Glutamate-rich protein 4

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Glutamate-rich protein 4 is encoded by the gene ERICH4 and can be otherwise known as chromosome 19 open reading frame 69 (C19orf69). [1] ERICH4 is highly conserved in mammals and exhibits overexpression in tissues of the kidneys, terminal ileum, and duodenum. [1] [2] The function of ERICH4 has yet to be well understood by the scientific community but is suggested to contribute to immune inflammatory responses.

Contents

Gene

ERICH4 is located on the sense strand of 19q13.2 in humans, consists of 2,340 base pairs, and contains 2 exons. [3] ERICH4, on the sense strand, is located within DMAC2 and next PCAT19 and B3NT8 which are all on the antisense strand. [1]

Genomic Neighborhood for ERICH4 ERICH4 Genomic Neighborhood.png
Genomic Neighborhood for ERICH4

Promoter & Predicted Transcription Factors (TF)

The promoter is predicted to begin 1,806 bp upstream from the 5' UTR and consists of 1,819 bp which overlaps with the coding sequence by 13 bp. [4]

Conceptual Promoter Sequence and Transcription Factors for ERICH4 ERICH4TFs.png
Conceptual Promoter Sequence and Transcription Factors for ERICH4
Matrix IDTF NameGenomic Position with Human ERICH4 PromoterStrand of q19Matrix SimilarityLiterature Supported Function
V$CEBPA.01 CCAAT/Enhancer-binding Protein Alpha 41,441,752-41,441,766Sense (+)0.962Recruit co-activators that in turn can open up chromatin structure or recruit basal transcription factors. [5] [6]
O$VTATA.01 Vertebrate TATA-binding Factor 41,442,466-41,442,482Antisense (-)0.915Required for initiation of transcription and is associated with a variety of different transcription factors. [7]
V$SOX1.04 SRY (Sex Determining Region)-Box 141,442,480-41,442,502Sense (+)0.801Involved in the regulation of embryonic development and in the determination of the cell fate. [8]
V$HSF1.04 Heat Shock Factor 1 41,442,536-41,442,560Sense (+)0.769Activation in cellular stress. [9]
V$BTEB3.01 Krueppel-like Factor 13 (KLF13) 41,442,243-41,442,261Sense (+)0.934KLF13 knock-out mice show a defect in lymphocyte survival as KLF13 is a regulator of Bcl-xL expression. [10]
V$PAX5.01 B-cell Specific Activator Protein 41,442,955-41,442,983Sense (+)0.796Key role in B-lymphocyte development. [11]
V$GLI3.02 GLI-Kruppel Family Member GLI3 41,443,115-41,443,131Sense (+)0.915Thought to play a role during embryogenesis. [12]
V$NR2F6.01 Nuclear Receptor subfamily 2 group F member 6 (NR2F6) 41,442,507-41,442,531Sense (+)0.851Transcriptional repressor of IL17 expression in Th17-differentiated CD4-positive T cells in-vitro and in-vivo. [13]
V$MAFB.01 MAFB/Leucine Zipper Transcription Factor 41,442,601-41,442,625Sense (+)0.923Regulation of lineage-specific hematopoiesis. Represses ETS1-mediated transcription of erythroid-specific genes in myeloid cells. [14]
V$AP4.03 Activating Enhancer Binding Protein 4 (TFAP4) 41,443,003-41,443,019Sense (+)0.993Regulates the expression of genes involved in the regulation of cellular proliferation, stemness, and epithelial-mesenchymal transition. [15]
V$EVI1.05 Ecotropic Viral Integration Site 1 (EVI1) Encoded Factor 41,442,583-41,442,599Sense (+)0.821Regulation of hematopoietic stem cell renewal. Controls several aspects of embryonic development. [16]
V$MRE.01 Mineralcorticoid Receptor Response Element41,442,844-41,442,862Sense (+)0.939Involved in water electrolyte homeostasis, blood pressure regulation, inflammation, and fibrosis in the renocardiovascular system. [17]
V$ARE.03 Androgene Receptor Binding Site, IR3 Sites41,442,844-41,442,862Antisense (-)0.946Ligand-dependent transcription factor that controls the expression of specific genes. The binding of the AR to its native ligands 5α-dihydrotestosterone (DHT) and testosterone initiates male sexual development and differentiation. [18]
V$ZNF217.01 Zinc Finger Protein 217 41,443,023-41,443,035Sense (+)0.911Promotes cell proliferation and antagonizes cell death. [19]
V$RORA.02 RAR-related Orphan Receptor Alpha, Homodimer DR5 Binding Site 41,442,783-41,442,807Sense (+)0.831Possible role in lymphocyte development. Possible function in negatively regulating inflammation due to a report of positive relation in the expression of IKBa, a negative regulator of the NF-kB signaling pathway. [20]
V$STAT6.01 Signal Transducer and Activator of Transcription 6 (STAT6) 41,443,042-41,443,060Sense (+)0.961Plays a central role in exerting IL4-mediated responses. [21]
V$ZF5.01 Zinc Finger/POZ Transcription Factor41,442,874-41,442,888Sense (+)0.957Role in development, oncogenesis, apoptosis, and transcription repression. [22]

mRNA

Conceptual Translation of ERICH4 ERICH4 Conc Translation.png
Conceptual Translation of ERICH4

