2A. Multiple sequence alignment of nine P. dolloi GR isoforms.
Figure 1 shows a multiple sequence alignment of the nine isoforms of P. dolloi GR. The nine P. dolloi GRs cluster into three groups: group I (GR-A1, GR-A2), group II (GR-B1, GR-B2, GR-B3) and group III (GR-C1, GR-C2, GR-C3, GR-C4). GR-A2 begins at “MMDP”, a sequence motif that is conserved in all nine GRs.
The multiple alignment reveals that these nine slender African lungfish GRs evolved through alternative splicing and gene duplications (Fig. 1). GR-A2 appears to be a product of alternative splicing of GR-A1. GR-C4 appears to be a product of alternative splicing of one or more GR-C isoforms, which supports a GR gene duplication in P. dolloi genome. There also is evidence for gene duplications among the P. dolloi GRs. MLSE at the beginning of GR-A1 is conserved in GR-B2 and GR-C2. A closely following YAPAD sequence is conserved in all P. dolloi GR isoforms. Fifteen of the first sixteen amino acids at the amino terminus of GR-A-1 are conserved in GR-B2 and GR-C2 (Fig. 1A). This amino acid sequence is highly conserved in the other seven GRs. The rest of GR-A2 beginning at MMDPAGALNSLNGTQSLNKY is identical in GR-A1, and this amino acid sequence is highly conserved in the other seven GRs. MPFESLKYYAPAD is conserved at the beginning of GR-B3 and GR-C3. Beginning at the conserved MMDP sequence in the N-terminal domain, the two GR-A isoforms differ at 55 positions from the three GR-B and the four GR-C isoforms.
Total RNA was isolated from P. dolloi ovary and translated into cDNA. PCR was performed using four primer sets based on the sequence of P. annectens GR, as described in the Methods section. The amplified DNA fragments were sub-cloned into a vector for sequence analysis. Similar to other steroid receptors, slender African lungfish GR can be divided into four functional domains [6, 8], consisting of a ligand-binding domain (LBD) at the C-terminus, a DNA-binding domain (DBD) in the center that is joined to the LBD by a short hinge domain (hinge), and a domain at the amino-terminus (NTD). GenBank accession no. BDF84376 for GR-A1, BDF84377 for GR-A2, BDF84378 for GR-B1, BDF84379 for GR-B2, BDF84380 for GR-B3, BDF84381 for GR-C1, BDF84382 for GR-C2, BDF84383 for GR-C3, and BDF84384 for GR-C4. Sequences were aligned with Clustal W , as described in the Methods section.
2B. Comparison of slender African lungfish GRs and West African lungfish GRs.
To begin to understand sequence conservation and divergence among lungfish GRs, we compared GR-A1, GR-B1 and GR-C1, which are the three longest slender African lungfish GRs, with the four West African lungfish glucocorticoid receptor sequences in GenBank (Fig. 2). The multiple sequence alignment, shown in Fig. 2, reveals strong sequence conservation in the DBD, with a difference at only one position containing a semi-conserved phenylalanine-tyrosine. The sequences in the LBD and hinge domains of slender African lungfish GR and West African lungfish GR also are highly conserved. There are small segments of sequence divergence in the NTD, but most of the NTD is conserved. Overall slender African lungfish GRs and African lungfish GRs are very similar to each other.
West African lungfish glucocorticoid receptor sequences were downloaded from GenBank (Accessions XP_043925084 for X1, XP_043925085 for X2, XP_043925087 for X3, XP_043925088 for X4). Sequences were aligned with Clustal W , as described in the Methods section.
2C. Comparison of the amino acid sequences of slender African lungfish GR, West African lungfish GR, coelacanth GR, zebrafish GR and human GR.
