BACKGROUND
in recent years, a family of molecules with roles in apoptosis and immune regulation has been discovered in mammalian genomes.
this gene family, is known under several pseudonyms, including the caterpiller , nacht, nod-lrr or nod-like receptor  family and is comprised of two major subfamilies of nod and nalp molecules, along with  <dig> divergent members; ipaf, the mhc class ii transactivator  and neuronal apoptosis inhibitory protein   <cit> .
official names have been recently assigned to many members of this family by the hugo gene nomenclature committee   <cit>  using the nlr prefix .
nlrs are recognized by the presence of three specific domains; an effector domain at the n-terminus that is involved in protein:protein interactions, a central nacht  domain and a c-terminal leucine-rich repeat  domain.
they are, therefore, structurally similar to disease resistance  proteins found in plants that are well known for their anti-microbial activities  <cit> .
in humans,  <dig> nlrs have been described including  <dig> nalps, with a pyrin effector domain, and  <dig> nods whose effector domain is typically a caspase recruitment domain .
the functions of the nlrs are presently not well defined.
however, based on their structural characteristics, these molecules are thought to be expressed in the cytosol of immune-related cells, and have been implicated in autoimmune diseases and responses to bacterial  <cit>  or viral molecules  <cit>  supporting their importance in host immunity.
some of these molecules activate caspase- <dig>  <cit> , while others initiate  <cit>  or inhibit nf-κb signaling  <cit> .
these two molecular pathways are fundamental to a molecular platform known as the inflammasome  <cit> , which coordinates the production and processing of important inflammatory cytokines such as interleukin - <dig>  il- <dig> and il- <dig> in mammals.
proteins that assemble in this caspase- <dig> inflammasome vary according to the cell type and stimulus  <cit> .
other molecules  that are necessary for inflammasome function are thought to be generated or recruited as a result of cross-talk between nlr and toll-like receptor  signaling  <cit> .
according to current hypotheses, the activation of nlrs occurs following recognition of specific ligands by their lrr domains similar to the way that tlrs recognize molecules from extracellular pathogens.
nlr proteins are, therefore, believed to represent cytosolic pattern recognition receptors  that use lrr regions to detect intracellular pathogens.
those nlrs that are better defined functionally include nod <dig>  nod <dig>  and nalp <dig>  nod <dig> and nod <dig>  have both been shown to play a role in immunity of the mammalian gut and are highly expressed in epithelial cells or macrophages associated with the intestine.
nod <dig> recognizes a molecule known as meso-dap , which is a peptidoglycan  component found in gram-negative and gram-positive bacteria  <cit> , while nod <dig> recognizes muramyl dipeptide, a peptidoglycan component found only in gram-positive bacteria  <cit> .
nalp <dig>  has been shown to recognize a wide range of molecules, including bacterial rna and synthetic viral rna/dna mimics   <cit> .
nalp <dig> becomes activated in tlr-primed macrophages in response to atp  and bacterial toxins that lower cytoplasmic k+  <cit> , which is thought to be the major mechanism in the nalp <dig> response to certain gram-positive bacteria.
in a distinct pathway, monosodium urate and calcium pyrophosphate dihydrate crystals have been shown to increase caspase- <dig> activity in a nalp3-dependent  manner  <cit> , representing potential 'danger signal' ligands for nalp <dig>  <cit>  and defining a further role for nlrs in recognizing cellular stress.
members of the nlr family have not been extensively studied in taxa other than mammals, although recent reports indicate some members of this family exist in lower vertebrates  <cit>  and in invertebrates  <cit> .
extending the knowledge of nlrs in ectotherms, this study reports an extensive overview of the nlr family in teleost fish, represented using information derived from the zebrafish danio rerio.
here, we describe the gene phylogeny and expression of three major subfamilies of nlrs in teleostei, which we designate nlr-a and nlr-b  and nlr-c, a large subfamily  that appears in all teleostei genomes, and is unique to bony fish.
the implications of all three subfamilies in immune regulation of fish are discussed.
RESULTS
many nlr-like sequences were identified in the genome and est databases of non-mammalian vertebrates.
these genes were compared by phylogenetic analysis of their deduced nacht domains .
mammalian nlrs are categorized into nod and nalp families according to previous publications  <cit>  and as depicted in table  <dig>  in the zebrafish genome, three distinct subfamilies were identified and highly supported by bootstrap analysis; some resembled mammalian nods , some resembled mammalian nalps  and some formed a unique clade, closely related to nod <dig>  which was restricted to teleostei .
a c = card, n = nacht, l = lrr, x = unknown effector domain.
b two copies of nlr-a <dig> situated at  <dig>  and  <dig>  m on chromosome  <dig> are 100% identical and likely represent errors in the assembly of this chromosome.
c nlr-a <dig> is also encoded within genscan prediction genscan <dig>
a c = card, n = nacht
a p = pyrin, n = nacht, l = lrr, x = unknown effector domain
subfamily a
teleost fish possess gene orthologs for all five members of the mammalian nod subfamily .
while chicken and xenopus genomes apparently lack the nod <dig> gene , both are in possession of the remaining four nods.
the gene predictions for zebrafish nod sequences were corrected using corresponding ests identified in the tigr database, and missing sequence found with assistance from other fish nod-like sequences using the blat  program.
following assembly, zebrafish nods were highly structurally conserved relative to human nods.
zebrafish nod <dig>  has an n-terminal card domain, and nine highly conserved leucine-rich repeats   although the 5' and 3' exons were not identified.
two card domains were identified at the n-terminal end of zebrafish nod <dig> , and eight lrr domains were recognizable by their lrr-like motifs  that align exactly with the lrrs of human nod <dig> .
although the n-terminal end of nod <dig>  was not recognized by the cdd, it shares some similarity with the human nod <dig> effector domain with two conserved sequence signatures, mrk and eag .