The ERICH4 mRNA sequence is 955 nucleotides in length with a fold energy predicted as -139.80 kcal/mol with -0.258 energy/base. [23]

Alternative Splicing

ERICH4 has one different protein-encoding transcript variant, or isoform. [1]

NamemRNA Length (bp)Protein Length (aa)Mass (Da)
Glutamate-rich protein 495513014,447
Glutamate-rich protein 4 isoform X11741155N/A

Protein

General Properties

The primary encoded protein consists of 130 amino acids and has a predicted molecular mass of 14.5 kDa and isoelectric point of 4 pI. [24] As suggested by the protein's name, glutamate-rich protein 4, the protein is most highly composed of glutamic acid amino acids at 17.7% of the protein's composition followed by leucine at 14.6%, and then proline at 9.2%. [25] ERICH4 has no positive or negative charge clusters. [25] The human protein has one identifiable mixed cluster from amino acid 91 to 116 with 3 positively-charged, 15 negatively-charged, and 8 neutral amino acids. [25] The same mixed cluster region in humans is frequently negative within ERICH4's orthologous proteins. [25] This protein contains no significant hydrophobic or transmembrane segments which are supported with comparison to five of ERICH4's orthologs (Graymouse lemur, Sheep, House mouse, African elephant, and Opossum). [25]

Domains

ERICH4 has one identified domain of unknown function, DUF4530, which is found in eukaryotes. [26] Proteins in this family are typically 140 amino acids in length and ERICH4 is a known human member of this family. [27]

Proposed Tertiary Structure for ERICH4 ERICH4TertStruct.png
Proposed Tertiary Structure for ERICH4

Secondary Structure

A cross-program analysis determines ERICH4 protein to be composed of five separated alpha helixes and five interspersing coils. The alpha helix segments span from amino acids 2-9, 21-24, 47-58, 61-94, and 104-111 in the protein sequence. ERICH4 is not predicted to contain beta-sheets. [28] [29] [30] [31]

Tertiary Structure

Program analysis in SWISS-Model proposes a tertiary structure for ERICH4 by matching the protein against the template of NLRP6 with a sequence identity of 25.79%, sequence similarity of 0.30, and coverage of 0.43 for amino acids 43-92 in ERICH4. [32]

Post-translational Regulation

ERICH4 has proposed phosphorylation at serine amino acids 28 and 96 and amino acid 36, a threonine, by casein kinase II and protein kinase c, respectively. [33] [34] ERICH4 is not predicted to be undergo a methionine cleavage or acetylation. [35]

Localization

This protein is predicted to be intracellular without any transmembrane regions. Sub-cellular localization is predicted to be mostly localized to the cytoplasm with a reliability score of 70.6 via the Reinhardt's method. [36] No significant O-GlcNAc site and N-myristoylation predictions. [37]

Tissue Expression

ERICH4’s highest levels of expression are within human tissue of the duodenum and small intestine, followed by the kidneys. [1] [38] Notably, expression within the small intestines is highest in the twentieth week of human fetal development. [1] [39] Within a representative set of mouse (Mus musculus) tissues, Erich4 is most highly expressed within the kidneys, followed by and in decreasing expression, the large intestines, adult duodenum, and adult small intestine. [40] The Sigma-Aldrich antibody product, HPA042632, derived from rabbit, has a strong granular cytoplasmic positivity in cytoplasmic structure in glandular cells (goblet cells) of the rectum. [41]

Tissue specificity of ERICH4 determined from RNA sequencing of human tissue. ERICH4TissueExp.png
Tissue specificity of ERICH4 determined from RNA sequencing of human tissue.
Tissue specificity of ERICH4 in human fetal samples between ten and twenty weeks gestational time. ERICH4TissueExpFetal.png
Tissue specificity of ERICH4 in human fetal samples between ten and twenty weeks gestational time.


Abnormal Tissue Expression

ERICH4 has high expression within normal tissue and low-to-medium expression with renal cell carcinoma tissue. [42]

An analysis examining ERICH4 was reviewed in tissues of the ileum and colon that were either normal or afflicted with Crohn's disease or ulcerative colitis. ERICH4 had high (~90%) expression within the ileum for all states (normal/control, Crohn's disease, and ulcerative colitis). [43] ERICH4 also has a higher expression in Crohn's disease than in either normal tissue or ulcerative colitis.

ERICH4 gene expression in clear-cell renal carcinoma including tumors and tumografts deficient for tumor suppressor BAP1 or PBRM1. Renal ERICH4.png
ERICH4 gene expression in clear-cell renal carcinoma including tumors and tumografts deficient for tumor suppressor BAP1 or PBRM1.
Microarray analysis of ERICH4 gene expression within intestinal tissue of the ileum and colon from probands with Crohn's disease, Ulcerative Colitis, or control patients. IBS ERICH4.png
Microarray analysis of ERICH4 gene expression within intestinal tissue of the ileum and colon from probands with Crohn's disease, Ulcerative Colitis, or control patients.

