Phenotypic Mutation 'Marigold'

• Allele: Marigold
• Mutation Type: critical splice donor site
• Chromosome: 10
• Coordinate: 19,477,233 bp (GRCm39)
• Base Change: T ⇒ C (forward strand)
• Gene: Ifngr1
• Gene Name: interferon gamma receptor 1
• Synonym(s): IFN-gammaR, Ifgr, IFN-gamma R, Ifngr, Nktar, CD119
• Chromosomal Location: 19,467,697-19,485,977 bp (+) (GRCm39)
• MGI Phenotype: FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene (IFNGR1) encodes the ligand-binding chain (alpha) of the gamma interferon receptor. Human interferon-gamma receptor is a heterodimer of IFNGR1 and IFNGR2. A genetic variation in IFNGR1 is associated with susceptibility to Helicobacter pylori infection. In addition, defects in IFNGR1 are a cause of mendelian susceptibility to mycobacterial disease, also known as familial disseminated atypical mycobacterial infection. [provided by RefSeq, Jul 2008] ; PHENOTYPE: Mice homozygous for a mutant allele exhibit increased susceptibility to viral infection and experimental autoimmune uveoretinitis. [provided by MGI curators]
• Mapped: Yes
• Institutional Source: Beutler Lab
• Gene Model: predicted gene model for protein(s): [ENSMUSP00000020188 ^†] [ENSMUSP00000129309 ^†] † probably from a misspliced transcript
• AlphaFold: P15261
• SMART Domains: Protein: ENSMUSP00000020188; Gene: ENSMUSG00000020009

Domain	Start	End	E-Value	Type
Pfam:Tissue_fac	9	119	2.2e-27	PFAM
Pfam:Interfer-bind	131	245	8.5e-9	PFAM
Pfam:IFNGR1	168	331	1.6e-53	PFAM
low complexity region	401	416	N/A	INTRINSIC

• Predicted Effect: probably null
• SMART Domains: Protein: ENSMUSP00000020188; Gene: ENSMUSG00000020009

Domain	Start	End	E-Value	Type
Pfam:Tissue_fac	9	119	2.2e-27	PFAM
Pfam:Interfer-bind	131	245	8.5e-9	PFAM
Pfam:IFNGR1	168	331	1.6e-53	PFAM
low complexity region	401	416	N/A	INTRINSIC

• Predicted Effect: probably null
• SMART Domains: Protein: ENSMUSP00000129309; Gene: ENSMUSG00000020009

Domain	Start	End	E-Value	Type
Pfam:Tissue_fac	9	74	2.3e-10	PFAM

• Predicted Effect: probably benign
• SMART Domains: Protein: ENSMUSP00000127219; Gene: ENSMUSG00000020009

Domain	Start	End	E-Value	Type
Pfam:Tissue_fac	9	94	1e-11	PFAM

• Predicted Effect: noncoding transcript
• SMART Domains: Protein: ENSMUSP00000127484; Gene: ENSMUSG00000020009

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
transmembrane domain	42	64	N/A	INTRINSIC

• Predicted Effect: noncoding transcript
• Meta Mutation Damage Score: 0.9589
• Is this an essential gene?: Non Essential (E-score: 0.000)
• Phenotypic Category: Autosomal Recessive
• Mode of Inheritance: Autosomal Recessive
• Last Updated: 2020-07-29 6:45 PM by External Program
• Record Created: 2016-02-28 11:28 AM by Bruce Beutler
• Record Posted: 2016-09-27
• Science Writers: Anne Murray
• Illustrators: Katherine Timer
• Authors: Lei Sun, Ying Wang, Bruce Beutler

Accession Number

NCBI RefSeq: NM_010511; MGI:107655

Alleles Listed at MGI

All Mutations and Alleles(8) : Chemically induced (other)(1) Targeted(7)

Phenotypic Description

Figure 1. Marigold mice exhibit increased frequencies of peripheral B cells. Flow cytometric analysis of peripheral blood was utilized to determine B cell frequency. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Figure 2. Marigold mice exhibit an increased percentage of peripheral IgD+ B cells. Flow cytometric analysis of peripheral blood was utilized to determine IgD+ B cell percentage. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Figure 3. Marigold mice exhibit reduced frequencies of peripheral IgM+ B cells. Flow cytometric analysis of peripheral blood was utilized to determine IgM+ B cell frequency. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Figure 4. Marigold mice exhibit redcued frequencies of peripheral macrophages. Flow cytometric analysis of peripheral blood was utilized to determine macrophage frequency. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Figure 5. Marigold mice exhibit reduced TNFα secretion from macrophages in response to the Toll-like receptor 3 (TLR3) ligand, poly(I:C), and priming with interferon-gamma. ELISA was utilized to determine TNFα concentration. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

