IRGM Human
Description
Introduction to IRGM Human
IRGM belongs to the immunity-related GTPase (IRG) family, which represents one of the strongest early resistance systems against intracellular pathogens in mammals . While the mouse genome contains 21 IRG gene copies arranged as tandem clusters on two chromosomes, the human genome has retained only two copies: IRGC and IRGM . IRGC is not involved in immunity, but IRGM plays a crucial role in autophagy-targeted destruction of intracellular pathogens, including Mycobacterium tuberculosis and Salmonella typhimurium .
The human IRGM gene has undergone a fascinating evolutionary journey, making it a unique example of gene "death and resurrection" in the primate lineage. This gene has developed critical functions in regulating autophagy and inflammation, with genetic variations in IRGM now recognized as risk factors for several inflammatory conditions.
2.1. Protein Structure and Expression
IRGM encodes a protein that promotes autophagy and suppresses innate immune responses . The human IRGM protein is distinct from other classical IRG proteins due to truncations in both the N- and C-terminal regions . In human cells, IRGM appears as a 20 kDa band on immunoblotting and is expressed in various cell types, including U937 macrophage cells, 293T cells, and HeLa cells .
2.2. Mechanistic Basis of IRGM Function
IRGM plays a direct role in organizing the core autophagy machinery, endowing it with antimicrobial and anti-inflammatory functions . It interacts with key autophagy regulators, including ULK1 and Beclin 1, promoting their co-assembly and governing the formation of autophagy initiation complexes .
Specifically, IRGM co-immunoprecipitates and co-localizes with both endogenous and overexpressed ULK1 and Beclin 1 . IRGM complexes with ULK1 are enriched for the activated, AMPK-dependent Ser-317 form of ULK1 relative to the inhibitory, mTOR-dependent, Ser-757 form . Furthermore, expression of IRGM enriches ULK1 in immunoprecipitated Beclin 1 complexes .
IRGM also interacts with pattern recognition receptors, including NOD2 . Together with NOD2 and ATG16L1 (all Crohn's disease risk factors), IRGM forms a molecular complex that modulates autophagic responses to microbial products . NOD2 enhances K63-linked polyubiquitination of IRGM, which is required for its interactions with core autophagy factors and for microbial clearance .
3.1. Gene Pseudogenization and Resurrection
The evolutionary history of IRGM represents a rare and remarkable case of gene death and resurrection. Most of the IRG gene cluster was deleted early in primate evolution, approximately 50 million years ago, after the divergence of anthropoids from prosimians . Comparative sequence analysis shows that the single-copy IRGM gene became pseudogenized (non-functional) in the anthropoid common ancestor due to an Alu retrotransposition event that disrupted its open reading frame (ORF) .
4.1. Key Polymorphisms and Their Effects
Several IRGM single nucleotide polymorphisms (SNPs) have been identified and associated with disease risk, particularly for Crohn's disease. Table 1 summarizes the key IRGM variants and their associations.
Table 1: Key IRGM Variants and Their Associations
The minor allele of rs13361189 (-4299T>C) has been associated with several diseases, including Crohn's disease and tuberculosis . This polymorphism is perfectly correlated (r²=1.0) with a structural deletion polymorphism located 20.1 kb upstream of the human IRGM gene . This structural variant is significantly associated with Crohn's disease and the deletion allele correlates with differential expression of IRGM in cultured cells .
4.2. Population Differences
Patterns of linkage disequilibrium and minor allele frequency for IRGM polymorphisms differ dramatically between subjects of European and African descent . Studies of rs13361189 have predominantly been conducted in Europeans, but the mechanism of association and potential racial differences remain poorly understood .
Research has shown that minor allele carriers of rs13361189 have increased serum immunoglobulin M, C-reactive protein, and circulating CD8+ T cells . Interestingly, the effect of this polymorphism on cytokine production appears to vary by race. Minor allele status is associated with increased induction of a subset of cytokines among African American subjects but decreased induction among White subjects . These findings underline the importance of broad racial inclusion in genetic studies of immunity .
