prior to spraying on the instrument. For the pET28a construct, the imidazole-eluted fractions were concentrated and subjected to size exclusion chromatography by a gel filtrations 16/60 Superdex column (GE Healthcare, Chicago, IL). For crystallization, the purified Cne Prp8 intein was concentrated to 9.5 mg/mL in a buffer composed of 25 mM HEPES (pH 7.5) and 150 mM NaCl.

Mass spectrometry of Prp8 intein

Purified Cne Prp8 intein was reduced with 40 mM TCEP and exchanged into deoxygenated exchange buffer (20 mM Tris [pH 7.5], 200 mM NaCl) using 7K MWCO Zeba spin desalting columns (Thermo Fisher, Waltham, MA) to remove TCEP. The protein concentration was measured and then treated with 10X of CuSO₄ and incubated at 30°C for 1 h. Following treatment, the purified intein was denatured with 6 M urea at 37°C for 30 min. The urea concentration was diluted down to less than 0.8 M with 50 mM Tris (pH 7.6) and 1 mM CaCl₂. Trypsin digest of the intein was performed by adding activated trypsin (Promega, Madison, WI) to a final ratio of 1:20 and incubating overnight at 37°C. The oxidation of Cne Prp8 intein cysteines after treatment was analyzed by multiple reaction monitoring-initiated detection and sequencing (MIDAS) as described by Unwin and colleagues [83]. The trypsin-digested mixture was acidified followed by LC-MS/MS analysis. LC-MS/MS analysis was performed on a microflow LC-MS/MS system configured with a 3-pumping Micromass/Waters CapLC system with an autosampler, a stream select module configured for precolumn plus analytical capillary column, and a QTRAP 6500 (ABSCIEX) mass spectrometer fitted with Turbo V microflow source, operated under Analyst 1.63 control. Injected samples were first trapped and desalted isocratically on an LC-Packings PepMa C18 μ-Precolum Cartridge (5 μm, 500 μm ID × 20 mm; Dionex, Sunnyvale, CA) for 7 min with 0.1% formic acid delivered by the auxiliary pump at 40 μL/min after which the peptides were eluted from the precolumn and separated on an analytical C18 capillary column (15 cm × 500 μm ID, packed with 5 μm, Jupiter 300 C18 particles, Phenomenex, CA) connected inline to the mass spectrometer at μL/min using a 50 min gradient of 5% to 80% acetonitrile in 0.1% formic acid. The oxidized peptide identification was conducted through multiple reaction monitoring (MRM) triggered enhanced product ion (EPI) scan using information dependent acquisition (IDA). The utilization of chromatographic separation, MRM transitions, and EPI scan allows accurate peptide identification and confirmation. The 2 MRM transitions including m/z 404.19 > 532.22 and m/z 786.04 > 895.41 for C[Oxi]LQNGTR.+2b5 and THEGLEDLVC[Oxi]THNHILSMYK.+3b8 were used to trigger the EPI experiment, respectively. The instrument was operated in a positive ion mode with a Turbo V ion drive electrospray source. The parameters for the operation were as follows: curtain gas, 20 psi; heated nebulizer temperature 180°C, ion spray voltage, 5,500 V; gas1, 18 psi; gas 2, 15 psi, declustering potential, 65 V, EP, 10 V and CAD gas, high.