the c-terminal end of nlr-a <dig> possessed  <dig> lrr motifs, which aligned exactly with lrr domains of human nod <dig> , with a similar motif  between the nacht domain and the first true lrr motif.
both nod <dig>  and nod <dig>  orthologs in zebrafish have conserved sequences within their lrr domains relative to their human equivalents, although the predicted lrr for zebrafish nlr-a <dig> is shorter than that of human nod <dig>  and less conserved relative other human and zebrafish nlr-a orthologs.
the n-terminal domains for nlr-a <dig> and nlr-a <dig>  as with nlr-a <dig>  were not identified within the cdd database set, but share some conserved features with the corresponding regions of mammalian nod <dig> and nod <dig>  nlr-a4/nod <dig> appears to represent the most divergent gene within the nlr-a subfamily, yet zebrafish nlr-a <dig> groups with high bootstrap support with human nod <dig> and its orthologs from chicken and xenopus during phylogenetic comparisons .
all five nlr-as are located on distinct chromosomes in zebrafish.
the nlr-a <dig> gene is located on chromosome  <dig> in version  <dig> of the zebrafish genome  , but is not mapped to a chromosome in version  <dig>  , nlr-a <dig> resides at chromosome  <dig> and nlr-a <dig>  nlr-a <dig> and nlr-a <dig> can be found on chromosomes  <dig>   <dig> and  <dig> respectively.
a identified using the conserved domain database,
b based on similarity to human ortholog,
c xenopus gene prediction scaffold_ <dig>  contains nacht domains from multiple nlrs.
subfamily b
six distinct genes encoding nacht domains were identified in zv <dig> that belong to subfamily b and form a separate cluster within the clade of mammalian nalps.
although zebrafish nlr-b <dig> and b <dig> were identified in distinct regions of the zebrafish genome  these genes are identical in the region of the nacht domain used for phylogenetic analysis.
several nalp-like sequences were also identified for xenopus tropicalis  that similarly formed their own cluster distinct from the human and zebrafish nalps .
gene predictions encoding putative nalps in zebrafish are short, with most lacking a recognizable effector domain and c-terminal lrr domain.
one exception is nlr-b <dig>  which appears to have an n-terminal region with low similarity to a card motif as identified by searching the cdd.
only one cdna sequence resembling this subfamily could be identified in the zebrafish est database  that, although highly similar in sequence, was not an exact match to any of the predicted nlr-b genes and appeared to encode only a portion of the nacht domain.
nlr subfamily b genes appear to be restricted to small clusters on chromosomes  <dig> and  <dig> in zebrafish.
furthermore, nlr-b <dig> and nlr-b <dig> reside close  to nlr-a <dig>  on chromosome  <dig>  later analysis of zv <dig> revealed removal of the nlr-b <dig> gene prediction, and its merger with the prediction for nlr-b <dig> .
subfamily c
database searches revealed multiple genes that possessed nacht domains and shared significant homology to human nod <dig> yet were distinct from the zebrafish nod <dig> molecule  described above.
this large number of highly similar genes clearly arose from several gene duplication events.
several hundred predicted genes/proteins were observed for this group in the databases for all teleost fish .
in zebrafish, these genes were found at numerous chromosomal loci, with large clusters evident on  chromosomes  <dig>   <dig>   <dig> and  <dig>  a small selection of these genes was subjected to further analysis .
these molecules divided into three clusters during phylogenetic analysis, which also corresponded to sequence differences identified in the n-terminal region.
representatives from chromosome  <dig> were identified in all three clusters, while nlrs from some other chromosomes  were restricted to one cluster, although not all genes were included in the analysis.
although the nacht domains of the c-group nlrs are clearly homologous to nod <dig>  many of these genes were found to encode a conserved pyrin domain at the n-terminus  showing some analogy to mammalian nalp genes.
the presence of this domain was confirmed by identifying an est sequence containing the pyrin domain and a partial nacht domain that resembled c-group nlrs.
other c-group nlrs had n-terminal sequences with no obvious gene ortholog.
while some are likely incorrectly predicted domains, est sequences confirm at least two of these predicted n-termini are transcribed in association with the nlr c-group nacht domain .
the nlr c-group molecules also possess an lrr region, as with other nlrs.
unexpectedly, a b <dig>   domain was identified in several of the predicted genes for nlrs of the c subfamily.
owing to nature of this large multigene family, a single representative est was sequenced to confirm domain structure, including the verification of the b <dig>  domain.
the b <dig> .
this domain was found at the c-terminus, following the lrr domain and was confirmed by completely sequencing est ; the  <dig>  bp sequence was submitted to genbank  and contained sequence from the nacht domain to the poly-a tail.
further overlapping ests/tcs identified in the tigr database provided additional confirmation for the nlr c-group, with an effector  domain, nacht domain, lrr domain and a c-terminal b <dig>  domain   although, due to the high number of closely related sequences for this subfamily and the current stage of the zebrafish genome sequence, it was not possible to ascertain whether the overlapping ests were generated from the same gene or distinct genes within the nlr-c family.
other nlrs
although the ciita was evident in the genomes of the pufferfishes, frog and chicken, this molecule was not readily identifiable in zebrafish zv <dig>  however, later analyses identified a ciita-like gene, in zv <dig> of the zebrafish genome, which resides on chromosome  <dig> at approximate position  <dig>  m .
sequences for naip were not identified in lower vertebrates during this study.
ipaf was identified in the frog genome , but not in the other non-mammalian genomes.
a recently described family of nlr-like genes from the sea urchin was found to cluster with mammalian ipaf and naip molecules during phylogenetic analyses .
expression of zebrafish nlrs
the spatial expression of nlr genes was evaluated in selected tissues from naïve zebrafish.
nlr-a <dig>  -a <dig>  -a <dig> -a <dig> and -a <dig> were all identified in zebrafish intestine using rt-pcr.
