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Proc. Nati. Acad. Sci. USA
Vol. 85, pp. 5136-5140, July 1988
Evolution
FIG. 2. The nucleotide sequence of the trout GH gene was determined from a series of clones carrying deletions originating from either end
of the Pst I fragment containing the trout GH gene. The gene spans a region of -4000 bp in the trout genome. The "TATA box" and the poly(A)
signal are shown overlined and in bold print. The putative cap site (+ 1), located 22 nucleotides downstream from the TATA box, was determined
by aligning the GH genomic and cDNA sequences. Exons are shown in uppercase; introns and flanking regions are in lowercase. Sequences
capable of forming hairpin structures and a tandemly repeated sequence are underlined.
deletions (150-200 bases) originating from either end of the M13mpl9 (17). The nucleotide sequence of the GH gene was
6.8-kbp Pst I fragment were created by using BAL-31 (16) and determined from these deletion derivatives by using the
resulting fragments were recloned into either M13mpl8 or Sanger sequencing procedure (18).
5138 Evolution: Agellon et al. Proc. Natl. Acad. Sci. USA 85 (1988)
RESULTS introns (intron 1, 485 bp; intron 2, 138 bp; intron 3, 443 bp;
intron 4, 1115 bp; intron 5, 245 bp) make up the trout GH
Isolation and Characterization of the Rainbow Trout GH gene. The intron boundaries are located at positions 76/560,
Gene. Thirty clones (out of 500,000 clones screened) were 701/838, 956/1398, 1555/2669, and 2817/3061. All donor and
isolated from a rainbow trout genomic library by virtue of acceptor sites resemble consensus sequences (30). The ac-
their hybridization to the 900-bp EcoRI/Pst I fragment of the ceptor site of intron 5 is interesting in that it is preceded by
rainbow trout GH cDNA clone (pAF51) (11). One clone an exceptionally cytidine-rich region.
(RTGH14B2), which contains a 14.8-kbp EcoRI fragment, The sequence was searched for perfect and imperfect,
was selected for detailed analysis. Fig. 1 shows the hybrid- direct and inverted repeats >6 nucleotides. A 17-bp tandem
ization pattern of trout testes DNA and RTGH14B2 DNA. repeat, beginning at position +458, and a region of dyad
Trout testes DNA digested with EcoRI produced several symmetry (stem of 8 bp, loop of 6 nucleotides) beginning at
fragments, ranging in size from 6 to 15 kbp, which hybridize position + 395 were found in intron 1. Two other regions of
with pAF51. The largest of these fragments comigrates with dyad symmetry were found in intron 4, the largest of the six
the EcoRI fragment carried by clone RTGH14B2. The hy- introns. The first region, capable of forming a stem and loop
bridization pattern of RTGH14B2 DNA treated with EcoRI with 7 bp and 7 nucleotides, respectively, begins at position
and HindIII or with EcoRI and Pst I is a subset of the pattern + 2394. The second region, capable of forming a stem of 11
observed in the corresponding genomic lanes (Fig. 1). The bp and a loop of 8 nucleotides, begins at position + 2420. The
additional hybridizing fragments in the trout testes DNA (Fig. significance of these structures is unknown.
1, lanes A-) represent the other copy of the GH gene Alignment of trout and human GH gene sequences, so that
(unpublished data) and not the PrI gene. Salmonid GH and Prl the polypeptides share maximum sequence similarity, indi-
share no detectable immunological relatedness (19). cates that the first four exons ofboth genes encode analogous
The smallest single fragment of clone RTGH14B2 shown in portions of the GH polypeptide. Trout exons V and VI, which
Fig. 1 that carries the GH transcription unit is a 6.8-kbp Pst are interrupted by the additional intron (i.e., intron 5), encode
I fragment. After subcloning this fragment, deletion deriva- a region ofthe GH polypeptide that is equivalent to the region
tives originating from either end of the fragment were encoded by the last exon of the human GH gene. The
constructed and sequenced (Fig. 2). introduction of intron 5 into the trout gene likely took place
The organization of the trout GH gene was determined by after the divergence of fish and tetrapods because the
aligning the trout GH cDNA sequence (11) with the corre- mammalian GH, Prl, and PL genes all contain five exons (9,
sponding regions of the GH genomic gene. The 5' region of 27-29, 31). Testing of this hypothesis, however, must await
the GH gene contains the sequence 5' TATAAAAA 3' (20) 22 the characterization of the trout Prl gene.
