Comparative analysis of somitogenesis related genes of the hairy/Enhancer of split class in Fugu and zebrafish
© Gajewski and Voolstra; licensee BioMed Central Ltd. 2002
Received: 11 June 2002
Accepted: 5 August 2002
Published: 5 August 2002
Members of a class of bHLH transcription factors, namely the hairy (h), Enhancer of split (E(spl)) and hairy-related with YRPW motif (hey) (h/E(spl)/hey) genes are involved in vertebrate somitogenesis and some of them show cycling expression. By sequence comparison, identified orthologues of cycling somitogenesis genes from higher vertebrates do not show an appropriate expression pattern in zebrafish. The zebrafish genomic sequence is not available yet but the genome of Fugu rubripes was recently published. To allow comparative analysis, the currently known Her proteins from zebrafish were used to screen the genomic sequence database of Fugu rubripes.
20 h/E(spl)/hey-related genes were identified in Fugu, which is twice the number of corresponding zebrafish genes known so far. A novel class of c-Hairy proteins was identified in the genomes of Fugu and Tetraodon. A screen of the human genome database with the Fugu proteins yielded 10 h/E(spl)/hey-related genes. By analysing the upstream sequences of the c-hairy class genes in zebrafish, Fugu and Tetraodon highly similar sequence stretches were identified that harbour Suppressor of hairless paired binding sites (SPS). This motif was also discovered in the upstream sequences of the her1 gene in the examined fish species. Here, the Su(h) sites are separated by longer intervening sequences.
Our study indicates that not all her homologues in zebrafish have been isolated. Comparison to the human genome suggests a selective duplication of h/E(spl) genes in pufferfish or loss of members of these genes during evolution to the human lineage.
Somitogenesis is the phase in embryonic development of vertebrates during which the somites, that is segmented mesodermal tissue along each side of the notochord, are successively generated. Besides other models , the "clock-and-wavefront" model  is able to explain somite formation. This model proposes the existence of a cellular clock that interacts with a slowly progressing wave (wavefront) moving along the presomitic mesoderm (PSM) from anterior to posterior. Genes of the h/E(spl)/hey family have been identified in chicken and mouse that show a cycling expression pattern, namely c-hairy1, c-hairy2, c-hey2, mhes1 and mhes7[3–9]. These bHLH proteins are thought to obey the proposed molecular clock.
Analysis of the family of h/E(spl)-related genes in zebrafish has yielded 9 her-genes so far (her1-6: [10, 11], her7 and her8 unpublished own work, accession numbers: AF240772, AY007990, her9: ) and one member of the hey class, called gridlock. her1, her4, her6 and her7 are thought to play a role in somite formation [14–16]. her4 and her6 are expressed in the developing nervous system and in the anterior PSM of zebrafish embryos but they do not cycle [10, 17]. The her1[15, 18] and the her7 gene (unpublished) are both cyclically expressed in the PSM during somitogenesis. Both genes are only distantly related to the cycling c-hairy type genes from higher vertebrates. In zebrafish, her9, the apparent orthologue of the cycling genes from chicken and mouse does not show any expression at all in the PSM . Therefore, it has been suggested that the zebrafish her1 gene is the functional homologue to the cycling c-hairy type genes and thus an element of the molecular clock. Alternatively, more than two c-hairy type genes (her6 and her9) exist in zebrafish. Since whole genome sequence information for zebrafish is still missing, we chose to exploit the publicly available draft sequence of the Fugu genome  to identify all the H/E(spl)/Hey-related proteins of this organism. The evolutionary divergence time of both fish species is about 180 myr compared to 430 myr to tetrapods . Hence, the emerging picture might give us a clearer view on the situation of the h/E(spl)/hey-related gene family in zebrafish than from comparison to higher vertebrates. Due to a remarkable conservation of exon-intron structure of the h/E(spl)-related genes from insects up to man, it is possible to annotate the proteins of this family on the level of genomic sequence for Fugu rubripes. Since the automatically performed annotation was not able to correctly predict the protein sequences (the N- and/or C-termini often were missing), it became necessary for comparative analysis to re-compile the sequences on the basis of an exon-intron dataset of known h/E(spl) genes.