all five genes were also expressed in liver although expression of nlr-a <dig> was extremely weak.
nlr-a <dig> expression was not detected in the spleen following  <dig> pcr cycles, but the four other nlr-a genes were expressed in this tissue .
as a representative of the nlr-b subfamily, nlr-b <dig> expression was investigated and detected in all three tissues.
similarly, mrna was detected for an nlr-c gene in all three tissues using primers based on the completely sequenced est clone.
the primers used to detect these genes amplified no products in control reactions whose templates were sterile water  or from cdna syntheses performed in the absence of reverse transcriptase .
arp was amplified from all tissues confirming the integrity of the cdnas and the success of rt-pcr.
genomic products were amplified for all nlr-a genes that were larger than the cdna amplicons and supported the presence of intron between the primer regions.
discussion
new insight into the regulation of essential developmental, inflammatory and apoptotic pathways was achieved with the discovery and characterization of the nlr gene family of putative cytoplasmic pattern recognition molecules.
while an increasing amount of information exists for these molecules in mammals, this gene family is poorly studied in other vertebrates with little to no information available even at the gene level for birds, amphibians and fish.
this study resolves this issue by identifying and characterizing many nlr-like genes from these three classes of animals and uncovering a unique subfamily of nlrs in teleost fish.
our evidence shows early evolution and high conservation of the nod  subfamily of nlrs.
all species of teleost fish that were analyzed had five distinct members of this subfamily designated nlr-a <dig>  nlr-a <dig>  nlr-a <dig>  nlr-a <dig> and nlr-a <dig> that were clear gene orthologs of human nod <dig> to nod <dig>  <cit> .
a nod <dig> ortholog was also described during an earlier screen of zebrafish ests for molecules similar to apoptosis regulators  <cit> .
in addition to encoded nacht domains, the effector domains and lrr regions were highly conserved in the fish nlr-a genes relative to their human equivalents, suggesting retained function.
nlr-a <dig> and nlr-a <dig>  the fish orthologs of human nod <dig> and nod <dig> respectively, both possessed clear card domains  with high amino acid identity to the equivalent regions of human molecules.
in mammalian nod <dig> , the card domains are necessary for the interaction with rick kinase, an enzyme that participates in nfκb activation and, ultimately, the generation of pro-inflammatory molecules  <cit> .
since rick is also present in fish genomes , it would appear that this inflammatory cascade was established prior to the divergence of teleost fish from the tetrapod lineage, assuming that the same interaction occurs between these molecules in fish.
the highly conserved sequences in the lrr domains implies these zebrafish nlr-a <dig> and nlr-a <dig> may also be able to recognize meso-dap and muramyl dipeptide as mammalian nod <dig> and nod <dig> respectively  <cit>  although this requires formal confirmation.
nlr-a <dig> transcript was detected equally in intestine, liver and spleen, reflecting the wide-spread distribution observed for murine nod <dig>  <cit> , while nlr-a <dig> was strongly expressed in intestine, with some expression in spleen and barely detectable levels in liver.
similar to the highest expression of nlr-a <dig> in zebrafish intestine, human nod <dig> has a more restricted expression pattern, with predominant expression in cells of myeloid origin including monocytes  <cit>  and paneth cells  <cit>  that are associated with the gut, although expression of nod <dig> can also be induced in epithelial cells  <cit> .
zebrafish nlr-a <dig> is clearly an ortholog of mammalian nod <dig>  with similarity in the effector and nacht domains and an equal number of lrr domains.
at the genomic level, nod <dig> is flanked by rhot <dig>  sbk <dig> and pdpk <dig>  gnptg respectively in zebrafish and fugu further supporting the orthologous relationship for nod <dig> between fish species.
expression of nlr-a <dig> was strong in zebrafish intestine, with some expression also in liver and little to no expression observed in the spleen.
interestingly, the kidney  did not express nlr-a <dig> as well suggesting that it is not expressed by lymphocytes .
in mammals, nod <dig> expression occurs primarily in lymphocytes and is attributed to inhibition of t-cell activity  <cit> .
two other nlr-a subfamily members were also identified in zebrafish that were designated nlr-a <dig> and nlr-a <dig> with nlr-a <dig> resembling human nod <dig> and nlr-a <dig> being highly conserved to human nod <dig>  nlr-a4/nod <dig> genes represent the most divergent members of this subfamily based on amino acid conservation within the n-terminal and lrr regions between different vertebrate orthologs.
both nlr-a <dig> and nlr-a <dig> genes were constitutively expressed in intestine, spleen and liver of naïve zebrafish, although there is clearly some fish to fish variation preventing their detection in some individuals under the conditions used for rt-pcr.
currently, there is no information concerning the expression patterns or functions of these latter two nlrs in mammals.
whereas nod <dig>  nod <dig>  nod <dig> and nod <dig> appear to be conserved in bird and amphibian genomes, the gene for nod <dig> was identified in neither the chicken nor the frog genomes.
this would suggest that nod <dig> has been deleted from the genomes in these species, although the genome of xenopus tropicalis is, at present, incomplete.
this is surprising since nod <dig>  in mammals, appears to be a highly important sensor for intracellular microbial molecules.
however, chickens do possess a nalp <dig> ortholog  representing another potential prr for muramyl dipeptide  <cit>  and may functionally replace nod <dig> in this species.
members of the nalp subfamily are also evident in lower vertebrates.
six genes were identified in zebrafish  for nalp-like molecules , and ten predicted nalp-like genes  were found for xenopus.
these genes clustered separately for each species, suggesting recent duplication events formed the nalp subfamilies independently in fish, amphibians and mammals.
the closest human ortholog of the amphibian and fish nalps appears to be nalp <dig>  a single nalp-like sequence predicted in the chicken genome  and in the uniprot database  clusters closest to the group of human nalps  <dig>   <dig>   <dig>  and  <dig> when analyzed phylogenetically  and has recently been given the name nlrp <dig> .