nucleotides from the putative transcription start site. Anal-
ysis of the 5' sequence, up to 332 nucleotides upstream from
the cap site, did not reveal the existence of any sequence DISCUSSION
similar to other consensus promoter elements. The DNA The current model for GH gene evolution is schematically
binding sites of the glucocorticoid- and thyroid hormone- represented in Fig. 4. Niall et al. (3) were first to suggest that
receptor complexes have been localized in the mammalian a small primordial gene was repeatedly duplicated to form a
GH genes (21, 22). Sequences with structural similarity to larger gene that became the "precursor gene." We have
these sites were not obvious in the trout GH gene. However,
it is currently not clear whether thyroid and glucocorticoid Phase / -IZI- primordial gene
hormones control fish GH gene expression in a manner
similar to that in mammals (23-25). The poly(A) signal 5'
AATAAA 3' (26) is located at the 3' region of the gene -in-it Ii-
(position + 3615). Thus, the rainbow trout GH gene spans a
region of =4000 bases, nearly twice the size of its mammalian -t-I + [}C}
counterparts (Fig. 3).
Six exons (exon 1, 75 bp; exon II, 140 bp; exon III, 117 bp; V- intron
exon IV, 156 bp; exon V, 147 bp; exon VI, 568 bp) and five + -{I}
intron
p p
I ME I m I rtGH
E E
1 lhE..I hGH I III IV V
~ Lii Z~uZ
rc
precursor gene
E E
Phase //
duplication, divergence
I bGH
E H I GH Prl PL
I rGH FIG. 4. Current model for evolution of the GH gene family,
adapted from Barta et al. (9), Miller and Eberhardt (7), Selby et al.
FIG. 3. Organization of fish and mammalian GH genes. Restric- (10), and Slater et al. (8). During phase I, a primordial gene (or coding
tion fragments containing GH genes are shown. Boxes represent region) was repeatedly duplicated. Subsequently, an intervening
exons; lines between boxes are introns. The trout GH gene contains sequence separating two of the duplicated domains was lost. Later,
an additional intron (intron 5) that interrupts a region equivalent to two other domains were incorporated to form the precursor gene
exon 5 of mammalian GH genes. The region of the trout gene that containing five exons. In phase II, the precursor gene was dupli-
encodes the untranslated portion ofGH mRNA is approximately four cated. Divergence gave rise to the genes that presently encode GH
times larger than its mammalian counterpart. rtGH, trout; hGH (27), and Prl and eventually PL. Hatched boxes represent exons that are
human; bGH (28), cow; rGH (9, 29), rat; E, EcoRI; H, HindlI; P, thought to have separate origins. Roman numerals represent exons
Pst I. Scale bar represents 500 bp. in the present gene structure.
Evolution: Agellon et A Proc. Natl. Acad. Sci. USA 85 (1988) 5139
Table 1. Alignment of the internally repeating regions in human GH and corresponding regions in trout GH
Trout GH
E1/E2 15 Lj1J- - - - A H L A F D T -
E 32 30.4 47.8
El 12 N RI- V Q
-
L H LL
- -
Q K M (i- E29
E2 93[LR - - - - S V F Nf L ®G[-@
)- S®G 110 21.7 52.2
E2 89 NJ-T-- ---TI~ S L )R IJ-9-()I 103
Alignment of the internally repeated regions in human GH, equivalent regions in trout GH, and comparison between the human and trout
GH segments are shown. The internally repeated regions in human GH were taken from Niall et al. (3). Gaps (-) were introduced in the sequences
to obtain the best alignment. Each gap was counted as one position in the calculation of % similarity and % identity. Spaces (:) in the human
GH sequence were added for clarity of alignments and were not included in the calculations. Identical amino acid residues are shown in boxes.
