Tetratrico peptide repeat interactions: to TPR or not to TPR?

Yeast ortholog of the Drosophila crooked neck protein promotes spliceosome assembly through stable U4/U6.U5 snRNP addition

“…The basic unit of TPR-ligand association remains poorly understood+ A single TPR repeat or a set of clustered repeats may mediate specific protein interactions+ For proteins with directly iterated TPR elements, individual cassettes may bind the same target (cooperatively or independently) or associate with different surfaces on one or more ligands+ In the case of Clf1p, at least five of the C-terminal TPR elements are dispensable and possibly redundant in function+ In contrast, TPR2 is critical for Mud2p association yet unnecessary for the Prp40p interaction+ Of the few proteins characterized that interact with TPR repeats the only common feature appears to be the presence of alpha helical sequence (e+g+, see Lamb et al+, 1995;Smith et al+, 1995;Tzamarias & Struhl, 1995;Shpungin et al+, 1996)+ This observation is consistent with the interaction of Clf1p with the Prp40p helix I, II, III regions located directly downstream of its WW repeats+ The Mud2p binding domains are less clearly defined+ However, secondary structure analysis (Smith et al+, 1996) suggests that significant alpha helical structure exists in both the amino and carboxyl halves of Mud2p and these sequences may support the Clf1p interaction+ This study confirms that four yeast proteins with multiple copies of the crn-like TPR motif (i+e+, Clf1p, Prp39p, Prp42p, and Rna14p) contribute to cellular pre-mRNA processing+ A fifth protein, Rrp5p, with related repeats was shown necessary for proper 18S and 5+8S rRNA biosynthesis (Torchet et al+, 1998)+ Although a human counterpart to Clf1p has yet to be reported, likely Clf1p/ crn orthologs are present in Schizosaccharomyces pombe (accession number P87312) and Caenorhabditis elegans (accession number O16376)+ Presumably, sequences within the crn-like TPR motif have evolved to accommodate interactions with RNA or RNA-bound proteins+ Precedent exists for a nonprotein ligand of the TPR motif+ Activation of the PP5 phosphatase can be achieved by the specific association of polyunsaturated fatty acids with the PP5 TPR domain, thus inducing a favorable conformation change within this enzyme (Chen & Cohen, 1997)+ Although several TPR proteins associate with RNA or DNA complexes (e+g+, Ssn6p, Prp6p, Prp39p, Prp42p, TFIIIC, and Rrp5p), none have been shown to directly bind nucleic acids+ Intriguingly, however, in addition to its TPR elements, the Rrp5p protein contains 12 copies of the S1 RNA binding motif+ Independent of whether Clf1p directly binds RNA, we believe that the crn TPR motif serves as a good predictor of RNP association for eukaryotic proteins+ Spliceosomes form only where the cis-and transacting factors are present and compatible, that is, found in the correct location, orientation, and stoichiometry+ The step-wise assembly process both reduces the likelihood of mRNA cleavage at improper sites and provides the means for cellular control of gene expression through regulated splice site selection (Lopez, 1998)+ Clf1p is clearly established as an essential factor in spliceosome assembly+ Yet, several intriguing questions remain regarding its function+ For instance, our model shows a "swap" of Clf1p for BBP/SF1 in early spliceosome assembly+ This order agrees with the commitment complex arrest observed in the absence of BBP/SF1 and the prespliceosome arrest noted in the absence of Clf1p+ However, it remains to be shown that the Mud2p/Prp40p contacts of Clf1p and BBP/SF1 are temporally distinct or mutually ex...…”

Two mutant forms of the S1/TPR-containing protein Rrp5p affect the 18S rRNA synthesis in Saccharomyces cerevisiae