5.1. Crohn's Disease
IRGM has been strongly implicated as a risk factor for Crohn's disease (CD) through genome-wide association studies . Variant IRGM haplotypes have been associated with increased risk for CD and correlated with differential expression of IRGM transcripts .
Multiple studies have confirmed IRGM as a susceptibility gene for CD in different populations, including British, German, New Zealander, Italian, Dutch, Belgian, and Spanish populations . In the German population, the IRGM SNPs rs13361189, rs10065172 (p.Leu105Leu), and rs1000113 have been associated with CD susceptibility with odds ratios of 1.31, 1.33, and 1.27, respectively .
Subjects with risk alleles at rs13361189 and rs10065172 have reduced IRGM expression in whole blood and terminal ileum, as well as dysregulated expression of a wide array of additional genes that regulate inflammation and autophagy . In particular, ileum-specific upregulation in risk allele carriers of a long intergenic noncoding RNA (lincRNA) encoded by ZNF300P1, a locus neighboring IRGM, has been observed, along with altered tissue-specific expression of TNF and other genes previously implicated in colitis and/or autophagy .
5.2. Infectious Diseases
IRGM plays a crucial role in autophagy-targeted destruction of intracellular pathogens. Human IRGM induces autophagy to eliminate intracellular Mycobacterium bovis (BCG) and Salmonella typhimurium . The association between IRGM variants and tuberculosis susceptibility suggests that alterations in IRGM function may impact the ability to control mycobacterial infections .
Human IFN-γ (hIFN-γ) induces autophagy in human macrophage cell line U937, and this process is dependent on critical autophagy factors, including IRGM . When IRGM is knocked down by siRNA, hIFN-γ-dependent autophagy (measured by GFP-LC3 puncta formation and LC3-I to LC3-II conversion) is significantly reduced .
Molecular Interactions and Pathways
IRGM participates in a complex network of interactions with other proteins involved in autophagy and immune response. It forms a molecular complex with NOD2 and ATG16L1, all of which are Crohn's disease risk factors, to modulate autophagic responses to microbial products .
There is evidence for weak gene-gene interaction between several SNPs of the autophagy genes IRGM and ATG16L1, though these interactions did not remain significant after Bonferroni correction in some studies . This suggests potential epistatic effects between different autophagy pathway genes in the pathogenesis of inflammatory bowel disease.
Table 2: IRGM Interactions with Autophagy Machinery
Future Research Directions
The unique evolutionary history and functional significance of IRGM in human immunity present several avenues for future research:
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Further investigation of the mechanism by which IRGM variants alter gene expression and affect autophagy function
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Exploration of population-specific effects of IRGM variants on immune responses
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Development of targeted therapeutics that modulate IRGM function for the treatment of inflammatory conditions like Crohn's disease
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Comprehensive analysis of IRGM's role in defense against a broader range of intracellular pathogens
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Better understanding of the evolutionary pressures that led to the resurrection of the IRGM gene in the human lineage
Product Specs
Immunity-related GTPase family M protein, Immunity-related GTPase family M protein1, LPS-stimulated RAW 264.7 macrophage protein 47 homolog, LRG-47, IRGM, IFI1, IRGM1, LRG47.
Q&A
What is the human IRGM gene and what is its functional significance?
The IRGM gene belongs to the immunity-related GTPase (IRG) family, one of the strongest early resistance systems against intracellular pathogens. While the mouse genome contains 21 IRG gene copies arranged as tandem clusters on two chromosomes, the human genome has been reduced to only two copies: IRGC (not involved in immunity) and IRGM . Human IRGM plays a crucial role in autophagy-targeted destruction of pathogens including Mycobacterium tuberculosis and Salmonella typhimurium, making it an essential component of the innate immune response . Unlike other members of the IRG family, human IRGM has truncations in both the N- and C-terminal regions and is not induced by interferons, which initially led researchers to believe it was a pseudogene .
What is the evolutionary history of the human IRGM gene?