It has been shown, that the pufferfish Fugu rubripes possesses a very small genome with a size of only 400 Mb . Compared to zebrafish or man the genome size in pufferfish is 4 to 8 times reduced. This reduction refers mostly to the intergenic regions and repetitive elements, while Fugu seems to possess a similar gene set with the same structure than mammalian organisms . Comparison of promoter sequences from homologous genes in both fish species should facilitate the identification of candidate transcription factor binding sites.
Results and Discussion
In the genome of Fugu rubripes significantly more h/E(spl)/hey-related genes were identified than in Danio rerio are currently known
In more detail: Deduced from the intronless genomic structure, which is indicative for E(spl) genes in Drosophila melanogaster, FrHer2 (T002603/1) and both Her4 proteins (T002603/2, T002289) were identified as Enhancer of split type proteins. Fugu her2 and one of the her4 genes are located close to each other in a head to tail orientation on contig T002603 (see additional file 2). However, FrHer2 (T002603/1) does not cluster with the other 2 Enhancer of split type proteins in the tree.
Five Fugu proteins were classified as Hey (4) or Hey-related (1) compared to only one currently known zebrafish member of that class, called Gridlock . Homologues for each of the hey or hey-related genes in Fugu have already been isolated in higher vertebrates [5, 25, 26] or were previously annotated in the genbank database (accession number: XM_068025 for "bHLH protein similar to hhesr1/hey1"). The C-terminal consensus sequence of the Hey proteins is KPYRPW GTE(IHey1/VHey2)GAF. Focussing on this consensus, FrHey1.1 (contig T004546), FrHey1.2 (contig T000531) and FrHey2 (contig T014948) could be determined for the pufferfish (table 1 and fig. 1). Interestingly, all 3 proteins show at least one exchange to the C-terminal consensus sequence. According to the similarity in the bHLH-domain the two other proteins in contig T003476 and T005657 belong also to the Hey type proteins (fig. 1). However, like mouse HRT3 (, accession number: AF172288) FrHey3 (contig T005657) possesses the TEIGAF motif but deviates to a higher degree from the YRPW-motif. The other protein (in contig T003476) does not possess a KPYRPW GTE(IHey1/VHey2)GAF motif at the C-terminal end. Instead a completely diverged amino acid sequence is present. Furthermore, the basic domain is somehow truncated (fig. 1, see additional file 4). Interestingly, this protein consists of 4 exons. This is in contrast to the other identified Hey-genes, which have 5 exons in human and Fugu (see table 1). Nevertheless, the human orthologue, defined as "bHLH protein similar to Hesr-1/Hey1" (accession number: XM_068025, table 1, additional file 4) shows equal aberrant features from the Hey-type genes. Therefore, we will refer to the hey-related gene in Fugu as Frhhesr1-related.
12 identified pufferfish proteins belong to the Hairy class of bHLH transcription factors that can be further subdivided into 3 branches. 5 proteins belong to the c-hairy type class compared to two genes known so far from zebrafish (fig. 2: bluegreen box). At a first glance, in the second branch at least two of three proteins seem to be the zebrafish orthologues Her1 and Her7, which are involved in somitogenesis (fig. 2: violet box). A detailed analysis of the c-Hairy type class as well as of the Her1/5/7 is given in the following sections. The third branch consists of three proteins that are related to the zebrafish Her8 (table 1, fig. 2: light green box).
Comparing both fish species, the number of h/E(spl)/hey-related genes in pufferfish is twice the number of these genes currently known from zebrafish. Evidence from Hox cluster analysis suggests that the extent of duplication in Fugu, if any, is far less extensive than in zebrafish . Therefore, it is likely that more h/E(spl)/hey-related genes in zebrafish exist. Deduced from the comparative tree it can be estimated that at least for hey type genes and in particular for genes of the c-hairy type class further zebrafish homologues have to be expected.