chicken nalp was identified on chromosome  <dig>  separate to the chicken nod <dig> gene .
although sequence variation makes accurate comparisons difficult, it is likely that this chicken gene arose from a distinct nalp than the fish and amphibian nalps, with the ancestral nalp possibly lost from the genome.
the discovery of multiple nalp-like proteins in lower vertebrates contradicts a recent hypothesis by hughes suggesting that the nalp subfamily evolved only in mammals  <cit> , with clear evidence that a gene encoding the nacht domain of at least one nalp  was present prior to the fish-tetrapod split.
zebrafish nalps are situated at two distinct chromosomal locations, four of these genes  are located on chromosome  <dig>  and the other two  can be found near nlr-a <dig> on chromosome 15; the new assembly of the zebrafish genome  suggests these two sequences may represent the same gene.
it should be pointed out that although chicken nlrp <dig> has an n-terminal pyrin domain, the n-terminal domains for the xenopus and zebrafish nalps were not identified.
one exception was nlr-b <dig>  which appears to have a domain that resembles a card and not a pyrin domain as would be expected from its similarity to the mammalian nalps.
no pyrin domains are observed for the xenopus nalp-like sequences and, other than the py-card protein , no pyrin domains were predicted in the xenopus genome.
these observations may reflect that early ancestors of nalps lacked these effector domains and later acquired the pyrin domain .
whether these nalp-like genes encode functional prrs in poikilotherms remains uncertain, however, nlr-b <dig> transcript was detectable in zebrafish intestine, spleen and liver suggesting this may represent a functional gene.
in addition to the nod- and nalp-like subfamilies, a unique subfamily of nlrs was identified in teleost fish, and designated nlr subfamily c .
this subfamily is interesting for several reasons.
firstly, all teleostei genome  databases show numerous nlr-c genes, amounting to several hundred of these genes in a single species.
secondly, these genes all possess a central nacht domain that is highly similar to the nacht domain of nod <dig>  suggesting they evolved from a nlr-a3-like molecule, yet many of these genes possess a pyrin domain at their n-terminus making them more structurally similar to mammalian nalp molecules.
finally, following the lrr domain many of these molecules  possess a b <dig>   domain, which may allow them to interact with distinct molecules to standard nlrs and thus perform some novel function.
b <dig>  domains are also found on some tripartite motif containing  proteins  <cit>  and on the pyrin molecule  <cit>   and have several roles related to immunity.
trim5a has been shown to inhibit retroviral activity by directly binding the capsid of the hiv retrovirus  <cit> , and pyrin has been shown to inhibit the activity of caspase- <dig> by directly binding to the active site of this enzyme  <cit> , both using their b <dig>  domains for these interactions.
each of these functions would fit with the role of nlrs as intracellular prrs; the ability to bind viruses could be an extension of the pattern detection system attributed to the neighboring lrr domain, while the potential to inhibit caspase- <dig> activity may make nlr-c molecules important negative regulators of the inflammasome in teleost fish.
the latter function would reflect gene families of cell surface receptors such as killer immunoglobulin-like receptors   <cit>  or novel immune-type receptors   <cit>  that possess many inhibitory receptors and a small number of stimulatory receptors for controlling cellular activation.
it is also interesting that these molecules all contain a nacht domain similar to nod <dig>  since mammalian nod <dig> has an inhibitory role in t cells  <cit> .
importantly, since the predicted n- and c-termini of some nlr-cs are structurally similar to the two domains of the pyrin molecule, this would also fit with a potential function of mimicking pyrin.
however, additional studies are required to determine what, if any, role in the immune system nlr-c molecules may play.
the evolutionary processes generating the vast subfamily of nlr-c genes are not clear and appear very complex.
the relationships are further confused by apparent errors in the assembly of the zebrafish genome , as evidenced by clear differences in the mapping of some nlr-c genes to their predicted chromosomes between assembly versions .
however, evidence suggesting tandem duplications of individual genes within a chromosomal locus is consistent between zv <dig> and zv <dig>  which result in nlr-c genes adopting new exons encoding distinct n-terminal domains and/or c-terminal domains via exon-shuffling.
the clusters of tandem nlr-c genes appear to have undergone en bloc duplication, to generate further clusters in the same locus , or within distinct loci or chromosomes  through translocation.
single genes may also have duplicated independently multiple times, within established loci and to create new loci, prior to and following formation of new gene structures.
a large scale duplication of this gene family may be explained by the teleost-specific genome duplication event  occurring early in the evolution of teleost fish, which followed two rounds of complete genome duplication  observed early in the evolution of the vertebrate lineage  <cit> .
should this be the case, mutations and deletions of many of the duplicated genes would be expected, to remove redundancy from the genome  <cit> .
therefore, many nlr-c genes may be non-functional genes or pseudogenes, although a small number have likely established new functions.
clearly, it is too early to assign functionality to these genes, except to note that many are transcribed and are presumably translated into protein products.
transcripts for nlr-c were detected, in this study, in three distinct tissues in naïve zebrafish, and many more can be identified in the est databases for this fish species.
a ciita-like gene was identified in the zebrafish genome  and is an important molecule, in mammals, for controlling the expression of both major histocompatibility complex class i and class ii molecules and therefore is significant for antigen presentation to t lymphocytes.
defects in human ciita gene expression have been linked to several immune disorders  <cit> .
however, alternative molecules have been implicated in the induction of antigen presentation pathways  <cit> , including other members of the nlr family, such as nalp <dig>  <cit> .
naip/ipaf homologs have been identified in the sea urchin  <cit>  implying that the ancestral nlr resembled one of these molecules.
however, neither naip nor ipaf was identified in the fish genomes at this time, although ipaf was evident in the frog genome, suggesting that the genes for these molecules may have been lost from the fish genomes during the teleost-specific genome duplication event.
