Characterization of the Functional Domain of β2-Microglobulin from the Asian Seabass, Lates calcarifer

Abstract

Background

β2-Microglobulin (β₂M) is the light chain of major histocompatibility class I (MHC I) that binds non-covalently with the α heavy chain. Both proteins attach to the antigen peptide, presenting a complex to the T cell to be destroyed via the immune mechanism.

Methodology/Principal Findings

In this study, a cDNA sequence encoding β₂M in the Asian seabass (Lates calcarifer) was identified and analyzed using in silico approaches to predict and characterize its functional domain. The β₂M cDNA contains an open reading frame (ORF) of 351 bases with a coding capacity of 116 amino acids. A large portion of the protein consists of the IG constant domain (IGc1), similar to β₂M sequences from other species studied thus far. Alignment of the IGc1 domains of β₂M from L. calcarifer and other species shows a high degree of overall conservation. Seven amino acids were found to be conserved across taxa whereas conservation between L. calcarifer and other fish species was restricted to 14 amino acids at identical conserved positions.

Conclusion/Significance

As the L. calcarifer β₂M protein analyzed in this study contains a functional domain similar to that of β₂M proteins in other species, it can be postulated that the β₂M proteins from L. calcarifer and other organisms are derived from a common ancestor and thus have a similar immune function. Interestingly, fish β₂M genes could also be classified according to the ecological habitat of the species, i.e. whether it is from a freshwater, marine or euryhaline environment.

Introduction

β₂M is the light chain component of the class I major histocompatibility complex (MHC I) molecule. It consists of about 99 residues with a seven-stranded β-sandwich fold and a central disulfide bond [1] and belongs to the antibody constant domain-like family of proteins (immunoglobulin superfamily). At the cell surface, the MHC I complex is comprised of three extracellular domains from the α chain (α1, α2 and α3) plus the β₂M protein domain. β₂M ensures the proper folding and cell surface display of the MHC I molecule [2]. The classical MHC I molecule mainly functions as a component that binds antigenic peptides, presenting them to the T-cell receptor to trigger the cellular immune response [3].

It has been reported that there is a high degree of conservation of β₂M sequences of mammalian species as well as between mammalian and avian species [4], [5]. The teleost β₂M sequences also exhibit high sequence similarity overall and conserved regions with warm-blooded vertebrates [6]. Previous phylogenetic analysis revealed the evolutionary diversion of the β₂M protein in warm-blooded vertebrates and fish [7], [8]. Meanwhile, another earlier phylogenetic analysis indicated that the freshwater fish β₂M gene diverged from the common ancestor gene earlier than the seawater fish β₂M gene [6].

In an effort to improve our understanding of the molecular biology of L. calcarifer, several thousand expressed sequence tags (ESTs) have been derived from various cDNA libraries from several tissues [9]. Analyses of the EST data enabled us to identify novel gene sequences, including those with significant similarity to β₂M. Using the numerous β₂M sequences that are available in the public databases, we analyzed the protein sequence in an effort to better understand the immune system of L. calcarifer.

Materials and Methods

The cDNA sequence of L. calcarifer β₂M obtained from the spleen EST library was translated into its potential open reading frame (ORF) using the ORF Finder algorithm (http://www.ncbi.nlm.nih.gov/gorf/). Domain analyses were carried out using several resources, including Simple Modular Architecture Research Tools (SMART) (http://smart.embl-heidelberg.de/) [10], Pfam 20.0 (http://pfam.wustl.edu/) [11] and Prosite 19.36 (http://www.expasy.org/prosite/) [12]. The profile of the IGc1 domain obtained from the Pfam domain database was used to search for other homologous proteins using the hmmsearch program in HMMER version 2.3.2 (http://hmmer.janelia.org) [13], [14] in both the Swiss-Prot database Release 54 (http://www.ncbi.nlm.nih.gov) and the fish genomes at Ensembl database Release 49 (http://www.ensembl.org). The IGc1 domain sequences of the homologous proteins thus identified were extracted for subsequent analyses.

The sequence alignment for the IGc1 domains was built using the hmmalign program in the HMMER package against the profile of the IGc1 domain obtained from Pfam to enable the pattern of β₂M protein change across the taxa to be examined. PHYLIP (http://evolution.genetics.washington.edu/phylip) [15] was then used to perform phylogenetic analyses. A neighbor-joining tree was built using the protdist and neighbor programs with the Jones-Taylor-Thornton substitution model. The robustness of the trees was evaluated by bootstrap analysis of 1000 random iterations using seqboot, while consense was used to generate the consensus tree. All programs used to construct the phylogenetic trees are contained in PHYLIP packages [15]. Subsequently, MEGA4 (http://megasoftware.net/) [16] was utilized to view the resultant phylogenetic trees. The L. calcarifer β₂M sequence analyzed in this study has been deposited in the GenBank database under the accession number FJ200516.

