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A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish.

Laing KJ, Purcell MK, Winton JR, Hansen JD - BMC Evol. Biol. (2008)

Bottom Line: Reverse-transcriptase (RT)-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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pathobiology, University of Washington, Seattle, Washington 98195, USA. klaing@fhcrc.org

ABSTRACT

Background: A large multigene family of NOD-like receptor (NLR) 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.

Results: Three distinct NLR subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily (NLR-A) resembles mammalian NODs, the second (NLR-B) resembles mammalian NALPs, while the third (NLR-C) 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 B30.2 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 (RT)-PCR analysis confirmed expression of representative genes from each subfamily in selected tissues.

Conclusion: 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.

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Phylogenetic comparison of vertebrate NLR molecules. Amino acid sequences of the NACHT domains (between the GxxGxGKS/T motif and the 'FAAFY' signature of human NOD2 or equivalent region in other NLRs) of vertebrate NLRs were aligned using CLUSTALW. Trees were constructed from these multiple alignments using the Maximum evolution and Neighbor-joining methods within the MEGA 3.1 program, using Poisson correction and complete deletion of gaps. Maximum evolution trees are shown. The resulting trees were bootstrapped 1000 times (shown as percentages). [A] Zebrafish NLRs were compared to human NLRs to estimate orthology. [B] The NALP subfamily was analyzed in more detail by comparing all zebrafish and Xenopus tropicalis predicted NALP-like molecules to human NALPs. [C] The NOD/NLR-A subfamilies of zebrafish, frog, chicken and humans were compared. DR = Danio rerio; XT = Xenopus tropicalis; GG = Gallus gallus; HS = Homo sapiens.
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Figure 1: Phylogenetic comparison of vertebrate NLR molecules. Amino acid sequences of the NACHT domains (between the GxxGxGKS/T motif and the 'FAAFY' signature of human NOD2 or equivalent region in other NLRs) of vertebrate NLRs were aligned using CLUSTALW. Trees were constructed from these multiple alignments using the Maximum evolution and Neighbor-joining methods within the MEGA 3.1 program, using Poisson correction and complete deletion of gaps. Maximum evolution trees are shown. The resulting trees were bootstrapped 1000 times (shown as percentages). [A] Zebrafish NLRs were compared to human NLRs to estimate orthology. [B] The NALP subfamily was analyzed in more detail by comparing all zebrafish and Xenopus tropicalis predicted NALP-like molecules to human NALPs. [C] The NOD/NLR-A subfamilies of zebrafish, frog, chicken and humans were compared. DR = Danio rerio; XT = Xenopus tropicalis; GG = Gallus gallus; HS = Homo sapiens.

Mentions: 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 (Fig 1). Mammalian NLRs are categorized into NOD and NALP families according to previous publications [1] and as depicted in Table 1. In the zebrafish genome, three distinct subfamilies were identified and highly supported by bootstrap analysis; some resembled mammalian NODs (designated subfamily A; Table 2; Fig 1C), some resembled mammalian NALPs (designated subfamily B; Table 3; Fig 1B) and some formed a unique clade, closely related to NOD3, which was restricted to teleostei (designated subfamily C; Table 4; Fig 1A).


A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish.

Laing KJ, Purcell MK, Winton JR, Hansen JD - BMC Evol. Biol. (2008)

Phylogenetic comparison of vertebrate NLR molecules. Amino acid sequences of the NACHT domains (between the GxxGxGKS/T motif and the 'FAAFY' signature of human NOD2 or equivalent region in other NLRs) of vertebrate NLRs were aligned using CLUSTALW. Trees were constructed from these multiple alignments using the Maximum evolution and Neighbor-joining methods within the MEGA 3.1 program, using Poisson correction and complete deletion of gaps. Maximum evolution trees are shown. The resulting trees were bootstrapped 1000 times (shown as percentages). [A] Zebrafish NLRs were compared to human NLRs to estimate orthology. [B] The NALP subfamily was analyzed in more detail by comparing all zebrafish and Xenopus tropicalis predicted NALP-like molecules to human NALPs. [C] The NOD/NLR-A subfamilies of zebrafish, frog, chicken and humans were compared. DR = Danio rerio; XT = Xenopus tropicalis; GG = Gallus gallus; HS = Homo sapiens.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2268669&req=5

Figure 1: Phylogenetic comparison of vertebrate NLR molecules. Amino acid sequences of the NACHT domains (between the GxxGxGKS/T motif and the 'FAAFY' signature of human NOD2 or equivalent region in other NLRs) of vertebrate NLRs were aligned using CLUSTALW. Trees were constructed from these multiple alignments using the Maximum evolution and Neighbor-joining methods within the MEGA 3.1 program, using Poisson correction and complete deletion of gaps. Maximum evolution trees are shown. The resulting trees were bootstrapped 1000 times (shown as percentages). [A] Zebrafish NLRs were compared to human NLRs to estimate orthology. [B] The NALP subfamily was analyzed in more detail by comparing all zebrafish and Xenopus tropicalis predicted NALP-like molecules to human NALPs. [C] The NOD/NLR-A subfamilies of zebrafish, frog, chicken and humans were compared. DR = Danio rerio; XT = Xenopus tropicalis; GG = Gallus gallus; HS = Homo sapiens.
Mentions: 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 (Fig 1). Mammalian NLRs are categorized into NOD and NALP families according to previous publications [1] and as depicted in Table 1. In the zebrafish genome, three distinct subfamilies were identified and highly supported by bootstrap analysis; some resembled mammalian NODs (designated subfamily A; Table 2; Fig 1C), some resembled mammalian NALPs (designated subfamily B; Table 3; Fig 1B) and some formed a unique clade, closely related to NOD3, which was restricted to teleostei (designated subfamily C; Table 4; Fig 1A).

Bottom Line: Reverse-transcriptase (RT)-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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Pathobiology, University of Washington, Seattle, Washington 98195, USA. klaing@fhcrc.org

ABSTRACT

Background: A large multigene family of NOD-like receptor (NLR) 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.

Results: Three distinct NLR subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily (NLR-A) resembles mammalian NODs, the second (NLR-B) resembles mammalian NALPs, while the third (NLR-C) 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 B30.2 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 (RT)-PCR analysis confirmed expression of representative genes from each subfamily in selected tissues.

Conclusion: 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.

Show MeSH
Related in: MedlinePlus