“…The carboxy-terminal part of Rrp5p contains seven tandem repeats of another motif: the tetratricopeptide repeat or TPR motif (Fig+ 2A,D) that is involved in protein-protein interactions in a large array of structurally and functionally diverse proteins (Lamb et al+, 1995)+ The TPR units are degenerated 34-amino-acid sequences that share a minimal homology limited to a few consensus residues (Sikorski et al+, 1990)+ Higher degrees of sequence conservation can be found outside the consensus residues, thus defining TPR subfamilies+ Database searches have revealed that the TPR domain of yeast Rrp5p is close to a part of the TPR domain of the Drosophila crooked neck (crn) protein that contains the longest tandem array of TPR units described to date (16 repeats; Zhang et al+, 1991)+ Figure 2D shows an alignment of the seven TPR units of the Rrp5p protein along with a consensus sequence that is compared to the consensus given for the cnr protein (Zhang et al+, 1991)+ The Rrp5p and cnr consensus share 41% identity and 68% similarity+ As previously reported (Venema & Tollervey, 1996), Rrp5p has homologues in human (accession number D80007) and Caenorhabditis elegans (accession num-FIGURE 1. Scheme of pre-rRNA processing in S. cerevisiae+ A: Structure and processing sites of the 35S pre-rRNA+ The 35S operon contains the sequences for the mature 18S, 5+8S, and 25S rRNAs separated by the two internal transcribed spacers ITS1 and ITS2+ Two external transcribed spacers, the 59 ETS and the 39 ETS, are present at either end+ The locations of the different oligonucleotide probes (numbered from 1 to 6) used in this study are indicated by small lines+ Black and white boxes represent mature rRNA species, and thin lines represent transcribed spacers+ Cleavage sites are indicated by vertical lines+ B: Pre-rRNA processing pathway+ The 35S primary transcript is cleaved at site A 0 to give the 33S pre-rRNA+ This molecule is rapidly processed at sites A 1 and A 2 , giving rise successively to the 32S pre-rRNA and to the 20S and 27SA 2 precursors+ Cleavage at A 2 separates the pre-rRNAs destined for the small and large ribosomal subunits+ The 20S precursor is matured by an endonucleolytic cleavage at site D to yield 18S rRNA+ The 27SA 2 precursor is processed by two alternative pathways, forming the mature 5+8S and 25S rRNAs+ In the major processing pathway cleavage at site A 3 occurs, giving the 27SA 3 species, which is then rapidly processed to site B1 S by an exonuclease activity, generating the 27SB S precursor+ A minor pathway involves direct cleavage of the 27SA 2 molecule at site B1 L , producing the 27SB L pre-rRNA+ At the same time as processing at B 1 is completed, the 39 end of mature 25S rRNA is generated by processing at site B 2 + The subsequent processing of both 27SB species appears to be identical+ Cleavage at sites C 1 and C 2 releases the mature 25S rRNA and 7S pre-rRNAs+ The 7S pre-rRNA undergoes rapid 39 r 59 exonuclease digestion to the 39 end of mature 5+8S rRNA (site E)+ C: rRNA processing associated with the bipartite allele+ Cleavage at site A 2 is inhibited and the 32S pre-rRNA is cleaved directly at site A 3 generating the aberrant 21S intermediate as well as the normal 27SA 3 precursor+ D: rRNA processing defects generated by the temperature-sensitive rrp5⌬6 allele+ Cleavage at sites A 0 , A 1 , and A 2 are altered as indicated by dotted lines+ ber U41534)+ These polypeptides present the same modular arrangement of S1 and TPR repeats (data not shown)+ The strongest similarity lies between each TPR domain of the three proteins+ TPR domains of yeast and human pro...…”

“…Rrp5p TPR motifs could be implicated in protein-protein interactions (Lamb et al+, 1995)+ The crystal structure of the TPR repeats was recently resolved (Das et al+, 1998) and revealed a spatial arrangement of one TPR unit in two antiparallel a-helices encompassing the A and B domains reported in Figure 2D+ The a-helices A and B were shown to constitute the inside and outside faces of the TPR repeats respectively, thereby indicating that the conserved residues of the B domain are probably essential residues to mediate protein-protein interactions (Das et al+, 1998)+ The rrp5⌬6 allele encodes a polypeptide deleted for two amino acids in TPR unit 1 (alanine 1494 and arginine 1495) which are conserved residues of the B domain of the TPR motif (Fig+ 2D)+ Therefore, the rrp5⌬6 allele could encode a defective protein-binding factor at restrictive temperature (37 8C) that would be impaired in the recruitment of important component(s) of the maturation process+ As already mentioned, a large number of trans-acting factors other than Rrp5p are required for the same rRNA-processing step (Venema & Tollervey, 1995)+ The Rok1p protein is an attractive candidate to interact with Rrp5p since it was isolated in this study as an extragenic multicopy and low-copy suppressor of the rrp5⌬6 temperature-sensitive mutation, and was also previously isolated with the same synthetic lethality screening used to isolate RRP5 (Venema & Tollervey, 1996;Venema et al+, 1997)+ Rrp5p and Rok1p tightly participate in rRNA processing at step A 2…”

Phosphodiesterases link the aryl hydrocarbon receptor complex to cyclic nucleotide signaling

“…Although XAP2 contains an immunophilin homology domain within its N-terminal region, no binding to immunosuppressant drugs was found [42]. The C-terminus of XAP2 contains multiple tetratricopeptide repeat (TPR) motifs that mediate protein-protein interactions [45]. Thus, XAP2 might serve to regulate the composition of the AHR complex.…”

“…Mapping studies revealed that the TPR containing carboxyl terminus of XAP2 is solely responsible for PDE2A binding. At present, the relationship between the number and arrangement of TPR repeats and their affinity and specificity for target proteins such as the various PDE subtypes is still unclear [45,46,89]. Initial experiments from our group indicate that XAP2 can bind simultaneously to PDE2A and HSP90 (unpublished data).…”