Results

Analysis of the L. calcarifer β₂M Sequence

Analyses of the cDNA sequence of L. calcarifer β₂M (clone LSE48F06) from the spleen EST library indicated the most probable ORF codes for a polypeptide of 116 amino acids in length. A domain search revealed that a large portion of the protein sequence matched the immunoglobulin C-type (IGc1) domain in the SMART, Pfam and Prosite databases. Almost half of the amino acid residues of β₂M form two large β structures, which are linked by a central disulfide bond. Its conformation thus strongly resembles the overall tertiary structure of the Igc1 domain [17]. In addition, analysis against the Prosite database showed the presence of an immunoglobulin and major histocompatibility complex protein signature, YSCRVTH, located at residues 97–103 in the L. calcarifer β₂M sequence.

A total of 81 IGc1 domains contained in β₂M sequences were obtained by protein search against the Swiss-Prot database (version 14 updated 23 October 2007) and the known proteins of five fish species (medaka, stickleback, zebrafish, pufferfish and spotted green pufferfish) in the Ensembl database (version 49 updated March 2008). Of these 81 domain sequences, only 56 were used to build the multiple sequence alignment (MSA) (see Table 1); the remaining sequences were excluded as they were considered identical, truncated or replicated between the two databases used. As the IGc1 domain is the functional domain in all β₂M sequences analyzed in this study, subsequent analyses focused on this domain as a representation of the β₂M protein.

Table 1. β₂M sequences used in this analysis.

Group	Protein ID	Protein Name	Species Name	Common Name	Reference
Fish	Q8AXA0	Reg	R. eglanteria	Clearnose skate	[19]
	P55076	Bin	L. intermedius	Lake Tana barbels	[26]
	O42197	Ipu	I. punctatus	Channel catfish	[6]
	Q04475	Dre1	D. rerio	Zebrafish	[4]
	Q03422	Cca	C. carpio	Common carp	[27]
	Q9PRF8	Aba	A. baerii	Siberian sturgeon	[18]
	Q8AYH8	Pol	P. olivaceus	Japanese flounder	[8]
	Q90ZJ6	Ola	O. latipes	Japanese medaka	[28]
	NP_998291	Dre2	D. rerio	zebrafish	[29]
Amphibian	Q9IA97	Xla	X. laevis	African clawed frog	[7]
Monotremes	Q864T7	Oan	O. anatinus	Platypus	[30]
	Q864T6	Tac	T. aculeatus	Australian echidna	[30]
Avians	P21611	Gga	Gallus gallus	Chicken	[31]
	P21612	Mga	M. gallopavo	Turkey	[32]
Marsupials	Q9GKM2	Tvu	T. vulpecula	Brushtail possum	[33]
	Q864T8	Mdo	M. domestica	Short-tailed opossum	[30]
Ruminants	Q6QAT4	Oar	O. aries	Sheep	Unpublished data
	P01888	Bta	B. taurus	Cattle	[34]
Equine	P30441	Eca	E. caballus	Horse	[35]
	Q861S3	Eas	E. asinus	Ass	[36]
Rodents	P01887	Mmu	M. musculus	Mouse	[37]
	P07151	Rno	R. norvegicus	Rat	[38]
	Q8CIQ3	Shi	S. hispidus	Hispid pocket mouse	Unpublished data
	Q9WV24	Cgr	C. griseus	Chinese hamster	[39]
	P01886	Cpo	C. porcellus	Domestic guinea pig	[40]
Primates	P55079	Soe	S. oedipus	Cotton-top tamarin	[41]
	Q9TSX4	Sfu	S. fuscicollis	Brown-headed tamarin	[41]
	O77517	Smn	S. niger	Black-handed tamarin	[41]
	O77518	Sim	S. imperator	Tamarin	[41]
	P63068	Sbb	S. bicolor	Pied bare-faced tamarin	[42]
	O77531	Pir	P. irrorata	Bald-faced saki	[41]
	Q6PZD3	Cae	C.aethiops	African green monkey	[43]
	O77529	Cho	C. hoffmannsi	Hoffmanns's titi	[41]
	O77532	Csa	C. satanas	Black-bearded saki	[41]
	Q71UN5	Cpe	C. penicillata	Black pencilled marmoset	[42]
	O77533	Cme	C. melanocephalus	Black headed Uacari	[42]
	O77519	Lch	L. chrysopygus	Golden-rumped lion tamarin	[42]
	O77535	Cpy	C. pygmaea	Pygmy marmoset	[42]
	O77530	Cto	C. torquatus	Yellow-handed titi	[42]
	O77526	Cpp	C. personatus	Masked titi	[42]
	O77528	Cpn	C. p. nigrifrons	Black titi	[42]
	O77521	Cem	C. emiliae	Emilia's marmoset	[42]
	O77536	Apa	A. paniscus	Black spider monkey	[42]
	O77534	Sbo	S. boliviensis	Bolivian squirrel monkey	[42]
	O77525	Lla	L. lagotricha	Brown woolly monkey	[42]
	O77523	Ase	A. seniculus	Howler monkey	[42]
	O77520	Cgo	C. goeldii	Goeldi's marmoset	[42]
	P63063	Ale	A. lemurinus	Lemurine night monkey	[42]
	O77537	Aaz	A. azarai	Azara's night monkey	[42]
	Q6T672	Pan	P. anubis	Olive baboon	Unpublished data
	Q8SPW0	Mfa	M. fascicularis	Crab-eating macaque	Unpublished data
	P61769	Has	H. sapiens	Human	[44]
Others	Q07717	Ssc	S. scrofa	Pig	[45]
	P01885	Ocu	O. cuniculus	Rabbit	[46]
	Q5MGS7	Fca	F. catus	Domestic cat	Unpublished data