Amino acid residues scored as similar (circled) are based on Dayhoffs highly acceptable substitutions (32).
designated these events as phase I. Subsequent duplication marks the end of phase I. At the beginning of phase II, the
and divergence of this precursor gene, which we designate as entire precursor structure was duplicated and subsequent
phase II, led to the evolution of GH, Prl, and PL. divergence gave rise to the genes that encode GH and Prl (see
The GH evolutionary model has been reviewed in detail bottom of Fig. 4).
elsewhere (6-8). We shall briefly summarize the key features The existence of an additional intron (intron 5) in the trout
of this model. Much of the rationale for phase I (Fig. 4) of the GH gene is a notable difference between fish and mammalian
GH evolutionary model is based on the existence of apparent GH genes. At first inspection, the presence of intron 5 in the
internally homologous regions within GH, Prl, and PL (3). In trout GH gene might appear to support phase I of the GH
human GH, for example, the first two of the four regions of evolutionary model. Closer examination of the sequence
internal homology are each encoded by separate exons data, however, reveals that the location of intron 5 interrupts
(exons II and IV) but the last two regions are encoded by one the last presumptive repeated segment in human GH (ESB,
larger exon (exon V). The latter exon may have been between Lys-172 and Val-173; Table 1). Intron 5 is likely a
generated after the deletion of the intervening sequence that recent introduction to the trout GH gene. Two observations
separated the two reduplicated coding domains either prior to support this hypothesis. (i) The event that gave rise to GH
or after its incorporation into the gene. The two other exons and Prl genes (phase II) occurred around 350-400 million
(exons I and III) of the human gene are thought to have years ago, before the divergence of fish and tetrapods. The
separate origins. Exon I, which eventually took over the existence of GH and Prl in these two groups of animals attests
controlling functions of the gene, was incorporated at the 5' to this notion. (it) Mammalian genes for GH and Prl are
upstream region, and exon III, which conferred the hormone organized in a similar manner-i.e., both genes have five
with carbohydrate-regulating properties, was incorporated exons and four introns. Thus, intron 5 of the trout GH gene
between the originally duplicated regions. Imperfect direct could not have existed prior to the divergence of fish and
repeats have also been found flanking exons I, III, and V of tetrapods.
rat GH, rat Prl, human GH, and human PL genes. This Comparison of regions in the trout GH polypeptide se-
observation was taken as further evidence that these regions quence, equivalent to those described by Niall et al. (3), do
arose by separate insertion events by a mechanism analogous not show the existence of internally homologous regions
to DNA transposition. The formation of the precursor gene (Table 1). Moreover, direct repeats similar to those flanking
5140 Evolution: Agellon et al. Proc. Natl. Acad. Sci. USA 85 (1988)
exons I, III, and V of the rat GH, rat Prl, human GH, and 130.
human PL genes were not found in the trout GH gene. 8. Slater, E. P., Baxter, J. D. & Eberhardt, N. L. (1986) Am.
Therefore, although the similarity between the polypeptide Zoo!. 26, 939-949.
sequences of fish GH and fish PrI (33, 34) is consistent with 9. Barta, A., Richards, R. I., Baxter, J. D. & Shine, J. (1981)
Proc. Natl. Acad. Sci. USA 78, 4867-4871.
phase II of the model (Fig. 4), the trout GH gene structure is 10. Selby, M. J., Barta, A., Baxter, J. D., Bell, G. I. & Eberhardt,
inconsistent with phase I. N. L. (1984) J. Biol. Chem. 259, 13131-13138.