ITC of Prp8 intein

ITC measurements were carried out on a TA Instruments Nano ITC (TA Instruments, Inc., New Castle, DE). Aqueous solutions of metal titrants (CuSO₄ or ZnSO₄) were prepared to be 0.3- to 30-fold higher than the concentration of the Cne Prp8 intein, in the range of 0.05 to 5.0 mM. The titrant and wild-type Cne Prp8 intein were degassed before each titration. The purified Cne Prp8 intein was concentrated from 10 μM to 16 μM in 300 μL and were placed in a 2.5 mL reaction cell, and the reference cell was filled with 300 μL deionized water. All titrations were carried out at 37°C. After baseline equilibration, successive injections of an indicated titrant were made into the reaction cell in 2.5 μL increments at 400 s intervals with stirring at 250 to 350 rpm to ensure an equilibrium was achieved for a return to baseline. The resulting heats of reaction were measured over 20 consecutive injections. Optimization of buffer was required for purified Cne Prp8 intein and found to be stable over long periods for ITC data collection only in 50 mM sodium acetate (pH 7.0), 100 mM NaCl, 10 mM TCEP. Buffer control experiments (50 mM sodium acetate [pH 7.0], 100 mM NaCl, ± 10 mM TCEP) to determine the heats of titrant dilution were carried out by making identical injections in the absence of the Cne Prp8 intein. The net reaction heat was obtained by subtracting the heats of dilution from the corresponding total heat of reaction. The titration data were deconvoluted based on best-fit binding models containing either 1 or 3 sets of interacting binding sites, using a nonlinear least-square algorithm through the NanoAnalyze software. The binding enthalpy change (ΔH), dissociation constant (K_d), and binding stoichiometry (n) were permitted to vary during the least-square minimization process and taken as best-fit values.

Crystallization, structure determination, and refinement of Prp8 intein

Initial crystallization conditions were obtained by screening the Hampton crystallization screens (I, II, and Research Index HT), using the hanging-drop vapor diffusion method. Upon optimization, large crystals were grown by mixing 1 μL of Cne Prp8 intein and 1 μL of reservoir solution containing 22% to 28% PEG4000, 0.1 M sodium acetate (pH 4.2), 0.2 M ammonium acetate. The Cne Prp8 intein crystallizes in space group P1 with 6 intein molecules per asymmetric unit (S4A Table). The crystals of the Cne Prp8 intein-Zn²⁺ complex were obtained by soaking native crystals in mother liquor supplemented with 4 mM zinc acetate. Prior to data collection, all crystals were transferred to a cryo-protectant solution containing crystallization buffer supplemented with 20% glycerol without (native) or with 4 mM zinc acetate (Prp8-Zn²⁺ complex). The crystals were flash-cooled directly in liquid nitrogen. Diffraction data for the native and the Prp8-Zn²⁺ complex crystals were collected at 100 K using a Pilatus detector at the BL9-2 beamline of the Stanford Synchrotron Radiation Laboratory (native) and using an ADSC HF-4M detector at the 19-ID NYX beamline of the National Synchrotron Light Source II (complex), respectively. Data were processed, scaled, and reduced using the programs HKL2000 [84] and PHENIX suite [85]. The structure of the Cne Prp8 intein was determined by molecular replacement, with the crystal structure of the C. gattii Prp8 intein [68] as a search model. The Prp8-Zn²⁺ complex structure was determined by molecular replacement, with the refined structure of the Cne Prp8 intein as a search model. The molecular replacement was carried out using the PHENIX program suite. Structure refinement was carried out using the PHENIX program suite and monitored using Coot [86] (S4B Table).

Generation of an inteinless Cne (Prp8ΔIn)

The synthetic inteinless PRP8 gene (designated PRP8ΔIn) was cloned into the Cne Safe Haven vector pSDMA25 [87]. Plasmid pSDMA25-Prp8ΔIn was linearized with PacI (NEB, Ipswitch, MA) and used for biolistic transformation of wild-type Cne H99. After selection on YPD agar plates containing nourseothricin (NAT), insertion at the Safe Haven site was validated by multiplex PCR. Both the intact wild-type locus of PRP8 as well as the PRP8ΔIn locus within the Safe Haven site were verified by PCR. To construct a knock-out of the wild-type PRP8 gene, a hygromycin (HYG) cassette flanked by 1 kb of PRP8 sequence was used to transform Cne harboring PRP8ΔIn at the Safe Haven site. HYG was used as the selection marker. Proper deletion of wild-type PRP8 and retention of PRP8ΔIn at the Safe Haven site, generating the strain Prp8ΔIn, was again validated by PCR amplification as well as by Southern blotting.