The marigold phenotype was identified among G3 mice of the pedigree R4089, some of which showed an increased frequency of B cells (Figure 1), an increased IgD⁺ B cell percentage (Figure 2), an increased frequency of IgM⁺ B cells (Figure 3), and a diminished macrophage frequency (Figure 4), all in the peripheral blood. Some mice also exhibited reduced TNFα secretion from macrophages in response to the Toll-like receptor 3 (TLR3) ligand, poly(I:C), and priming with interferon (IFN)-γ (Figure 5).

Nature of Mutation

Figure 6. Linkage mapping of the reduced TNFα secretion after poly(I:C) stimulation and IFN-γ priming using a recessive model of inheritance. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 50 mutations (X-axis) identified in the G1 male of pedigree R4089. Normalized phenotype data are shown for single locus linkage analysis without consideration of G2 dam identity. Horizontal pink and red lines represent thresholds of P = 0.05, and the threshold for P = 0.05 after applying Bonferroni correction, respectively.

Whole exome HiSeq sequencing of the G1 grandsire (R4089) identified 50 mutations. All of the above anomalies were linked by continuous variable mapping to a mutation in Ifngr1:  a T to C transition at base pair 19,601,485 (v38) on chromosome 10, or base pair 9,528 in the GenBank genomic region NC_000076 within the donor splice site of intron 3 in Ifngr1. The strongest association was found with a recessive model of linkage to the normalized amount of TNFα secretion from macrophages after poly(I:C) + IFN-γ treatment, wherein six variant homozygotes departed phenotypically from eight homozygous reference mice and 24 heterozygous mice with a P value of 2.608 x 10^-8 (Figure 6). A substantial semidominant effect was also observed in most of the assays and a dominant effect with seen in the B cell and IgD⁺ B cell assays. 

The effects of the mutation at the cDNA and protein level have not examined, but the mutation could result in skipping of the 164-nucleotide exon 3 (out of 7 total exons). Deletion of exon 3 would result in a frame-shift and coding of 24 aberrant amino acids followed by a premature stop codon after amino acid 100.

<--exon 2         <--exon 3 intron 3-->                ­<--exon 4--> 5556 ……GTAAAGGTGTATTC ……CTTATGTGCCTAAAGG gtaagtagattgtaca…… GAAAGGTCGGGCC……CGTATTTCACCCTGA 11858 72   ……-V--K--V--Y--S ……-L--M--C--L--K--                    --K--A--R--A-……-R--I--S--P--*- 100           correct          deleted                                    aberrant

Genomic numbering corresponds to NC_000076. The donor splice site of intron 3, which is destroyed by the marigold mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red. 

Protein Prediction

Figure 7. Protein domain organization of IFN-γR1. Abbreviations: SP, signal peptide; LBD, ligand-binding domain; TM, transmembrane domain. The location of JAK1 and STAT1 binding are indicated. The marigold mutation is in the donor splice site of intron 3.

Figure 8. Crystal structure of the extracellular domain of human IFN-γR1 bound to the monovalent form of IFN-γ. Figure was generated using UCSF Chimera, and modeled after PDB: 1FYH.

Ifngr1 encodes the ligand-binding chain of the IFN-γ receptor (IFN-γR1) that, along with IFN-γR2 (encoded by Ifngr2), forms the type II IFN receptor (IFN-γR). The IFN-γR binds to type II interferon, namely the IFN-γ homodimer (1). IFN-γR1 is a member of the class II cytokine receptor family, which includes IFNAR1, IFNAR2, tissue factor (TF), and interleukin (IL)-10 (2). IFN-γR1 has a single transmembrane domain at amino acids 255-275 (Figure 7). The extracellular ligand-binding regions of these receptors (amino acids 26-254 in IFN-γR1; amino acids 1-25 constitute a signal peptide) all share fibronectin type III (FNIII) domains similar to the constant region of immunoglobin (Ig). Most of these receptors contain two of these domains, each containing ~100 amino acids with seven β-strands and connecting loops. 