To begin to understand the relationship of lungfish GRs to other selected GRs, we constructed a multiple sequence alignment of slender African lungfish GR with West African lungfish GR, coelacanth GR, zebrafish GR and human GR (Fig. 3). The DBD and hinge domains are highly conserved in all GRs. There is good sequence conservation of the LBD in all six GRs. However, there is an interesting pattern of sequence conservation in the NTD. There is excellent sequence conservation in the NTD among slender African lungfish GR, West African lungfish GR, coelacanth GR and human GR. The stronger conservation of the NTD in lungfish GRs with human GR than with zebrafish GR, indicates that the NTD in zebrafish GR has diverged from the other GRs.
Glucocorticoid receptor sequences were downloaded from GenBank (Accession no. NP_000167 for human GR, XP_005996162 for coelacanth GR, and NP_001018547 for zebrafish GR) and aligned with Clustal W , as described in the Methods section. The NTD in zebrafish GR has gaps and sequence differences with the other GRs.
2D. Comparison of functional domains in slender African lungfish GR with domains in West African lungfish GR, coelacanth GR, zebrafish GR and human GR.
Figure 4 shows the percent identity in the comparison of the different functional domains on slender African lungfish GR with the GR and MR from other vertebrates.
Comparison of domains in slender African lungfish GR with GRs from West African lungfish, coelacanths, humans and zebrafish and MRs from slender African lungfish, West African lungfish, humans and zebrafish. The functional NTD (A/B), DBD (C), hinge (D) and LBD (E) domains are schematically represented with the numbers of amino acid residues and the percentage of amino acid identity depicted.
As shown in Fig. 4, the DBD and LBD are highly conserved in all GRs. For example, slender African lungfish GR and human GR have 98% and 66% identity in DBD and LBD, respectively. There are similar % identities between corresponding DBDs and LBDs in lungfish GR and other GRs. This strong conservation of the DBD and LBD contrasts with the lower sequence identity between the NTD of slender African lungfish GR and human GR (38%) and even lower sequence identity with the NTD in zebrafish GR (28%).
2E. Phylogenetic Analysis.
To better understand the relationships among the nine P. dolloi GRs and four P. annectens GRs, we constructed the phylogenetic tree, shown in Figs. 5. In this phylogeny, the four African lungfish GRs cluster into one group. Slender African lungfish GR-A1 and GR-A2 are in a separate branch from the other slender African lungfish GRs. GR-A2 appears to be formed by alternative splicing of GR-A1. GR-B1, GR-B2 and GR-B3 cluster. GR-C3 and GR-C4 cluster, and GR-C4 appears to be formed by alternative splicing of GR-C3.
2F. Basis for the failure to clone P. dolloi GR.
Figure 6 shows the location of the PCR primers that we used to successfully clone GRs from chicken, alligator and frog . Due to the strong conservation of the GR and MR these PCR primers retrieved partial sequences from both the GR and MR in chicken, alligator and frog. The full sequences of these GRs and MRs was achieved in the next step using RACE. Our failure to clone P. dolloi GR was due using WQRFYQ instead of WQRFFQ for the 1st /2nd -reverse primer. When we used WQRFFQ we were able to clone P. dolloi GR.
The correct 1st /2nd -reverse primer for PCR cloning of P. dolloi GR is WQRFFQ instead of WQRFYQ.
P. dolloi contains nine GR isoforms, in contrast to P. annectens, which contains four GR isoforms. We do not know how many GR isoforms are in Australian lungfish (Neoceratodus forsteri) because their GR sequences have not been deposited in GenBank. The availability of sequences of P. dolloi GRs and P. annectens GRs should permit using PCR to clone N. forsteri GRs, which would elucidate the number GR isoforms in this lungfish and the relationship of their GRs to the GRs of P. dolloi and P. annectens.
The response to corticosteroids of any lungfish GR is not known, nor are the functions of the multiple GR isoforms in P. dolloi GRs and P. annectens GRs. We have initiated studies to determine corticosteroid activation of P. dolloi GRs to begin to elucidate the functions of slender African lungfish GRs. It is interesting that there are multiple isoforms of human GR, due to alternative splicing of human GR, and these isoforms are important in achieving functional diversity of human GR [6, 8, 33, 36]. A similar scenario is likely for P. dolloi GRs and P. annectens GRs.