The IRGM gene has undergone a remarkable evolutionary journey often described as "death and resurrection":
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Approximately 50-60 million years ago, the IRG family existed as a multi-copy tandem gene family in mammals .
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Most of the IRG gene cluster was deleted after the divergence of anthropoids from prosimians (around 50 million years ago) .
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The remaining single-copy IRGM gene was pseudogenized by an Alu retrotransposition event in the anthropoid common ancestor that disrupted the open reading frame (ORF) .
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The gene remained non-functional in Old World and New World monkeys for approximately 25 million years .
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The ORF was reestablished in the common ancestor of humans and great apes .
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This functional restoration coincided with the insertion of an endogenous retrovirus (ERV9), which now serves as the functional promoter driving human IRGM expression .
This represents a rare case in primate evolution where a gene was pseudogenized for millions of years and then brought back to function .
How is IRGM implicated in human diseases?
IRGM has been strongly implicated in several inflammatory conditions:
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Crohn's disease: Genome-wide association studies have identified IRGM variants (rs13361189 and rs4958847) as contributing to Crohn's disease susceptibility . These associations have been replicated in multiple populations including British, German, New Zealand, Italian, Dutch, Belgian, and Spanish cohorts .
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Sepsis: Decreased expression of human IRGM has been linked to inflammatory responses in sepsis .
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Infectious diseases: IRGM plays a role in defense against intracellular pathogens, with implications for conditions such as tuberculosis .
The link between IRGM variants and disease appears to involve alterations in autophagy efficiency, with research showing that reduction in IRGM expression impairs the induction of autophagy and clearance of intracellular pathogens .
What molecular mechanisms link IRGM to autophagy and inflammation?
The molecular pathways connecting IRGM function to autophagy and inflammation involve multiple interconnected processes:
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Autophagy regulation: IRGM contributes to autophagy-targeted destruction of intracellular pathogens like M. tuberculosis and S. typhimurium .
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Inflammatory signaling: Decreased expression of IRGM leads to increased production of inflammatory chemokines and cytokines both in vivo and in cultured macrophages .
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Type I interferon dependence: RNA deep sequencing and quantitative PCR analyses have shown that increases in cytokine production and most transcriptional changes in IRGM-deficient cells are dependent on increased type I interferon production .
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Metabolic alterations: IRGM deficiency drives increased glycolysis and accumulation of acyl-carnitines, which occur independently of type I interferon signaling .
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Peroxisomal homeostasis: Dysregulation of peroxisomal function has been identified as a novel upstream pathway governing type I interferon production and inflammatory cytokine production in IRGM-deficient cells .
These findings highlight the complex biochemical changes triggered by IRGM deficiency that contribute to inflammatory diseases .
How do IRGM genetic variants impact susceptibility to Crohn's disease?
The relationship between IRGM variants and Crohn's disease involves several mechanisms:
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Structural variation: A 20.1 kb deletion polymorphism upstream of IRGM is perfectly correlated (r²=1.0) with the disease-associated SNP rs13361189 .
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Expression regulation: The deletion allele is associated with differential expression of IRGM in cultured cells .
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Functional consequences: Reduced IRGM expression has been shown to impair autophagy induction and the clearance of intracellular pathogens (S. typhimurium) .
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Promoter variants: Variations in the promoter region may be correlated with differential expression patterns .
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ERV9 element: The endogenous retrovirus that serves as the IRGM promoter may influence expression patterns in different cell types and conditions .
This multifaceted relationship underscores the complex mechanisms by which IRGM contributes to Crohn's disease pathogenesis.
What experimental models are most appropriate for studying IRGM function?
When designing experiments to investigate IRGM function, researchers should consider:
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Cell culture systems:
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Infection models:
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Analytical techniques:
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Comparative approaches:
How does the ERV9 element influence IRGM expression and function?
The ERV9 endogenous retroviral element plays a critical role in IRGM regulation:
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Promoter function: The ERV9 element serves as the functional promoter for human IRGM .
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Expression timing: The insertion of the ERV9 element coincided with the restoration of IRGM function in the human/ape lineage .