The 55 protein sequences used in this study were retrieved from the Swiss-Prot and Refseq databases. Protein ID shows the accession number of the sequence in the database while Protein Name is the protein name designated in this study. Equine, Rodents, Ruminants, Primates and Others are largely grouped as Eutheria.

Sequence Alignment

Alignment of the IGc1 domains of β₂M from L. calcarifer and other species showed a high degree of overall conservation across taxa (see Figure 1). The IGc1 domain of L. calcarifer starts with a Ser residue, which is conserved among the taxa, with the exception of domains from the Japanese flounder (Q8AYH8), Chinese hamster (Q9WV24), hispid pocket mouse (Q8CIQ3) and Australian echidna (Q864T6), in which the starting residue is a Thr. The fish sequences, with the exception of Siberian sturgeon (Q9PRF8), are two residues shorter (lacking residue-75 and residue-76) than the human (P61769) sequence. The deletions in the teleost sequences are located in the loop between the anti-parallel beta-strands S6 and S7 [18]. Seven positions or residues, Asn₁₁, Cys₁₅, Pro₂₂, Asp₄₄, Phe₄₇, Cys₇₀ and Val₇₂ (numbering refers to the position in the MSA) are found to be completely conserved. These residues or regions are believed to be in the active or binding site of the β₂M protein. A previous study reported that the two cysteine residues (Cys₁₅ and Cys₇₀), which covalently link to form a disulfide bridge (thus connecting the two β sheets), are important elements in protein folding that contribute to stabilization of the MHC class I molecule [1].

Figure 1. Multiple sequence alignment of IGc1 domains.

The alignment consists of IGc1 domain sequences from organisms of various taxa such as Eutheria, Marsupials, Monotremes, Avians, Chondrichthyes fish and Actinopterygii fishes. Lca is the L. calcarifer protein sequence and the conserved residues are marked by (*). S1, S2, S3, S4, S5, S6 and S7 indicate the regions of seven β strands in the IGc1 domain. Numbers at the top indicate amino acid positions. Information on the sequences is given in Table 1.

Phylogenetic Analysis

The phylogenetic tree built is an unrooted tree (see Figure 2) with two distinct clades, the mammalian β₂M and fish β₂M. The avian, marsupial and monotreme sequences form an intermediate group between the fish and the mammalian clades. All fish sequences are from the Actinopterygii class with the exception of the clearnose skate (Q8AXA0) [19], which is a cartilaginous fish (class Chondrichthyes). In order to clarify the relationships among the β₂M molecules of the Actinopterygii fish (Siberian sturgeon, channel catfish (O42197), Japanese medaka (Q90ZJ6), Japanese flounder, zebrafish (Q04475, NP_998291), common carp (Q03422) and Lake Tana barbel (P55076)), an NJ tree consisting of fish sequences only was constructed using the chicken (P21611) β₂M sequence as an outgroup (see Figure 3). The β₂M from L. calcarifer, which is a euryhaline and catadromous species, clustered together with Japanese medaka β₂M, forming a separate clade from the freshwater fishes (common carp, Lake Tana barbel, zebrafish and channel catfish). The phylogenetic trees also reveal a molecular signal of the ecological distinction between marine and freshwater fish. The Siberian sturgeon β₂M sequence is the most basal lineage, which is placed outside the main cluster of teleosts in the tree (see Figure 3).

Figure 2. NJ phylogenetic tree of β₂M protein sequences representing whole organisms.