CONCLUSIONS
in summary, the nlr gene family contains several members in all vertebrates, and at least one prototypical gene must have existed prior to the evolution of vertebrates.
clearly, there are some losses and gains of nlr genes in the genomes of distinct species thus shaping unique repertoires of these molecules throughout vertebrates and invertebrates.
although there are still many members of the nlr family that require functional characterization, their implication as regulators of immunity is highly intriguing and warrants future investigation.

 in recent years, a family of molecules with roles in apoptosis and immune regulation has been discovered in mammalian genomes. this gene family, is known under several pseudonyms, including the caterpiller, nacht, nod-lrr or nod-like receptor family and is comprised of two major subfamilies of nod and nalp molecules, along with divergent members; ipaf, the mhc class ii transactivator and neuronal apoptosis inhibitory protein. official names have been recently assigned to many members of this family by the hugo gene nomenclature committee using the nlr prefix. nlrs are recognized by the presence of three specific domains; an effector domain at the n-terminus that is involved in protein:protein interactions, a central nacht domain and a c-terminal leucine-rich repeat domain. they are, therefore, structurally similar to disease resistance proteins found in plants that are well known for their anti-microbial activities. in humans, nlrs have been described including nalps, with a pyrin effector domain, and nods whose effector domain is typically a caspase recruitment domain. the functions of the nlrs are presently not well defined. however, based on their structural characteristics, these molecules are thought to be expressed in the cytosol of immune-related cells, and have been implicated in autoimmune diseases and responses to bacterial or viral molecules supporting their importance in host immunity. some of these molecules activate caspase-, while others initiate or inhibit nf-κb signaling. these two molecular pathways are fundamental to a molecular platform known as the inflammasome, which coordinates the production and processing of important inflammatory cytokines such as interleukin - il- and il- in mammals. proteins that assemble in this caspase- inflammasome vary according to the cell type and stimulus. other molecules that are necessary for inflammasome function are thought to be generated or recruited as a result of cross-talk between nlr and toll-like receptor signaling. according to current hypotheses, the activation of nlrs occurs following recognition of specific ligands by their lrr domains similar to the way that tlrs recognize molecules from extracellular pathogens. nlr proteins are, therefore, believed to represent cytosolic pattern recognition receptors that use lrr regions to detect intracellular pathogens. those nlrs that are better defined functionally include nod nod and nalp nod and nod have both been shown to play a role in immunity of the mammalian gut and are highly expressed in epithelial cells or macrophages associated with the intestine. nod recognizes a molecule known as meso-dap, which is a peptidoglycan component found in gram-negative and gram-positive bacteria, while nod recognizes muramyl dipeptide, a peptidoglycan component found only in gram-positive bacteria. nalp has been shown to recognize a wide range of molecules, including bacterial rna and synthetic viral rna/dna mimics. nalp becomes activated in tlr-primed macrophages in response to atp and bacterial toxins that lower cytoplasmic k+, which is thought to be the major mechanism in the nalp response to certain gram-positive bacteria. in a distinct pathway, monosodium urate and calcium pyrophosphate dihydrate crystals have been shown to increase caspase- activity in a nalp3-dependent manner, representing potential'danger signal' ligands for nalp and defining a further role for nlrs in recognizing cellular stress. members of the nlr family have not been extensively studied in taxa other than mammals, although recent reports indicate some members of this family exist in lower vertebrates and in invertebrates. extending the knowledge of nlrs in ectotherms, this study reports an extensive overview of the nlr family in teleost fish, represented using information derived from the zebrafish danio rerio. here, we describe the gene phylogeny and expression of three major subfamilies of nlrs in teleostei, which we designate nlr-a and nlr-b and nlr-c, a large subfamily that appears in all teleostei genomes, and is unique to bony fish. the implications of all three subfamilies in immune regulation of fish are discussed.  many nlr-like sequences were identified in the genome and est databases of non-mammalian vertebrates. these genes were compared by phylogenetic analysis of their deduced nacht domains. mammalian nlrs are categorized into nod and nalp families according to previous publications and as depicted in table in the zebrafish genome, three distinct subfamilies were identified and highly supported by bootstrap analysis; some resembled mammalian nods, some resembled mammalian nalps and some formed a unique clade, closely related to nod which was restricted to teleostei. a c = card, n = nacht, l = lrr, x = unknown effector domain. b two copies of nlr-a situated at and m on chromosome are 100% identical and likely represent errors in the assembly of this chromosome. c nlr-a is also encoded within genscan prediction genscan a c = card, n = nacht a p = pyrin, n = nacht, l = lrr, x = unknown effector domain subfamily a teleost fish possess gene orthologs for all five members of the mammalian nod subfamily. while chicken and xenopus genomes apparently lack the nod gene, both are in possession of the remaining four nods. the gene predictions for zebrafish nod sequences were corrected using corresponding ests identified in the tigr database, and missing sequence found with assistance from other fish nod-like sequences using the blat program. following assembly, zebrafish nods were highly structurally conserved relative to human nods. zebrafish nod has an n-terminal card domain, and nine highly conserved leucine-rich repeats although the 5' and 3' exons were not identified. two card domains were identified at the n-terminal end of zebrafish nod, and eight lrr domains were recognizable by their lrr-like motifs that align exactly with the lrrs of human nod. although the n-terminal end of nod was not recognized by the cdd, it shares some similarity with the human nod effector domain with two conserved sequence signatures, mrk and eag. the c-terminal end of nlr-a possessed lrr motifs, which aligned exactly with lrr domains of human nod, with a similar motif between the nacht domain and the first true lrr motif. both nod and nod orthologs in zebrafish have conserved sequences within their lrr domains relative to their human equivalents, although the predicted lrr for zebrafish nlr-a is shorter than that of human nod and less conserved relative other human and zebrafish nlr-a orthologs. the n-terminal domains for nlr-a and nlr-a as with nlr-a were not identified within the cdd database set, but share some conserved