In human GH, the apparent internal repeats share 30%o 11. Agellon, L. B. & Chen, T. T. (1986) DNA 5, 463-471.
identical amino acid residues and 51.3% similarity when 12. Feinberg, A. P. & Vogelstein, B. (1983) Anal. Biochem. 132,6-
conservative substitutions are taken into account (Table 1). 13.
By comparison, the equivalent regions in the trout GH have 13. Benton, W. D. & Davis, R. W. (1977) Science 196, 180-182.
14. Maniatis, T., Fritsch, E. F. & Sambrook, J. (1982) Molecular
only 10.9%o identical residues and 39.1% similarity. Further- Cloning:A Laboratory Manual (Cold Spring Harbor Lab., Cold
more, the groups of similar amino acid residues among the Spring Harbor, NY).
selected regions in trout GH are not in the same category of 15. Vieira, J. & Messing, J. (1982) Gene 19, 259-268.
acceptable substitutions (32) as those found in the apparent 16. Poncz, M., Solowiejczyk, D., Ballantine, M., Schwartz, E. &
internally repetitive regions of human GH. Significant se- Surrey, S. (1982) Proc. Natl. Acad. Sci. USA 79, 4298-4302.
quence similarity, however, is observed between equivalent 17. Norrander, J., Kempe, T. & Messing, J. (1983) Gene 26, 101-
regions of trout and human GH (Table 1). These comparisons 106.
18. Sanger, F., Nicklen, S. & Coulson, A. R. (1977) Proc. Natl.
suggest that the presumed internal repeats in the human GH Acad. Sci. USA 74, 5463-5467.
are not present in trout GH. 19. Agellon, L. B., Chen, T. T., van Beneden, R. J., Sonstegard,
Nicoll et al. (35) have shown that similarity between R. A., Wagner, G. F. & McKeown, B. A. (1986) Can. J. Fish.
randomly selected regions in human GH, human PL, or ovine Aquat. Sci. 43, 1327-1331.
Prl can be demonstrated by the introduction of appropriate 20. Breathnach, R. & Chambon, P. (1981) Annu. Rev. Biochem. 50,
gaps in the sequence. In their example, the selected regions 349-383.
have at least the same extent of similarity as those described 21. Moore, D. D., Marks, A. R., Buckley, D. I., Kapler, G.,
Payvar, F. & Goodman, H. M. (1985) Proc. Natl. Acad. Sci.
by Niall et al. (3). Our analysis of the trout GH structure and USA 82, 699-702.
that of Nicoll et al. (35) do not support the hypothesis that 22. Barlow, J. W., Voz, M. L. J., Eliard, P. H., Mathy-Hartert,
internally repeated regions in GH, Prl, or PL arose from a M., De Nayer, P., Economidis, I. V., Belayew, A., Martial,
small primordial gene (phase I, Fig. 4). J. A. & Rousseau, G. G. (1986) Proc. Natl. Acad. Sci. USA 83,
It would be premature to generate an alternate model to 9021-9025.
account for the trout GH gene structure until the GH gene 23. Martial, J. A., Baxter, J. D., Goodman, H. M. & Seeburg,
structure from at least one organism, common to both P. H. (1977) Proc. Nat!. Acad. Sci. USA 74, 1816-1820.
24. Samuels, H. H., Stanley, F. & Shapiro, L. E. (1979) Biochem-
branches leading to teleostean and mammalian evolution, is istry 18, 715-721.
determined. 25. Dobner, P. R., Kawasaki, E. S., Yu, L.-Y. & Bancroft, F. C.
(1981) Proc. Nat!. Acad. Sci. USA 78, 2230-2234.
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technical assistance. This project was supported by a grant (DCB- 263, 211-214.
851-8069) from the National Science Foundation to D.A.P. and 27. DeNoto, F. M., Moore, D. D. & Goodman, H. M. (1981)
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the Center for Marine Biotechnology, University of Maryland. E. C. & Rottman, F. M. (1982) Nucleic Acids Res. 10, 7197-
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