A screen with the 20 conceptually translated Fugu proteins against the human genomic sequence database yielded 10 h/E(spl)/hey-related genes (for accession numbers see Materials and Methods). These 10 genes can be further divided into 6 h/E(spl) genes, 3 hey genes (hey1, hey2, heyL, ) and 1 hey-related gene (hhesr1, accession number: XM_068025). In Fugu, 15 h/E(spl) genes, 4 hey-genes and 1 hey-related gene were identified. Deduced from the sequence alignment of the Hey type proteins (see additional file 4), FrHey1.1 and FrHey1.2 are similar to human Hey1, FrHey2 is similar to human Hey2 and FrHey3 is similar to human HeyL. One copy of the hey-related gene exists in both genomes (hhesr1, accession number: XM_068025, and Frhhesr1). While the set of Hey- and Hey-related genes is quite comparable in both organisms, the number of h/E(spl) genes in Fugu (15) is 2.5 times higher than in the human genome (6). This indicates a duplication of those genes in Fugu or loss of members of the h/E(spl) genes in human. It is not known how these genes are expressed in Fugu but interestingly the majority of the zebrafish her genes is expressed in subsets of differentiating neuroblasts during nervous system development ([10, 12, 29]; her 8 unpublished). Since fish possess a unique set of neurons and sensory organs, compared to higher vertebrates, it might be that selective duplication of the hairy genes was one source that led to neuronal/sensory cell diversification.
A novel class of c-Hairy proteins exist in the genomes of two pufferfish species
In FrHer6.1 (in contig T007628) and FrHer6.2 (in contig T000396) a sequence stretch of around 30–40 amino acids just N-terminal of the WRPW-motif is missing compared to c-Hairy1 class members (fig. 3). This feature is indicative for c-Hairy2 class proteins . Thus, FrHer6.1 and FrHer6.2 belong to the c-Hairy2 class and can be considered as Her6 homologues.
Deduced from the high conservation in the bHLH domain to the other c-Hairy proteins, FrHer10.1 (in contig T000956) and FrHer10.2 (in contig T008912) constitute a third to our knowledge novel c-Hairy class. In both proteins a sequence stretch of around 40 amino acids is missing, like in the c-Hairy2 class. In addition, a second stretch just C-terminal to the orange domain is absent compared to the already known two classes (fig. 3). Proteins of this c-Hairy type are so far not known in other vertebrates. However, these two Fugu proteins show similarity to the Hes2 proteins from mouse and human (fig. 3). But in the Hes2 proteins the number of amino acids between the orange domain and the WRPW motif is even more reduced in comparison to the c-Hairy-related proteins. To elucidate whether the class of c-Hairy-related proteins is unique in Fugu, the shotgun sequences of Tetraodon nigroviridis were screened with the 5 Fugu c-hairy type nucleotide sequences. Like in Fugu, the two c-Hairy-related class members (TnHer10.1 and TnHer10.2, TnHer10_1 and TnHer10_2 in fig. 3) and also the second member of the c-Hairy2 class were found (TnHer6.2, TnHer6_2 in fig. 3) supporting that respective proteins have to be expected in zebrafish.
Is the zebrafish her1/7 gene complex conserved in pufferfish?
Promoters of c-hairy1 and c-hairy2 type genes can be classified into two distinct groups
Although the promoters consist of identical regulatory elements, on the level of nucleotide sequence they can be divided into two groups that correspond to the c-Hairy1 and c-Hairy2 protein classes (fig. 5). In particular, this classification is even reflected in the intervening regions of the two Su(h) sites of the identified SPS motifs. Thus, the promoters of the c-hairy class genes show more similarities within their classes in different species than among themselves in the same species.
Identification of potential regulatory motifs in zebrafish her1
In Xenopus, it has been shown that the SPS regulatory motif and a specific 3'UTR element are sufficient to drive mesoderm expression . Since the zebrafish her1 gene is exclusively expressed in the PSM, we assume that SPS sequences are specific mesoderm regulator elements in fish and presumably in vertebrates.