features with the corresponding regions of mammalian nod and nod nlr-a4/nod appears to represent the most divergent gene within the nlr-a subfamily, yet zebrafish nlr-a groups with high bootstrap support with human nod and its orthologs from chicken and xenopus during phylogenetic comparisons. all five nlr-as are located on distinct chromosomes in zebrafish. the nlr-a gene is located on chromosome in version of the zebrafish genome, but is not mapped to a chromosome in version, nlr-a resides at chromosome and nlr-a nlr-a and nlr-a can be found on chromosomes and respectively. a identified using the conserved domain database, b based on similarity to human ortholog, c xenopus gene prediction scaffold_ contains nacht domains from multiple nlrs. subfamily b six distinct genes encoding nacht domains were identified in zv that belong to subfamily b and form a separate cluster within the clade of mammalian nalps. although zebrafish nlr-b and b were identified in distinct regions of the zebrafish genome these genes are identical in the region of the nacht domain used for phylogenetic analysis. several nalp-like sequences were also identified for xenopus tropicalis that similarly formed their own cluster distinct from the human and zebrafish nalps. gene predictions encoding putative nalps in zebrafish are short, with most lacking a recognizable effector domain and c-terminal lrr domain. one exception is nlr-b which appears to have an n-terminal region with low similarity to a card motif as identified by searching the cdd. only one cdna sequence resembling this subfamily could be identified in the zebrafish est database that, although highly similar in sequence, was not an exact match to any of the predicted nlr-b genes and appeared to encode only a portion of the nacht domain. nlr subfamily b genes appear to be restricted to small clusters on chromosomes and in zebrafish. furthermore, nlr-b and nlr-b reside close to nlr-a on chromosome later analysis of zv revealed removal of the nlr-b gene prediction, and its merger with the prediction for nlr-b. subfamily c database searches revealed multiple genes that possessed nacht domains and shared significant homology to human nod yet were distinct from the zebrafish nod molecule described above. this large number of highly similar genes clearly arose from several gene duplication events. several hundred predicted genes/proteins were observed for this group in the databases for all teleost fish. in zebrafish, these genes were found at numerous chromosomal loci, with large clusters evident on chromosomes and a small selection of these genes was subjected to further analysis. these molecules divided into three clusters during phylogenetic analysis, which also corresponded to sequence differences identified in the n-terminal region. representatives from chromosome were identified in all three clusters, while nlrs from some other chromosomes were restricted to one cluster, although not all genes were included in the analysis. although the nacht domains of the c-group nlrs are clearly homologous to nod many of these genes were found to encode a conserved pyrin domain at the n-terminus showing some analogy to mammalian nalp genes. the presence of this domain was confirmed by identifying an est sequence containing the pyrin domain and a partial nacht domain that resembled c-group nlrs. other c-group nlrs had n-terminal sequences with no obvious gene ortholog. while some are likely incorrectly predicted domains, est sequences confirm at least two of these predicted n-termini are transcribed in association with the nlr c-group nacht domain. the nlr c-group molecules also possess an lrr region, as with other nlrs. unexpectedly, a b domain was identified in several of the predicted genes for nlrs of the c subfamily. owing to nature of this large multigene family, a single representative est was sequenced to confirm domain structure, including the verification of the b domain. the b. this domain was found at the c-terminus, following the lrr domain and was confirmed by completely sequencing est; the bp sequence was submitted to genbank and contained sequence from the nacht domain to the poly-a tail. further overlapping ests/tcs identified in the tigr database provided additional confirmation for the nlr c-group, with an effector domain, nacht domain, lrr domain and a c-terminal b domain although, due to the high number of closely related sequences for this subfamily and the current stage of the zebrafish genome sequence, it was not possible to ascertain whether the overlapping ests were generated from the same gene or distinct genes within the nlr-c family. other nlrs although the ciita was evident in the genomes of the pufferfishes, frog and chicken, this molecule was not readily identifiable in zebrafish zv however, later analyses identified a ciita-like gene, in zv of the zebrafish genome, which resides on chromosome at approximate position m. sequences for naip were not identified in lower vertebrates during this study. ipaf was identified in the frog genome, but not in the other non-mammalian genomes. a recently described family of nlr-like genes from the sea urchin was found to cluster with mammalian ipaf and naip molecules during phylogenetic analyses. expression of zebrafish nlrs the spatial expression of nlr genes was evaluated in selected tissues from naïve zebrafish. nlr-a -a -a -a and -a were all identified in zebrafish intestine using rt-pcr. all five genes were also expressed in liver although expression of nlr-a was extremely weak. nlr-a expression was not detected in the spleen following pcr cycles, but the four other nlr-a genes were expressed in this tissue. as a representative of the nlr-b subfamily, nlr-b expression was investigated and detected in all three tissues. similarly, mrna was detected for an nlr-c gene in all three tissues using primers based on the completely sequenced est clone. the primers used to detect these genes amplified no products in control reactions whose templates were sterile water or from cdna syntheses performed in the absence of reverse transcriptase. arp was amplified from all tissues confirming the integrity of the cdnas and the success of rt-pcr. genomic products were amplified for all nlr-a genes that were larger than the cdna amplicons and supported the presence of intron between the primer regions. discussion new insight into the regulation of essential developmental, inflammatory and apoptotic pathways was achieved with the discovery and characterization of the nlr gene family of putative cytoplasmic pattern recognition molecules. while an increasing amount of information exists for these molecules in mammals, this gene family is poorly studied in other vertebrates with little to no information available even at the gene level for birds, amphibians and fish. this study resolves this issue by identifying and characterizing many nlr-like genes from these three classes of animals and uncovering a unique subfamily of nlrs in teleost fish. our evidence shows early evolution and high conservation of the nod subfamily of nlrs. all species of teleost fish that were analyzed had five distinct members of this subfamily designated nlr-a nlr-a nlr-a nlr-a and nlr-a that were