The phylogenetic tree shown is the collapsed tree of 55 sets of sequence data. This tree shows that β₂M sequences are clustered together according to their taxons. β₂M sequences from Eutheria are clustered together and consist of sequences from Primates, Equine, Rodents, Ruminants, SscQ07717, OcuP01885 and FcaQ5MGS7. Marsupials, Monotremes and Avians are the intermediate taxons between Eutheria and Fish. Amphibian Xla protein Q9IA97 is clustered together with Actinopterygii fishes while the outgroup in this tree is a cartilaginous fish Reg Q8AXA0. The divergence of fish and mammalian β₂M received a high bootstrap value (89) to support the reliability of this phylogenetic tree.

Figure 3. NJ phylogenetic tree of IGc1 domains present in β₂M protein sequences from fish.

The phylogenetic tree shows that fish β₂M proteins are clustered according to the fish's ecological habitat, which may be fresh water, euryhaline or marine. The chicken sequence was used as the outgroup. Information on the sequences is given in Table 1.

Discussion

Our analysis of the novel L. calcarifer β₂M gene recovered in this study indicates that, overall, fish β₂M sequences have high sequence similarity and share many conserved features with published sequences from mammals and birds. Using β₂M as both a phylogenetic marker and a source of information, we confirmed previous studies indicating that the β₂M proteins of mammals and fish represent clearly distinct evolutionary paths, with fish β₂M genes more closely related to avian sequences than to those of mammals [7], [8]. The divergence between fish and mammals is partially a consequence of several unreversed changes in the ORF. For example, at site-14 (S2) in all mammalian β₂M sequences, the residue is Arg, whereas in Actinopteygii fish β₂M sequences it is Ile. The Ser residue in mammalian sequences is substituted by Ala at site-45 (S4) in all Actinopterygii fish, whereas Lys at position 55 (S5) in mammalian β₂M is consistently replaced by Thr in all Actinopterygii fish. Although these changes of amino acids are located within the mature protein region, the residues at those sites are not involved in any important stabilizing interactions of the protein [20].

Our analyses of the Actinopterygii fish β₂M sequences employed sequences representing two subclasses: Neopterygii (teleosts) and Chondrostei. Within the Neopterygii, two superorders are evident: Ostariophsi and Acanthopterygii. The molecular results showed phylogenetic relationships that support those established based on fish morphology [21]. Ostariophsi includes two different orders (Cypriniformes and Siluriformes), whereas Acanthopterygii includes three different fish orders (Beloniformes, Perciformes and Pleuronectiformes). With the exception of Siberian sturgeon, our results also showed that fishes included in Ostariophsi are mainly freshwater fishes, whereas those of Acanthopterygii are marine or euryhaline fishes (see Figure 3). The results reconfirm a previous paper that indicated an evolutionary divergence had occurred between freshwater and marine or euryhaline fish β₂M sequences [8]. At the molecular level among the Actinopterygii fishes studied, Asian seabass, Japanese medaka and Japanese flounder sequences share synapomorphic amino acids at three sites: Thr_73, (S6) Gly₇₈ (loop between S6 and S7) and Asp₈₂ (S7). Siberian sturgeon (Chondrost) resolves as the most basal lineage in agreement with other studies [21], [18], confirming this fish is the most primitive member of the subclass Actinopterygii. Indeed, a two-codon (residues 75 and 76 in the alignment) deletion is synapomorphic in all teleost β₂M sequences in contrast to Siberian sturgeon β₂M.

Given the preponderance of analytical results and qualitative comparative results, we suggest that the L. calcarifer β₂M gene recovered here is likely to function similarly to previously characterized β₂M genes, and that the protein it encodes acts as a light chain that binds non-covalently to the heavy chain of the MHC class I molecule. The two proteins would then create a complex with the antigen peptide and present the antigen to T cells to be destroyed by the immune mechanism [22]. β₂M is also involved in stabilizing the MHC class I molecules [23], [24]. Since β₂M is clearly most closely related to the IGc1-type domains of MHC class I and II, its gene must have been linked to that of the MHC at some point of evolution [7]. Furthermore, the similarity between the structures of β₂M and the IGc1-type domains of MHC I and II suggests that they share a common ancestor encoded in MHC genes [25]. In this study, we have identified the β₂M gene in L. calcarifer and confirm its phylogenetic placement within a group of related fish species. We believe that, as more fish β₂M sequences become available, reanalysis of the data may be able to better resolve the evolutionary history of the seeming ecological divergence detected among fish sequences and that of the L. calcarifer β₂M gene from the rest of the β₂M gene tree. Again, the overall utility of our approach in the detection, recovery and delineation of genes within L. calcarifer is emphasized by its success in our study of β₂M.