Unusual high degree of conservation in the promoter of the hesr1-related gene of zebrafish, human, mouse and Fugu
By analysing the genome database of Fugu http://Fugu.hgmp.mrc.ac.uk/ 20 h/E(spl)/hey genes in Fugu were determined, compared to 10 currently known members of this family in zebrafish. Deduced from this data, at least for hey type genes and in particular for genes of the c-hairy type class further zebrafish homologues have to be expected. A novel c-hairy type class could be identified in Fugu and Tetraodon that is so far not known in other vertebrates. Since no apparent orthologue from chicken exists, we refer to this class as the c-hairy-related class. Indicative for this class is the difference in length of the amino acid sequence between the orange domain and the WRPW motif compared to the already known two classes. Although the upstream sequences of the c-hairy 1 and c-hairy 2 class genes show identical composition of regulatory elements in zebrafish, Fugu and Tetraodon, the classification coming from protein sequence analysis is reflected in the promoter regions on the level of nucleotide sequence. Furthermore, the identified SPS motifs in the promoters of the analysed c-hairy1 and c-hairy2 type genes are highly conserved, shown by comparison with higher vertebrates. For the SPS motif in the her1 upstream sequences of the analysed fish species longer intervening sequences between the Su(h) sites were observed. Deduced from mesoderm specific expression of the her1 gene in zebrafish, we suppose that the "Suppressor of hairless paired binding site" is a specific mesoderm regulator in fish and presumably in vertebrates.
Materials and Methods
Gene identification and sequence retrieval
By using the TBLASTN program  the Fugu database (first release from 25.10.01) at the UK HGMP Resource Centre http://Fugu.hgmp.mrc.ac.uk/ was screened with the 9 different Her proteins of Danio rerio. The accession numbers of the used zebrafish bHLH genes are: her1: X97329, her2: X97330, her3: X97331, her4: X97332, her5: X95301, her6: X97333, her7: AF240772, her8: AY007990, her9: AF301264. The TBLASTN results were screened manually for the occurrence of sequence motifs known to be conserved in H/E(spl)-related proteins. These motifs are the basic domain with the consensus sequence KPx(M/V/I)E(K/R)(R/K)R, the highly conserved second loop with the consensus sequence (L/V)EKA(D/E)(I/V)LE and the WRPW motif located at the C-terminal end of the proteins. For further analysis, at least two of these motifs had to occur in a reasonable distance within a contig. Because the N- and/or C-termini often were missing in the automatically annotated proteins http://www.jgi.doe.gov/fugu/index.html, a training set for identification of the exonic regions was created, which contains the following known hairy genes: Drosophila hairy: X15904, human hes1: L19314, mouse hes1: D16464, mouse hes7: AB050104, zebrafish her1 and her7: AF292032 (see additional file 5). The regions of coding sequences, which we have conceptually translated into the respective proteins of Fugu rubripes, are depicted in table 1. Sequence LGS99222 was used for identification of the FrHer6.1 C-terminus (PAAVSPGAPSGNTDSVWRPW). Sequence LGS286123 was used for identification of the FrHey1 C-terminus (WGLEIGAF). The BLASTX algorithm  was used to identify the closest relatives to the Fugu Her proteins in zebrafish and higher vertebrates (table 1).
