The mammalian PYHIN gene family: phylogeny, evolution and expression - PubMed (original) (raw)

The mammalian PYHIN gene family: phylogeny, evolution and expression

Jasmyn A Cridland et al. BMC Evol Biol. 2012.

Abstract

Background: Proteins of the mammalian PYHIN (IFI200/HIN-200) family are involved in defence against infection through recognition of foreign DNA. The family member absent in melanoma 2 (AIM2) binds cytosolic DNA via its HIN domain and initiates inflammasome formation via its pyrin domain. AIM2 lies within a cluster of related genes, many of which are uncharacterised in mouse. To better understand the evolution, orthology and function of these genes, we have documented the range of PYHIN genes present in representative mammalian species, and undertaken phylogenetic and expression analyses.

Results: No PYHIN genes are evident in non-mammals or monotremes, with a single member found in each of three marsupial genomes. Placental mammals show variable family expansions, from one gene in cow to four in human and 14 in mouse. A single HIN domain appears to have evolved in the common ancestor of marsupials and placental mammals, and duplicated to give rise to three distinct forms (HIN-A, -B and -C) in the placental mammal ancestor. Phylogenetic analyses showed that AIM2 HIN-C and pyrin domains clearly diverge from the rest of the family, and it is the only PYHIN protein with orthology across many species. Interestingly, although AIM2 is important in defence against some bacteria and viruses in mice, AIM2 is a pseudogene in cow, sheep, llama, dolphin, dog and elephant. The other 13 mouse genes have arisen by duplication and rearrangement within the lineage, which has allowed some diversification in expression patterns.

Conclusions: The role of AIM2 in forming the inflammasome is relatively well understood, but molecular interactions of other PYHIN proteins involved in defence against foreign DNA remain to be defined. The non-AIM2 PYHIN protein sequences are very distinct from AIM2, suggesting they vary in effector mechanism in response to foreign DNA, and may bind different DNA structures. The PYHIN family has highly varied gene composition between mammalian species due to lineage-specific duplication and loss, which probably indicates different adaptations for fighting infectious disease. Non-genomic DNA can indicate infection, or a mutagenic threat. We hypothesise that defence of the genome against endogenous retroelements has been an additional evolutionary driver for PYHIN proteins.

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Figures

Figure 1

Figure 1

Maps of the human, C57BL/6 mouse and rat PYHIN gene loci, based on NCBI human v36.3, mouse MGSCv37.2 and rat RGSCv3.4 assemblies. The boundaries of the gene cluster in all three species are defined by the CADM3 gene and an olfactory receptor gene cluster. A number of bridged gaps are present in the rat locus, denoted by white boxes. The asterisk on the mouse locus denotes a HIN domain sequence, with expression supported by EST data. Accession numbers and alternative names for genes are provided in Table 1.

Figure 2

Figure 2

Predicted protein domain organisation derived from cDNA sequences for human and mouse and predicted genes for rat. Pyrin domains are indicated by stippled boxes, and the HIN domain subtypes (A, B or C) are shown. Only a single splice variant is shown for human IFI16 and IFIX, with complete details summarised previously [22]. Mouse p203 also has known splice variants [63]. Regions of sequence similarity among mouse proteins and the relationship between mouse and rat proteins are summarised in Additional Files 1 and 6.

Figure 3

Figure 3

Bayesian phylogenetic tree of HIN domains from a range of placental and marsupial mammals rooted with marsupial sequences. Posterior probabilities ≥0.7 in this analysis are shown above the nodes. Clades that were supported by PhyML analysis (with likelihood-ratio test values >0.85, except as indicated) are shown by dots on the nodes. For a limited number of important nodes the PhyML likelihood-ratio test values are shown as a number below the node. Dotted lines separate observable HIN clades: placental HIN-A, -B, and -C, and marsupial HIN-D. Sequences used are specified in Table 1 and Additional File 2: Table S2, and the alignment is shown in Additional File 3: Figure S3.

Figure 4

Figure 4

Bayesian phylogenetic tree of PYHIN pyrin domains across placental and marsupial mammals, rooted with marsupial sequences. Where a pyrin domain is clearly from the same gene as a HIN domain, labels are the same as Figure 3 (e.g. Cow 1). Some pyrin domains from low coverage genomes cannot definitively be linked to particular HIN domains, and are indicated with letters (e.g. Hyrax a). Posterior probabilities >0.7 are shown above nodes. Clades which were supported by PhyML analysis with likelihood-ratio test values >0.74 are shown by dots on the nodes. For a limited number of important nodes the PhyML likelihood-ratio test values are shown as a number below the node. Dotted lines indicate the three distinct clades: marsupial pyrin, pyrin domains from placental AIM2 sequences, and pyrin domains from placental non-AIM2 (IFI) sequences. Sequences used are defined in Table 1 and Additional File 2: Table S1, and alignment in Additional File 4: Figure S4.

Figure 5

Figure 5

Presence and absence of HIN domains in individual species, mapped onto a mammalian species tree[64,67]. The number of HIN domains indicated must be considered a minimum estimate of the true number of HIN domains, particularly for the genomes with only 2-fold sequence coverage (dolphin, sloth, armadillo, hyrax and wallaby). The duplication of the ancestral gene to generate HIN-A, -B, and -C domains is indicated. Putative points of loss of a functional AIM2 HIN-C domain are marked, consistent with the presence of pseudogenes in a number of species, and likely absence of a gene in pig. Independent loss of AIM2 in dog as indicated, cannot be confirmed due to uncertainty in the phylogenetic relationship between horse, dog and Cetartiodactyla [65]. Armadillo has evidence for an Aim2 HIN-C sequence, but as only one exon is available, this sequence was not used in phylogenetic analysis. Duplications and losses of HIN-A and HIN-B domains are numerous and are not indicated on the species branches here.

Figure 6

Figure 6

Northern blots for Aim2 expression in C57BL/6 mouse tissues, as well as bone marrow derived macrophages (BMM) from three mouse strains. Results for 18 S rRNA are shown as a loading control. Tissues were perfused with saline to reduce blood cell contamination. Results are representative of two independent tissue samples.

Figure 7

Figure 7

Expression of mouse PYHIN genes in perfused C57BL/6 mouse tissues (a), in various C57BL/6 mouse immune cells – splenic T and B cells, BMM and thioglycollate elicited peritoneal macrophages (TEPM) (b), and in BMM from three different mouse strains (c). Real time PCR results for each gene were normalised to the average of four housekeeping genes, which was found to give a relatively stable signal between tissues. Primers were tested to ensure lack of significant amplification of non-target PYHIN cDNAs. Results shown are the mean and range derived from duplicate RNA preparations.

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