IFN-γR1 binds IFN-γ in a 1:2 complex (3;4). Subsequently, two copies of IFN-γR2 bind forming a 1:2:2 signaling complex (5). The crystal structure of a single copy of 229 amino acids of the extracellular domain of human IFN-γR1 bound to the monovalent form of IFN-γ has been solved (Figure 8; PDB:1FYH; (6;7)). The IFN-γR monomer folds into six α-helices connected by short loops (6). In the IFN-γR dimer, the first four helices of one monomer (helices A–D) and the last two helices of the second monomer (helices E' and F') form a structural domain. A short linker connects the two FNIII domains in the extracellular domain of IFN-γR1. The β-sandwich formed by each FNIII repeat consists of a three-stranded (A, B, E) and a four-stranded (G, F, C, C') β-sheet. The receptor interface that mediates the interaction with IFN-γ consists of strands C, F, and G, as well as the CC' and EF loops of the first FNIII domain (D1; membrane distal); the short helix (α2) of the interdomain linker; and strand F, as well as the BC, C'E, and FG loops of the second FNIII domain (D2; membrane proximal). Each D domain folds into two β-strands consisting of β-pleated sheets. The D domains are separated by an 11 amino acid linker and are oriented at an angle of 120° relative to one another. The membrane proximal D2 domain is positioned at a 60° angle relative to the cell membrane (4).

The IFN-γR receptor is typical of class II helical cytokine receptors and lacks intrinsic kinase activity. Instead, the intracellular domains of the IFN-γR receptor subunits are associated with Janus activating kinases (JAKs) that phosphorylate receptors and signal transducing molecules (see Background). In particular, IFN-γR1 binds to JAK1 and IFN-γR2 binds to JAK2. Once phosphorylated, JAK1 recruits signal transducer and activator of transcription (STAT)1 (see the records for domino and poison). Tyr441 of IFNAR1 associates with negative regulators of type I IFN signaling such as suppressor of cytokine signaling 1 (SOCS1) (8). Mutation of Tyr441 to phenylalanine (Tyr441Phe) resulted in impaired negative regulation of IFN-γ signaling. IFN-γ-induced STAT1 was prolonged in the Tyr441Phe cells.

A YVSLI motif at amino acids 287-291 is essential for IFN-γ-induced IFN-γR1 internalization (see Expression and Localization) and function (9). IFN-γR1 is N-linked glycosylated at Asn61 and Asn85 within the extracellular domain (10;11).

The marigold mutation is predicted to result in deletion of exon 3. Deletion of exon 3 would result in a frame-shift and coding of 24 aberrant amino acids followed by a premature stop codon after amino acid 100 within the ligand-binding domain. Expression and function of IFNGR1^marigold have not been assessed.

Expression/Localization

IFN-γR1 is constitutively expressed at moderate levels on the surface of most cells. Upon exposure to IFN-γ, IFN-γR1 translocates to the nucleus (12-14). IFN-γ has a nuclear localization sequence at its C-terminus that mediates the translocation of the IFN-γR1/IFN-γ complex to the nucleus via receptor-mediated endocytosis (12). After endocytosis, the C-terminus of IFN-γ interacts with the intracellular domain of IFN-γR1 (amino acids 253-287) (15). IFN-γ, IFN-γR1, and STAT1 all can bind to IFN-γ-activated sequence response (GAS) element in the promoter region of IFN-γ-activated genes (e.g., IRF-1 and indoleamine dioxygenase) (16). Upon binding to the GAS element, IFN-γ and IFN-γR1 enhance transcription. IFN-γR1 does not have a DNA-binding domain, but binding to STAT1 at the GAS element may result in the IFN-γR1-associated increased transcriptional activity.

Background

Figure 9. Inflammatory cytokine signaling pathways promote transcriptional changes to drive immune responses in hematopoietic cells. IFNα/β and IFNγ activate parallel signaling pathways. IFNα/β binding to the type I IFN receptor activates TYK2 and JAK1 to phosphorylate STAT1 and STAT2, which heterodimerize, associate with IRF9 and bind to IFN-stimulated response elements (ISREs) to activate transcription. Signaling through the type II IFN receptor occurs in a parallel pathway. When IFNγ binds its receptor, associated JAK1 and JAK2 kinases phosphorylate STAT1, which homodimerizes and translocates to the nucleus for transcriptional activation at IFNγ-activated site (GAS) sequences. The TNFα and TLR signaling pathways act similarly to promote transcriptional changes; these pathways exhibit extensive crosstalk. TNFα receptor binding causes TRADD to recruit RIP and TRAF2, which activate IKK to phosphorylate IκBa, thereby releasing NFκB. TNFα receptor signaling also activates MEKK1, which causes JNK to stimulate AP-1 and ATF2. AP-1 binds TPA DNA-response elements (TRE), while ATF2 binds cAMP-responsive elements (CRE). Infectious particles activate TLRs to signal through MyD88. This recruits IRAK, which binds TRAF6 and activates NFκB and JNK pathways. This figure and legend were adapted from Baldridge et al (2011). Please see text for further details. This image is interactive. Click on the image to view mutations within the pathway (red) and the genes affected by these mutations (black). Click on the mutations for more specific information.