Function

The function of ERICH4 has yet to be well understood by the scientific community and therefore, requires further research.

Interactions

According to STRING analysis, ERICH4 has multiple predicted interactions with other proteins including proteins with associated immune function and expression within the gastrointestinal tract or testes from textmining. [44] No experimentally confirmed protein interactions yet.

Predicted Partner ProteinScoreAssociated Functions
Tetratricopeptide Repeat Domain 29 (TTC29)0.680Shown to be significantly upregulated during wound healing of human masticatory mucosa. [45]
Transmembrane Protein 184A (TMEM184A)0.552Functions as a heparin receptor and mediates anti-inflammatory responses of ECs involving decreased JNK and p38 activity. [46]
Insulin-like Growth Factor binding protein Acid Labile Subunit (IGFALS) 0.509Serum protein that binds insulin-like growth factors, increasing their half-life and their vascular localization. [47]
Serine Peptidase Inhibitor, Kazal type 4 (SPINK4)0.500Has been shown to exhibit Celiac disease pathology-related differential gene expression, likely derived from altered goblet cell activity. [48]
Protein Disulfide-Isomerase-Like protein of the Testis (PDILT)0.497Catalyzes protein folding and thiol-disulfide interchange reactions. This protein lacks oxidoreductase activity in vitro and is suspected to function as a chaperone. [49]

Homology

Paralogs

No human paralogs were found for the gene. [2]

Orthologs

Orthologs have been identified in most mammals for which complete genome data is available. Notably, ERICH4 orthologs are only present in placental and marsupial mammals but absent in monotremes. [2] The most distant ortholog was identified in the gray short-tailed opossum which is a marsupial mammal. [2]

No significant similarities were found in the vertebrates Aves, Reptilia, Amphibia, Chondrichthyes, Osteichthyes or Agnatha. Searching to exclude vertebrates in BLAST and BLAT produced no significant ortholog findings for invertebrates, fungi, and bacteria. [2]

SpeciesCommon NameNCBI Accession NumberSequence Length (AA)Millions of Years since LCA  % Identity % SimilarityTaxonomic Group
Homo sapiens HumanNP_001123986.1130---100100 Primates
Microcebus murinus Gray mouse lemurXP_012616209.1179737280Primates
Tupaia chinensis Northern treeshrewXP_006165343.1137856372 Scandentia
Mus pahari Gairdner's shrewmouseXP_021075502.1141885763 Rodentia
Meriones unguiculatus Mongolian gerbilXP_021519873.1141886064Rodentia
Rattus norvegicus Brown ratNP_001102923.1147886165Rodentia
Mus musculus House mouseNP_001034332.2140886271Rodentia
Microtus ochrogaster Prairie voleXP_005361243.1140886271Rodentia
Erinaceus europaeus European hedgehogXP_007536664.1129946168 Eulipotyphla
Orcinus orca Killer whaleXP_004271419.2121946272 Cetacea
Physeter catodon Sperm whaleXP_007128192.1121946472Cetacea
Desmodus rotundus Common vampire batXP_024433457.1180946673 Chiroptera
Ovis aries SheepXP_012045823.2131946975 Artiodactyla
Bos taurus CattleXP_002695042.1131946975Artiodactyla
Pteropus alecto Black flying foxXP_006910763.1133947178Chiroptera
Hipposideros armiger Great roundleaf batXP_019488166.1134947179Chiroptera
Loxodonta africana African bush elephantXP_003420798.11271025866 Proboscidea
Monodelphis domestica Gray short-tailed opossumXP_007492011.11061604561 Didelphimorphia
Phascolarctos cinereus KoalaXP_020834126.11091604863 Diprotodontia
Vombatus ursinus Common wombatXP_027701859.11091604964Diprotodontia

Molecular Evolution

The m value, or number of corrected amino acid changes per 100 residues, for the gene ERICH4 was plotted against the divergence of species in millions of years. When compared to the data of hemoglobin, fibrinogen alpha chain, and cytochrome C, it was determined that the gene has the closest progression to fibrinogen alpha chain, suggesting a relatively rapid pace of evolution. M values for ERICH4 were derived from percentage of identity of species protein sequences compared to the human sequence using the formula derived from the Molecular Clock Hypothesis.

References

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  2. 1 2 3 4 5 "ERICH4 Orthologs". NCBI - BLAST.
  3. ↑ "ERICH4 Gene (Protein Coding)". GeneCards. Retrieved 7 February 2019.
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  5. ↑ Kovaks K, Steinmann M, Magistretti P, Halfon O, Cardinaux J (2003). "CCAAT/Enhancer-binding Protein Family Members Recruit the Coactivator CREB-binding Protein and Trigger Its Phosphorylation". The Journal of Biological Chemistry. 278 (38): 36959–36965. doi: 10.1074/jbc.M303147200 . PMID   12857754.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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  34. ↑ "SIB Motif Scan".
  35. ↑ "SIB Terminus, N-Terminal PTM Prediction".[ permanent dead link ]
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