For identification of the c-hairy homologues as well as her1, her5 and her7 in Tetraodon nigroviridis the corresponding Fugu sequences were used to screen the shotgun sequence database at genoscope by BLASTN http://www.genoscope.cns.fr/externe/tetraodon/Ressource.html and the trace archive http://www.ncbi.nlm.nih.gov/Traces/trace.cgi? at NCBI using megaBLAST. The Sequences, which are described here, can be retrieved at the Ensembl Trace Server http://trace.ensembl.org or at the NCBI Trace archive http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?. Sequences with the accession numbers 89970374, 89981571, 90016949, 90052606, 90066642, 90222617, 90222618, 90275465, 90275466, 90351844, 90421676, 90430225, 95723915, 95738908, 95996399, 97329806, 97457947, 97625306, 99082743, 99085687, 99124118, 99344199, 99379652, 99390932, 99545674 and 101019329 were assembled for 1 kb upstream of the first exon up to 5 kb downstream of the third exon of Tetraodon her1. The fourth exon of Tetraodon her1 was identified in sequence COAG1029AA11SP1 (reverse complement) at position 97–614. For Tetraodon her5 the sequences with the following accession numbers were assembled: C0AH037AD02SP1, C0AG530DE07SP1, C0AG873DH06LP1, C0AG1038AA11SP1, C0AG1120DA10SP1 and 90098825, 90098826, 90176607, 90411020, 90411021, 95688576, 95703158, 96052770, 97373175, 97658773, 99123371, 99159494, 99248382, 99288485, 101130421. For Tetraodon her6.1 the sequences with the following accession numbers were assembled: 89972279, 90058082, 90064995, 90119043, 90135880, 90238776, 90289277, 90444073, 90476831 and C0AG202CG02SP1, C0AG336DF02SP1, C0AG465AB08LP1, C0AG467BE05LP1, C0AG600DE09LP1, C0AG635CC05LP1, C0AG1333AE06SP1. Tetraodon her6.2 was assembled with sequences of the following accession numbers: 97704800, C0AG515DB08SP1 and C0AG1340BB02SP1. For Tetraodon her7 the sequences with the accession numbers C0BG101CF02LP1, C0AG256AH01SP1, C0AG325AF02LP1, C0AG542AG07SP1, C0AG575CF01SP1, C0AG735BC08SP1, C0AG793CF06SP1, C0AG799AD01LP1, C0AG900AF01SP1, C0AG1022CB06LP1, C0AG1034AH05SP1, C0AG1243AA03SP1, C0AG1342BE07LP1, C0AG1541DH04LP1, C0AH109BE02LP1 and C0BG045CF02SP1 were used. For Tetraodon her9 the sequences with the accession numbers C0AA019AG08C1, C0AG201DA11SP1, C0AG302BF10LP1, C0AG622DB06LP1, C0AG997DB09LP1, C0AG1070BF12SP1, C0AG1174AH07SP1, C0AG1255CB09SP1 and C0AG1350CB05LP1 were utilised. For Tetraodon her10.1 the sequences with the accession numbers C0AG132BG03LP1, C0AG214BF08LP1, C0AG471CC07SP1, C0AG852AF01LP1, C0AG1268AC03SP1, C0BG067CF10LP1, 97442563 and 100725254 were assembled. For Tetraodon her10.2 the following sequences were assembled and the reverse complement of it was analysed: 101123589, C0AG438BH03LP1, C0AG859BF07LP1, C0AH077AD07SP1, C0BG092BE02LP1 (see additional file 6).
The human genome database was screened with the 20 Fugu proteins by TBLASTN http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsBlast.html&&ORG=Hs. The accession numbers (contig id, protein id) in which the human H/E(spl)/Hey-related proteins were identified, are: Hes1/Hry (NT_005571, gi: 20536141, XP_039925), Hes2 (AL031848, gi: 4914512, CAB46198), Hes4 (NT_032954, gi: 20472908, NP_066993), Hes5 (NT_004350, gi: 20535853, not annotated yet, 1. exon 161111–161164 and 2. exon 161264–161803), Hes6 (NT_005120, gi: 20535565, NP_061115), Hes7 (NT_010823, gi: 20560291, NP_115969). Hey1 (NT_008209, gi: 20544348, XP_113553), Hey2 (NT_030710, gi: 20550030, NP_036391), HeyL (NT_004511, gi: 20537057, NP_055386), protein similar to Hesr-1 (NT_006169, gi: 20535686, XP_068025).
Promoter identification and sequence retrieval
For examination of the corresponding promoter regions 2 kb upstream of the Start-Methionine were used in a BLASTN search  to detect conserved regulatory elements. Search for potential transcription factor binding sites was done using the MatInspector program . Due to bad sequence reads we were not able to identify the first exon in 4 genes (indicated with n.d. in table 1), which were therefore excluded from upstream sequence analysis.