clear gene orthologs of human nod to nod. a nod ortholog was also described during an earlier screen of zebrafish ests for molecules similar to apoptosis regulators. in addition to encoded nacht domains, the effector domains and lrr regions were highly conserved in the fish nlr-a genes relative to their human equivalents, suggesting retained function. nlr-a and nlr-a the fish orthologs of human nod and nod respectively, both possessed clear card domains with high amino acid identity to the equivalent regions of human molecules. in mammalian nod, the card domains are necessary for the interaction with rick kinase, an enzyme that participates in nfκb activation and, ultimately, the generation of pro-inflammatory molecules. since rick is also present in fish genomes, it would appear that this inflammatory cascade was established prior to the divergence of teleost fish from the tetrapod lineage, assuming that the same interaction occurs between these molecules in fish. the highly conserved sequences in the lrr domains implies these zebrafish nlr-a and nlr-a may also be able to recognize meso-dap and muramyl dipeptide as mammalian nod and nod respectively although this requires formal confirmation. nlr-a transcript was detected equally in intestine, liver and spleen, reflecting the wide-spread distribution observed for murine nod, while nlr-a was strongly expressed in intestine, with some expression in spleen and barely detectable levels in liver. similar to the highest expression of nlr-a in zebrafish intestine, human nod has a more restricted expression pattern, with predominant expression in cells of myeloid origin including monocytes and paneth cells that are associated with the gut, although expression of nod can also be induced in epithelial cells. zebrafish nlr-a is clearly an ortholog of mammalian nod with similarity in the effector and nacht domains and an equal number of lrr domains. at the genomic level, nod is flanked by rhot sbk and pdpk gnptg respectively in zebrafish and fugu further supporting the orthologous relationship for nod between fish species. expression of nlr-a was strong in zebrafish intestine, with some expression also in liver and little to no expression observed in the spleen. interestingly, the kidney did not express nlr-a as well suggesting that it is not expressed by lymphocytes. in mammals, nod expression occurs primarily in lymphocytes and is attributed to inhibition of t-cell activity. two other nlr-a subfamily members were also identified in zebrafish that were designated nlr-a and nlr-a with nlr-a resembling human nod and nlr-a being highly conserved to human nod nlr-a4/nod genes represent the most divergent members of this subfamily based on amino acid conservation within the n-terminal and lrr regions between different vertebrate orthologs. both nlr-a and nlr-a genes were constitutively expressed in intestine, spleen and liver of naïve zebrafish, although there is clearly some fish to fish variation preventing their detection in some individuals under the conditions used for rt-pcr. currently, there is no information concerning the expression patterns or functions of these latter two nlrs in mammals. whereas nod nod nod and nod appear to be conserved in bird and amphibian genomes, the gene for nod was identified in neither the chicken nor the frog genomes. this would suggest that nod has been deleted from the genomes in these species, although the genome of xenopus tropicalis is, at present, incomplete. this is surprising since nod in mammals, appears to be a highly important sensor for intracellular microbial molecules. however, chickens do possess a nalp ortholog representing another potential prr for muramyl dipeptide and may functionally replace nod in this species. members of the nalp subfamily are also evident in lower vertebrates. six genes were identified in zebrafish for nalp-like molecules, and ten predicted nalp-like genes were found for xenopus. these genes clustered separately for each species, suggesting recent duplication events formed the nalp subfamilies independently in fish, amphibians and mammals. the closest human ortholog of the amphibian and fish nalps appears to be nalp a single nalp-like sequence predicted in the chicken genome and in the uniprot database clusters closest to the group of human nalps and when analyzed phylogenetically and has recently been given the name nlrp. chicken nalp was identified on chromosome separate to the chicken nod gene. although sequence variation makes accurate comparisons difficult, it is likely that this chicken gene arose from a distinct nalp than the fish and amphibian nalps, with the ancestral nalp possibly lost from the genome. the discovery of multiple nalp-like proteins in lower vertebrates contradicts a recent hypothesis by hughes suggesting that the nalp subfamily evolved only in mammals, with clear evidence that a gene encoding the nacht domain of at least one nalp was present prior to the fish-tetrapod split. zebrafish nalps are situated at two distinct chromosomal locations, four of these genes are located on chromosome and the other two can be found near nlr-a on chromosome 15; the new assembly of the zebrafish genome suggests these two sequences may represent the same gene. it should be pointed out that although chicken nlrp has an n-terminal pyrin domain, the n-terminal domains for the xenopus and zebrafish nalps were not identified. one exception was nlr-b which appears to have a domain that resembles a card and not a pyrin domain as would be expected from its similarity to the mammalian nalps. no pyrin domains are observed for the xenopus nalp-like sequences and, other than the py-card protein, no pyrin domains were predicted in the xenopus genome. these observations may reflect that early ancestors of nalps lacked these effector domains and later acquired the pyrin domain. whether these nalp-like genes encode functional prrs in poikilotherms remains uncertain, however, nlr-b transcript was detectable in zebrafish intestine, spleen and liver suggesting this may represent a functional gene. in addition to the nod- and nalp-like subfamilies, a unique subfamily of nlrs was identified in teleost fish, and designated nlr subfamily c. this subfamily is interesting for several reasons. firstly, all teleostei genome databases show numerous nlr-c genes, amounting to several hundred of these genes in a single species. secondly, these genes all possess a central nacht domain that is highly similar to the nacht domain of nod suggesting they evolved from a nlr-a3-like molecule, yet many of these genes possess a pyrin domain at their n-terminus making them more structurally similar to mammalian nalp molecules. finally, following the lrr domain many of these molecules possess a b domain, which may allow them to interact with distinct molecules to standard nlrs and thus perform some novel function. b domains are also found on some tripartite motif containing proteins and on the pyrin molecule and have several roles related to immunity. trim5a has been shown to inhibit retroviral activity by directly binding the capsid of the hiv retrovirus, and pyrin has been shown to inhibit the activity of caspase- by directly binding to the active site of this