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Letter to the Editor Letter to the Editor Evolution of Ribonuclease Inhibitor by Exon Duplication Marcia C. Haigis,* Eric S. Haag,* and Ronald T. Raines*² *Department of Biochemistry and ²Department of Chemistry, University of Wisconsin±Madison The leucine-rich repeat (LRR) is a prevalent struc- Shapiro, and Acharya 1997; Kajava 1998) (®g. 1A and tural motif that mediates speci®c protein-protein inter- B). By using the National Center for Biotechnology In- actions (Kobe and Deisenhofer 1995b). The LRR is de- formation (NCBI) nr database (http://www.ncbi.nlm. ®ned by a region of 20±29 residues that contains the nih.gov), we identi®ed three potential transcripts ob- consensus sequence: XLXXLXLXXN, where L, N, and tained from human placental, HeLa, and testis cDNA X are leucine, asparagine, and any residue, respectively. libraries (GI 5 186260, 35843, and 7328055, respec- Typically, LRRs are displayed in 1±30 tandem copies tively). These clones are 1,682, 1,921, and 2,982 bp, within a protein. respectively. Although alternative splice forms of the 59- The ®rst crystalline structure of an LRR-containing untranslated region have been identi®ed in placenta, protein revealed a new protein fold (Kobe and Deisen- Northern blot analysis revealed that the RI gene is ex- hofer 1993) (®g. 1A and B). In porcine ribonuclease in- pressed as a single transcript in placental and HeLa cells hibitor (RI [Hofsteenge 1997]), the LRRs are arranged (Lee et al. 1988; Schneider et al. 1988; Crawford, Hag- tandemly in a horseshoe shape with 16 a-helices encas- erty, and Beutler 1989). Using these transcripts, we ing a parallel b-sheet of 17 strands. Hydrophobic forces searched the NCBI database for a corresponding geno- between the consensus leucine residues appear to sta- mic sequence and identi®ed a region of DNA on human bilize the b-sheet. RI is able to bind tightly to members chromosome 11 that overlaps cosmids cSRL125c1 and of the ribonuclease (RNase) A superfamily, which not cSRL135f4 and contains the RI gene (GI 5 2281060). only catalyze RNA degradation but also mediate angio- The genomic locus of human RI spans more than genesis, cytotoxicity, and the host-defense response 12 kb (®g. 1C). All three transcripts that we identi®ed (D'Alessio and Riordan 1997; Raines 1998; Leland and possess a colinear open reading frame encoded by nine Raines 2001). 39-terminal exons, numbered 2±10, as determined by the The RI fold is conserved in other proteins contain- presence of consensus splice donor and acceptor sites. ing LRRs. Human U2A9 is a small nuclear protein that The transcripts differ in their 59-untranslated region and contains ®ve LRRs and binds to U2B0 to form an active contain zero, one, or two alternatively spliced exons. As spliceosomal complex. Another protein, Skp2, contains all transcripts encode an identical protein sequence, the both 10 LRRs that function as a protein-binding domain functional signi®cance of alternative splice forms is un- and an F-box motif that binds to the catalytic core of known. Remarkably, all but the ®rst and last coding ex- ubiquitin-protein ligases. The LRRs in U2A9 and Skp2 ons are exactly 171 bp in length. In addition, all introns adopt an RI-like fold (Price, Evans, and Nagai 1998; are of phase 2, which denotes codon interruption after Schulman et al. 2000). The crystalline structures of the second nucleotide. Hence, any of the internal exons U2A9 bound to U2B0 and those of RI bound to RNase could be moved or removed without disrupting the A and angiogenin reveal that the parallel b-sheet formed alignment of LRRs encoded by neighboring exons. by the LRRs furnishes the surface for interacting with A striking relationship exists between the intron- other proteins (Kobe and Deisenhofer 1995a; Papageor- exon structure and the tertiary structure of RI (®g. 1). giou, Shapiro, and Acharya 1997; Price, Evans, and Na- Each of the internal exons encodes 57 residues. Except gai 1998). for the junction after the N-terminus, which occurs with- The modularity of the LRR is consistent with the in a longer b-strand, every exon translation product cor- evolution of RI by gene duplication. To test this hy- relates with a pair of b-strands and a-helices without pothesis, we investigated the genomic structure of hu- any disruption (®g. 1A and B). Thus, the LRR motif man RI. Our ®ndings provide a new insight into the within RI is de®ned completely by its intron-exon evolution of RI as well as the many proteins containing structure. LRRs or other modules. The phasing and position of the RI introns are con- Human RI consists of alternating 28- or 29-residue sistent with exon ampli®cation during evolution (de LRR units (Kobe and Deisenhofer 1993; Papageorgiou, Souza et al. 1997; Gilbert, de Souza, and Long 1997; Fedorov et al. 1998). To test this hypothesis, we inves- tigated the similarity of the coding exons. RI exons were Abbreviations: LRR, leucine-rich repeat; RI, ribonuclease aligned using the PILEUP program from the Wisconsin inhibitor. Package of Genetics Computer Group (Madison, Wis.). Key words: angiogenin, exon duplication, leucine-rich repeat, ri- Although the terminal exons (2 and 10) have low se- bonuclease A, ribonuclease inhibitor, RNA. quence identity, the internal exons (3±9) can be aligned Address for correspondence and reprints: Ronald T. Raines, De- without gaps and have considerable sequence identity partment of Biochemistry, University of Wisconsin±Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544. (®g. 2A). Pairwise comparisons revealed that exons 3± E-mail: [email protected]. 