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Transcriptional structure: The beginning of the 5'-UTR of the IRGM transcript corresponds to the U5 region of an ERV9 element .
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Lack of interferon response elements: The ERV9-derived promoter lacks interferon response elements, explaining why human IRGM is not interferon-inducible unlike mouse Irgm genes .
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Cell-type specificity: ERV9-driven expression is particularly efficient in embryonic and hematopoietic cells, potentially conferring tissue-specific expression patterns to IRGM .
This represents a fascinating example of how retroviral elements can be co-opted for host gene regulation with significant functional consequences for immunity.
What are the key IRGM variants associated with disease risk?
How do metabolic alterations contribute to IRGM-related inflammatory responses?
Research has revealed important connections between IRGM, metabolism, and inflammation:
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Increased glycolysis: IRGM-deficient bone marrow-derived macrophages (BMM) exhibit enhanced glycolytic activity .
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Acyl-carnitine accumulation: IRGM deficiency leads to increased accumulation of acyl-carnitines .
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Interferon independence: These metabolic alterations occur independently of the increased type I interferon signaling seen in IRGM-deficient cells .
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Peroxisomal dysfunction: Dysregulation of peroxisomal homeostasis appears to be a novel upstream pathway influencing both interferon production and inflammatory cytokine responses .
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Mitochondrial effects: Prior research has indicated that IRGM deficiency affects mitochondrial homeostasis, which may contribute to metabolic disruptions .
Understanding these metabolic pathways provides insights into potential therapeutic targets for inflammatory conditions associated with IRGM dysfunction.
What are the critical unanswered questions about human IRGM biology?
Despite significant advances, several important questions remain:
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Molecular mechanisms: How exactly does IRGM coordinate autophagosome formation and pathogen targeting?
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Cell-type specificity: Does IRGM function differently in various immune and non-immune cell types?
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Evolutionary advantages: What selective pressures drove the resurrection of IRGM in the human/ape lineage after 25 million years of pseudogenization?
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Therapeutic potential: Can modulation of IRGM function or its downstream pathways offer therapeutic benefits for Crohn's disease or other inflammatory conditions?
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Regulatory networks: How does IRGM interact with other autophagy and immunity genes, and how are these interactions influenced by genetic variants?
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Peroxisome-mitochondria cross-talk: What is the precise relationship between peroxisomal dysfunction, mitochondrial homeostasis, and IRGM-mediated inflammatory responses?
Addressing these questions will require integrated approaches combining genomics, cell biology, immunology, and evolutionary analyses.
Product Science Overview
The Immunity-Related GTPase Family, M (IRGM), also known as interferon-inducible protein 1 (IFI1), is an enzyme encoded by the IRGM gene in humans . This protein is a member of the interferon-inducible GTPase family, which plays a crucial role in the innate immune response by regulating autophagy formation in response to intracellular pathogens .
The IRGM gene is located on chromosome 5 in humans . The protein encoded by this gene is involved in various cellular processes, including the remodeling and trafficking of intracellular membranes . This dynamin-like protein binds to intracellular membranes and promotes their remodeling, which is essential for the clearance of acute protozoan and bacterial infections .
IRGM is required for the efficient degradation of intracellular pathogens through autophagy. It interacts with autophagy and lysosome regulatory proteins to promote the fusion of phagosomes with lysosomes . This process ensures the degradation of microbial cargo, thereby playing a vital role in antimicrobial defense .
IRGM also regulates selective autophagy, including xenophagy and mitophagy, both directly and indirectly . It acts as a molecular adapter that promotes the coassembly of the core autophagy machinery. This includes activating AMPK, which phosphorylates ULK1 and BECN1 to induce autophagy . Additionally, IRGM influences the composition of the BECN1 complex by competing with negative regulators like BCL2 and RUBCN .
Polymorphisms affecting the normal expression of the IRGM gene are associated with susceptibility to Crohn’s disease and tuberculosis . Elevated expression of IRGM has also been linked to the development of several cancers . Understanding the role of IRGM in these diseases can provide insights into potential therapeutic targets for treating these conditions.