enzyme, both using their b domains for these interactions. each of these functions would fit with the role of nlrs as intracellular prrs; the ability to bind viruses could be an extension of the pattern detection system attributed to the neighboring lrr domain, while the potential to inhibit caspase- activity may make nlr-c molecules important negative regulators of the inflammasome in teleost fish. the latter function would reflect gene families of cell surface receptors such as killer immunoglobulin-like receptors or novel immune-type receptors that possess many inhibitory receptors and a small number of stimulatory receptors for controlling cellular activation. it is also interesting that these molecules all contain a nacht domain similar to nod since mammalian nod has an inhibitory role in t cells. importantly, since the predicted n- and c-termini of some nlr-cs are structurally similar to the two domains of the pyrin molecule, this would also fit with a potential function of mimicking pyrin. however, additional studies are required to determine what, if any, role in the immune system nlr-c molecules may play. the evolutionary processes generating the vast subfamily of nlr-c genes are not clear and appear very complex. the relationships are further confused by apparent errors in the assembly of the zebrafish genome, as evidenced by clear differences in the mapping of some nlr-c genes to their predicted chromosomes between assembly versions. however, evidence suggesting tandem duplications of individual genes within a chromosomal locus is consistent between zv and zv which result in nlr-c genes adopting new exons encoding distinct n-terminal domains and/or c-terminal domains via exon-shuffling. the clusters of tandem nlr-c genes appear to have undergone en bloc duplication, to generate further clusters in the same locus, or within distinct loci or chromosomes through translocation. single genes may also have duplicated independently multiple times, within established loci and to create new loci, prior to and following formation of new gene structures. a large scale duplication of this gene family may be explained by the teleost-specific genome duplication event occurring early in the evolution of teleost fish, which followed two rounds of complete genome duplication observed early in the evolution of the vertebrate lineage. should this be the case, mutations and deletions of many of the duplicated genes would be expected, to remove redundancy from the genome. therefore, many nlr-c genes may be non-functional genes or pseudogenes, although a small number have likely established new functions. clearly, it is too early to assign functionality to these genes, except to note that many are transcribed and are presumably translated into protein products. transcripts for nlr-c were detected, in this study, in three distinct tissues in naïve zebrafish, and many more can be identified in the est databases for this fish species. a ciita-like gene was identified in the zebrafish genome and is an important molecule, in mammals, for controlling the expression of both major histocompatibility complex class i and class ii molecules and therefore is significant for antigen presentation to t lymphocytes. defects in human ciita gene expression have been linked to several immune disorders. however, alternative molecules have been implicated in the induction of antigen presentation pathways, including other members of the nlr family, such as nalp. naip/ipaf homologs have been identified in the sea urchin implying that the ancestral nlr resembled one of these molecules. however, neither naip nor ipaf was identified in the fish genomes at this time, although ipaf was evident in the frog genome, suggesting that the genes for these molecules may have been lost from the fish genomes during the teleost-specific genome duplication event.  in summary, the nlr gene family contains several members in all vertebrates, and at least one prototypical gene must have existed prior to the evolution of vertebrates. clearly, there are some losses and gains of nlr genes in the genomes of distinct species thus shaping unique repertoires of these molecules throughout vertebrates and invertebrates. although there are still many members of the nlr family that require functional characterization, their implication as regulators of immunity is highly intriguing and warrants future investigation. 
three distinct nlr subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily resembles mammalian nods, the second resembles mammalian nalps, while the third appears to be unique to teleost fish. although the functional significance of the three major nlr subfamilies is unclear, we speculate that conservation and abundance of nlr molecules in all teleostei genomes, reflects an essential role in cellular control, apoptosis or immunity throughout bony fish. this current study, therefore, provides an in-depth investigation of this gene family in lower vertebrates including extensive phylogenetic comparison of zebrafish nlrs with orthologs in tetrapods, and analysis of their tissue-specific expression. gene predictions for zebrafish nlrs were verified using sequence derived from ests or direct sequencing of cdna. the third subfamily is large, containing several hundred nlr-c genes, many of which are predicted to encode a c-terminal b domain. a large multigene family of nod-like receptor molecules have been described in mammals and implicated in immunity and apoptosis. little information, however, exists concerning this gene family in non-mammalian taxa. our findings confirm the presence of multiple nlr gene orthologs, which form a large multigene family in teleostei.
 a large multigene family of nod-like receptor molecules have been described in mammals and implicated in immunity and apoptosis. little information, however, exists concerning this gene family in non-mammalian taxa. this current study, therefore, provides an in-depth investigation of this gene family in lower vertebrates including extensive phylogenetic comparison of zebrafish nlrs with orthologs in tetrapods, and analysis of their tissue-specific expression.  three distinct nlr subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily resembles mammalian nods, the second resembles mammalian nalps, while the third appears to be unique to teleost fish. in zebrafish, nlr-a and nlr-b subfamilies contain five and six genes respectively. the third subfamily is large, containing several hundred nlr-c genes, many of which are predicted to encode a c-terminal b domain. this subfamily most likely evolved from a nod3-like molecule. gene predictions for zebrafish nlrs were verified using sequence derived from ests or direct sequencing of cdna. reverse-transcriptase -pcr analysis confirmed expression of representative genes from each subfamily in selected tissues.  our findings confirm the presence of multiple nlr gene orthologs, which form a large multigene family in teleostei. although the functional significance of the three major nlr subfamilies is unclear, we speculate that conservation and abundance of nlr molecules in all teleostei genomes, reflects an essential role in cellular control, apoptosis or immunity throughout bony fish. 