The IFN-γ-associated signaling pathway is a canonical signaling pathway activating STAT proteins, called the JAK (Janus kinase)-STAT pathway. Upon IFN-γ to the IFN-γR, the IFN-γR associates with JAK1 and JAK2 (17). The JAK tyrosine kinases are normally dephosphorylated and inactive. Receptor stimulation results in dimerization/oligomerization and subsequent apposition of JAK proteins, which are now capable of trans-phosphorylation as they are brought in close proximity (18). This activates JAKs to phosphorylate the receptor cytoplasmic domains, creating phosphotyrosine ligands for the SH2 domains of STAT proteins. In the IFN-γ-associated signaling pathway, the JAK1/JAK2 recruit STAT1. Once recruited to the receptor, STAT proteins are also tyrosine phosphorylated by JAKs, a phosphorylation event which occurs on a single tyrosine residue that is found at around residue 700 of all STATs. Tyrosine phosphorylation of STATs may allow formation and/or conformational reorganization of the activated STAT dimer, involving reciprocal SH2 domain-phosphotyrosine interactions between STAT monomers. In addition to tyrosine phosphorylation, several STATs including STAT1, also require phosphorylation on a serine in the TAD for full activation (19;20). In STAT1, this serine is residue 727, and it exists within a consensus MAPK phosphorylation site (19). Phosphorylated, activated STATs enter the nucleus and accumulate there to promote transcription (21). They do so by facilitated transport involving importin-α5, a subunit of the nucleocytoplasmic transport machinery (22). Termination of transcriptional activation appears to require nuclear dephosphorylation by at least one nuclear phosphatase, TC45 (23). Once dephosphorylated, STAT1 may be exported through the chromosome region maintenance 1 (CRM1) export receptor (24). Additional STAT protein nuclear inhibitors are the PIAS (protein inhibitor of activated STAT) proteins (25). PIAS proteins interact directly with phosphorylated STATs and block DNA binding.

Termination of STAT signaling requires ending both transcriptional activation and cytoplasmic STAT signaling. In the cytoplasm, there are several mechanisms to halt signaling. First, the suppressors of cytokine signaling (SOCS) proteins can directly bind and suppress JAKs or can compete with STATs for receptor binding (26;27). SOCS proteins are induced transcriptionally by cytokine stimulation, and recruited to active receptor complexes to induce inhibition. Second, protein tyrosine phosphatases including SHP1 and SHP2 prevent further cytoplasmic STAT tyrosine phosphorylation (28;29). Third, the β isoforms of some STATs can function as dominant negative inhibitors in certain circumstances. STAT1β apparently activates a distinct set of genes from STAT1α, and STAT1β fails to complement impaired IFN-γ-induced α-specific gene activation in STAT1-deficient cells (30).

IFN-γ has several known functions. IFN-γ mediates host defense against infectious agents and tumors, and is synthesized exclusively by T lymphocytes and natural killer cells upon immune and inflammatory stimuli. Similar to type I IFN, IFN-γ protects cells from viral infection and mediates antiproliferative effects on normal and neoplastic cells. IFN-γ is the primary cytokine that upregulates MHC class I protein expression and induces MHC class II proteins on leukocytes and epithelial cells. IFN-γ also promotes the activation and regulation of mononuclear phagocytes. During humoral immune responses, IFN-γ promotes IgG heavy chain switching. In addition, IFN-γ regulates proinflammatory cytokine production, including IL-12 and TNFα. IFN-γ induces macrophage activation, host defense against intracellular pathogens, and Th1 type cell-associated inflammation (31). IFN-γ signaling in dendritic cells controls T cell expansion. IFN-γ signaling has cell-specific functions. In neutrophils, IFN-γ signaling regulates T cell expansion and inflammation. In non-hematopoietic cells, IFN-γ signaling is proposed to control inflammation.  IFN-γ signaling is not necessary for the expansion, contraction, and memory differentiation of CD8⁺ T cells in response to peptide vaccination (32). However, IFN-γ signaling counterregulates CD8⁺ T cell responses and the generation of effector memory T cell processes. IFN-γ signaling limits the expansion of naïve CD8+ T cells and their differentiation into effector memory-like T cells.