For identification of the zebrafish her6 and her9 upstream sequences the corresponding cDNA sequences were used for a blastn search against the trace archive at NCBI. The sequences with the accession numbers 15682371 and 25608918 were assembled for the her6 promoter. The first 53 nucleotides of the published her6 cDNA sequence were found on a different sequence stretch. The sequences with the accession numbers 25425900, 98681634, 15611875, 98577137, 100352443 and 102690745 were assembled for around 1 kb upstream of her9 (see additional file 6).
For comparison of the promoter region of the Frhhesr1-related gene in contig T003476 (table 1) the corresponding human sequence (accession number: 16931048, nt 18662–20664) was used for a BLASTN search against the trace archive to obtain corresponding sequences of mouse and zebrafish. The mouse upstream region was assembled using trace archive files with the following accession numbers 34431248 nt 1–741 of 741, 20297240 nt 135–751 of 751 (reverse complement), 7193321 nt 1–628 of 705 (reverse complement) and 43361903 nt 272–942 of 942 (reverse complement). The zebrafish promoter was compiled by utilizing the following files (accession numbers): 83152916 nt 1–602 of 612 (reverse complement), 30330598 nt 191–612 of 612 and 42667125 nt 1–612 of 612. All sequences are immediate to the first ATG of the respective hhesr1-related coding sequence, except for zebrafish. Here, no sequence information about the 3'end of this promoter as well as the beginning of the coding sequence was available. Potential exonic regions in the upstream sequence of the Frhhesr1-related gene were investigated by GENSCAN http://genes.mit.edu/GENSCAN.html and potential ORFs were identified by BioEdit .
The SPS sequence in the upstream sequence of Frher9 (T000078) was identified at position 38130–38161. The SPS sequence in the promoter region of Frher6 (T007628) was localized at position 7320–7289 (reverse complement). The Frher1/5 gene complex was found in contig T002307 and a corresponding SPS sequence was identified at position 8677–8643 (reverse complement). Deduced from the created dataset of SPS sites, we used FASTM at Genomatix http://www.genomatix.de/cgi-bin/fastm2/fastm.pl to define a model for this motif for fish. The model consists of two binding site elements separated by 20 to 45 nucleotides (distance from start of element 1 to start of element 2). Both elements had to occur on one strand, the elements are defined as: GTGRRAR and WTYMCAC. With this dataset, we re-examined all available upstream sequences of the Fugu genes for the occurrence of SPS sites.
Sequence comparisons and phylogeny
Alignments of amino acid sequences were done making use of the CLUSTALW algorithm  in the program BioEdit or by using the Pileup program of the GCG software package [41, 42]. Phylogenetic trees based on these alignments were computed by the Neighbor-Joining method  with a bootstrap support of 100 replicates. For the tree calculations the program PHYLIP  was used. Trees were displayed using Treeview . The program GeneDoc was used for displaying the alignments . For the alignment of the c-hairy homologues the accession numbers of the compared genes are: c-hairy1: AF032966, c-hairy2: , mouse hes1: NM008235, x-hairy1: U36194, x-hairy2A: AF383159. For comparsion, the mouse hes2 (NM_008236) and human hes2 (CAB46198) were used.
For alignment of the upstream sequences the DIALIGN program  from Genomatix http://www.genomatix.de/cgi-bin/dialign/dialign.pl was used.
The authors wish to thank Diethard Tautz for giving helpful advice and critical comments to this work. Thanks also to Michael Kroiher for critically reading the manuscript. The Fugu sequence data has been provided freely by the Fugu Genome Consortium http://fugu.hgmp.mrc.ac.uk/. Genoscope and the Whitehead Institute for Genome Research http://www.genoscope.cns.fr/externe/Tetraodon/ made the sequence data of Tetraodon nigroviridis publicly available. This work was supported by the Deutsche Forschungsgemeinschaft (SFB 572).
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