9 are 50%±60% identical. In addition, translation prod- Mol. Biol. Evol. 19(6):959±963. 2002 ucts corresponding to exons 3±9 were aligned and de- q 2002 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038 termined to be 30%±50% identical (®g. 2C). 959 960 Haigis et al. ing genomes diverged. To distinguish between these dis- tinct mechanisms, we performed phylogenetic analyses on the internal coding exons of human, mouse, and pig RI. The mouse RI exons were identi®ed by a twofold approach: analyzing existing sequences and generating new sequence data. By using the NCBI mouse genome database, we identi®ed genomic sequences that contain several exons of mouse RI. In addition, we generated new sequence data to verify the remaining intron-exon junctions. To obtain the mouse RI locus, we screened a mouse 129 library (Genome Systems, St. Louis, Mo.) by the PCR using the primers: 59 GGTGCAAAGACA- TCAGCTCAGCAGTCCAAGC 39 and 59 CCTGGA- GCACCAGACCCACACC 39. Like the human gene, mouse RI consists of seven internal exons that are 171 bp in length and are separated by phase 2 introns. The pig exons were inferred from the cDNA for pig RI (GI 5 M58700) by using the genomic structures of human and mouse RI. The internal exons from human, pig, and mouse were aligned as described previously (®g. 2A). Sequence alignment reveals strong identity between analogous exons. Neighbor-Joining phylogenetic trees built by using a Kimura two-parameter correction have strongly supported clades for analogous exons between species with bootstrap values of 99%±100% (®g. 2B). A maximum parsimony analysis of the data set also strongly supports the existence of clades for each exon with bootstrap values of 98%±100%. Apparently, the tandem repeats within RI are extremely stable and ho- mogenization has not taken place, as that would have resulted in a tree in which the internal exons from each species form a strongly supported clade. A consistent internal branching pattern did not emerge with strong support from either analysis. Furthermore, the branches leading to each exon clade are extremely long, which is consistent with a nearly simultaneous divergence of each clade. Thus, we conclude from this analysis that exons 3±9 were most likely duplicated in a radiation that occurred rapidly early in the history of RI. Members of the RNase A superfamily apparently exist in all tetra- pods (D'Alessio and Riordan 1997). Thus, it is likely that RI was assembled after the origin of tetrapods in the late Devonian, approximately 360 MYA, but before the divergence of eutherian mammals. FIG. 1.ÐCorrelation of the exons of human RI with its LRR units. A, Our data indicate several unusual features about the Ribbon diagram of RI was created using the atomic coordinates de- evolution of RI. The internal exons of RI are homolo- rived by X-ray diffraction analysis (Papageorgiou, Shapiro, and Achar- gous and stable. In addition, the branching pattern sug- ya 1997) and the program MOLSCRIPT (Kraulis 1991). Each exon- gests that the internal exon duplications occurred rapidly encoded sequence is in a different color. The N- and C-termini are labeled. B, Same as A, except rotated by ;908 around the horizontal and then diverged over a long period of time. To assess axis. C, Physical map of the human RI gene. Alternate forms isolated whether positive selection has been a factor in the di- from placenta, HeLa cells, and testes are depicted as RIa,RIb, and vergence of the RI exons, we measured the rate of non- RIg, respectively. Exons and introns are drawn to scale. Start and stop synonymous versus synonymous changes in human ex- codons are indicated. Exon colors match those of exon-encoded se- ons 3±9 (Nei and Gojobori 1986). The ratios of non- quences in A and B. synonymous-to-synonymous changes range from 0.31 to 1.00. Although the nonsynonymous-to-synonymous ra- The high degree of similarity and their identical tio is not always a de®nitive indicator of positive selec- length strongly suggests that the internal exons of RI are tion (Wyckoff, Want, and Wu 2000), the low ratios for homologues related by exon duplication.
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