Ifngr1-deficient (Ifngr1^−/−) mice are overtly normal, but exhibit impaired resistance to infection by several microbial pathogens such as Listeria monocytogenes and Leishmania major as well as myocobacteria species, including M. bovis and M. avium (33;34). Ifngr1^−/− mice develop normal helper and cytotoxic T cell responses to the pathogens (33;35). Ifngr1^−/− mice are able to mount immune responses to many viruses (36). However, Ifngr1^−/− mice exposed to murine cytomegalovirus (MCMV) infection exhibit chronic aortic inflammation (37). In addition, the infected Ifngr1^−/− mice showed MCMV viral titers in the spleen, peritoneal exudate cells, and salivary gland up to six months after infection, while control mice cleared the infection. Ifngr1^−/− mice developed experimental autoimmune uveoretinitis after subcutaneous immunization with Bordetella pertussis toxin (38). Ifngr1^−/− mice exhibited an increased resistance to lipopolysaccharide [LPS]-induced shock  (39). A separate study found that Ifngr1^−/− mice failed to develop IFN-γ-mediated antiviral responses (40). Ifngr1^−/− mice exhibited delayed clearance of a neuroadapted strain of sindbis virus from the brain and spinal cord as well as lower levels of TNFα and IL-6 mRNAs than infected wild-type mice (40). In contrast, the Ifngr1^−/− mice exhibited more inflammation marked by increased expression of MHCII and IL-17A mRNAs than wild-type mice. Ifngr1^−/− mice treated with curprizone, a demyelination inducer, exhibited delayed demyelination compared to wild-type mice (41). After removal of the cuprizone from the diet, the Ifngr1^−/− mice exhibited accelerated remyelination in the corpus callosum due to enhanced recruitment of new oligodendrocytes in the demyelinated areas. Taken together, IFN-γ is proposed to regulate the development and resolution of demyelinating syndromes such as multiple sclerosis.

Polymorphisms in human IFNGR1 have been implicated in a number of diseases including autosomal recessive immunodeficiency 27A [OMIM: #209950; (42;43)] and autosomal dominant immunodeficiency 27B [OMIM: #615978; (44;45)]. Immunodeficiences 27A and 27B are predispositions to diseases caused by weakly virulent mycobacteria. Patients with immunodeficiency 27A or 27B are otherwise overtly normal. The mycobacteriosis usually begins in childhood and can cause either localized or disseminated infections upon exposure to mycobacteria. Polymorphisms in IFNGR1 also are linked to increased susceptibility to Helicobacter pylori [OMIM: #600263; (46)], hepatitis B [OMIM: #610424; (47)], and Tuberculosis infections (OMIM: #607948).

Putative Mechanism

The immune phenotypes observed in the marigold mice indicate loss of IFNGR1^marigold function.

Primers

PCR Primer
Marigold_pcr_F: TAGGGGTTCCTGGACTGATTCC
Marigold_pcr_R: CTGGAAGAAAGACATTGGCTCC

Sequencing Primer
Marigold_seq_F: TGGACTGATTCCTGCACCAAC
Marigold_seq_R: ACCCAGGTTTGGTTAACAGC

Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold

The following sequence of 624 nucleotides is amplified (chromosome 10, + strand):

1   taggggttcc tggactgatt cctgcaccaa catttctgat cattgttgta atatctatga
61  acaaattatg tatcctgatg tatctgcctg ggccagagtt aaagctaagg ttggacaaaa
121 agaatctgac tatgcacggt caaaagagtt ccttatgtgc ctaaagggta agtagattgt
181 acacataagt aacttttcag tgagtgtgtg tgtgtgtgtg tgtgtgtgtg tgtgtgtgtg
241 tgtgtattgg tgctttgtcc acatgtgtgt accacattca tgcagtactt gtgtgtgtgt
301 gtgtgtgtgt gtgtgtgtat tggtgctttg tccacatgtg tgtaccacat tcatgcagta
361 ccttcagagg ccagaagagg gcgccaaatc ctgtcactgc cattactggt agttaccaac
421 agacatatgg atgctgttaa ccaaacctgg gtcctctgga aatgcagcca ttgctcttaa
481 ccactaagcc ttctctctag ctcctacatg gatacatttt aattttgaag tacttacact
541 tccctgtatg cttgctttta ttggtagttg taacaagtgt ctaacagcat atgacaattt
601 aaggagccaa tgtctttctt ccag

Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References

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