Cne culture and Western blot

Cne H99 derivatives and Sce S288C were grown in defined synthetic complete media (SC) after diluting overnight cultures to an OD₆₀₀ of 0.2 in fresh SC. After 3 h at 30°C, 200 rpm, cells were supplemented with 1 mM CuSO₄ or ZnSO₄. Cells were incubated an additional 3 h at 30°C, 200 rpm, harvested, washed with 3 × 5 mL PBS and resuspended in 0.6 mL lysis buffer (25 mM Tris [pH 7.4], 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1 mM PMSF, and 1× fungal specific protease inhibitor [Sigma Aldrich, St. Louis, MO] and lysed with acid-washed glass beads in a Bead Ruptor 12 (Omni International, Keenesaw, GA). Cell debris was centrifuged for 10 min at 16,000g and soluble extracts were mixed with 4x Laemmli Sample Buffer (Bio-Rad, Hercules, CA) either with or without added β-mercaptoethanol. Samples were then boiled for 10 min at 90°C and 20 μg total protein loaded on a 4% to 20% Criterion TGX gel (Bio-Rad, Hercules, CA), electrophoresed at 150 V in SDS running buffer for 1 h, then transferred onto a nitrocellulose membrane using a TransBlot Turbo system (Bio-Rad, Hercules, CA). Transfer quality was assessed by Ponceau-S stain. Membranes were washed 2 × 10 min in PBS with Tween-20 (PBST), then blocked for 1 h in 5% milk PBST. Membranes were washed again 2 × 5 min in PBST, then probed with primary anti-Prp8 intein (1:1,000) or anti-Cdc2 (1:5,000) in 2% milk PBST overnight at 4°C. Membranes were washed 3 × 15 min with PBST and then applied with HRP-conjugated secondary antibodies (GE Healthcare, Chicago, IL; rabbit or mouse at 1:10,000) in 2% milk PBST and incubated for 1 h. Blots were washed again 3 × 15 min with PBST, and then applied with SuperSignal West Femto (Thermo Scientific, Waltham, MA) chemiluminescent reagents, and images developed using X-ray film at different exposures.

Precursor modeling

The Prp8 protein structure (chain A) in the 3.7 Å cryo-EM structure of the Sce spliceosomal tri-snRNP [61] (PDB 5GAN) was used as a structural template for constructing a homology model of the Cne Prp8 extein. A pair-wise Needleman-Wunsch [88] sequence alignment using EMBOSS Needle [89] shows 55.3% sequence identity and 68.3% sequence similarity between the full Sce and Cne extein sequences. The Cne Prp8 extein homology model was constructed using MODELLER [90] with the DOPE [91] and GA341 [92] energy functions to identify the best model. The 171-residue Cne intein sequence is an insert between residues 1530 and 1531 in the extein. The Cne Prp8 extein homology model was combined with the Cne Prp8 intein crystal structure to generate a model for the full Cne Prp8 precursor. The orientation of the intein with respect to the extein was manually adjusted using VMD software [93] to avoid any steric overlap and keep the intein and extein ends that are joined by peptide bonds sufficiently close together. This combined intein-extein structure was then used as a structural template to generate a continuous Cne Prp8 precursor homology model using MODELLER. Further minimization on this precursor homology model was performed using the program CHARMM, version c35b3 [94,95] with the CHARMM36 force field for proteins [96]. All atoms not within the precursor amino acid sequence range encompassing the intein and its neighboring extein regions (residues 1520–1720) were initially held fixed, and a low-temperature (150 K) optimization protocol was used to improve the homology model. This protocol included 5 iterations of the following steps: (a) 5,000 steps of Steepest Descent (SD) minimization followed by 5,000 steps of Adapted-Basis Newton-Raphson (ABNR) minimization, each with an energy change tolerance of 0.001 kcal/mol; (b) 1,000 steps of Langevin dynamics at a temperature of 150 K and a friction coefficient of 5.0 ps⁻¹; (c) another 5,000 steps of SD and 5,000 steps of ABNR minimization. All nonhydrogen atoms were then restrained using harmonic restraints with a force constant of 1.0 kcal/mol/Ų. SHAKE constraints [97] were applied on all hydrogen atoms, and 5,000 steps of SD and 5,000 steps of ABNR minimization were performed to obtain the final Cne Prp8 precursor model.