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DnaJ homolog subfamily C member 28 (DNAJC28) is a protein that in humans is encoded by the DNAJC28 gene.[1] It is a member of chaperone DnaJ family. The family is also known as Hsp40 (heat shock protein 40 kDa).

Gene

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DNAJC28 human gene location with surrounding genes.[1] IFNGR2 encodes the beta chain of the gamma interferon receptor, and defects in it cause extreme immunodeficiency.[2] TMEM50B is hypothesized to be involved in endosome to vacuole transportation. Neighboring GART is involved in de novo purine synthesis.[3] SON encodes a protein that binds RNA, promotes pre-mRNA splicing, and recognizes a human Hepatitis B virus DNA sequence, repressing its core promoter activity.[4]

The DNAJC28 gene is located on the negative strand of Chromosome 21 (21q22.11), spanning 3,784 base pairs.[5] Also known as C21orf78 or (previously) C21orf55 in humans, this gene has orthologs in animals, plants, and fungi.[6] DNAJC28 has only 2 exons, the first of which is the only one that differs between transcript variants.

RNA and Transcriptional variants

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DNAJC28 has a total of 3 transcriptional variants, all of which differ from transcript variant 1 in the 5’ UTR and encode an identical protein. All transcripts contain the same 2 exons, with exon 2 completely containing the coding sequence.[7]

DNAJC28 transcriptional variants, numerically labeled on the left. The 2 exons are also labeled. Light green regions are untranslated while the dark green regions are the coding sequence.
RNA and Protein Products of Each DNAJC28 Transcript Variant
DNAJC28 Transcript Variant Number Accession Number mRNA length (nucleotides) 5'UTR length (nucleotides) Protein Length (amino acids)
1 NM_017833.5 1706 367 388
2 NM_001040192.3 1485 146 388
3 NM_001320746.3 1462 123 388

Protein

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The protein DNAJC28 is 388 amino acids long and contains a conserved N-terminal DnaJ domain, which is critical for interaction with Hsp70s, a family of heat shock proteins that act as chaperones[8]. Molecular weight and isoelectric point of human DNAJC28 without post-translational modification are 45.8 kDal and 9.57 pI, respectively.[9][10] DNAJC28 has no isoforms. No pattern was found across orthologs for amino acid composition.

Conserved Regions

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DNAJC28 contains a J (DnaJ) domain, which is a defining feature of the DnaJ/HSP40 family. J domains are highly conserved and are an integral part of protein translation, folding, translocation, and degradation through stimulating the ATPase activity of members of the HSP70 family.[11] Each J domain is around 70 base pairs long, composed of four alpha helices, and have a highly conserved His-Pro-Asp (HPD) tripeptide motif between the second and third helices.[12][13]

There is a conserved domain of unknown function (DUF1992) from amino acids 203-272.[14]

There is a coiled-coil region from approximately amino acids 288-318 that is conserved throughout all listed orthologs (through fungi and plants).[15][16]

Tertiary Structure

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Predicted DNAJC28 J domain annotated with helices and HPD motif. Helix locations and shape were predicted using E. coli DnaJ protein. HPD motif is highlighted.

The E. coli DnaJ protein's J domain has been extensively analyzed and found to be of very similar tertiary structure to J domains of other members of the DnaJ family.[17] DNAJC28's J domain tertiary structure was predicted based off of the characteristics of other J domains.

Interacting Proteins

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DNAJC28 was found to mostly interact with proteins involved with the mitochondria and mitochondrial ATPases. Mitochondrial HSP70 is also known to control F1F0 ATP synthase assembly and control the quality of F1F0 ATP synthase components.[18][19] Other protein interactions were found on BioGrid.[20][21]

DNAJC28 Protein Interactions[20]
Hit Full Name Function Location Score
IARS2 isoleucyl-tRNA synthetase 2, mitochondrial Catalyze aminoacylation of tRNA by linking cognate amino acid Mitochondria, cytoplasm 935
LETM1 leucine zipper and EF-hand containing transmembrane protein 1 Maintains mitochondrial tubular shapes, required for cellular viability Inner mitochondrial membrane 1535
SLC30A9 solute carrier family 30 member 9 Enables zinc ion transmembrane transporter activity, regulates mitochondria organization Mitochondrial membrane, ER, cytoplasm 1570
TIMM44 translocase of inner mitochondrial membrane 44 Mediates binding of HSP70 to translocase of inner mitochondrial membrane 23 complex Mitochondrial membrane 2270

Expression and localization

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DNAJC28 iTasser Model 2. N-terminus is colored red. The predicted mitochondrial presequence is pictured in green (amino acids 7-39), light green is the NCBI listed DnaJ domain, yellow is Helix 1 (52-56), teal is Helix 2 (64-78), orange is the HPD motif, blue is Helix 3 (85-99), purple is Helix 4 (105-112).

A mitochondrial presequence was predicted from amino acids 7-39. Amino acids 7-16 are a highly positively charged amphiphilicity region. A mitochondrial targeting signal presequence traditionally has a high composition of arginine, a very low amount of negatively charged residues at the N-terminus, and forms an amphipathic helix with a positively charged side and a hydrophobic side opposite it.[22][23] The mitochondrial presequence cleavage site is predicted to be at amino acid 48.[24]

There is low, ubiquitous expression of DNAJC28 in all human tissues.[25] DNAJC28 is also expressed in almost all parts of the mouse brain, excluding the hypothalamus and pons.[26]

Function

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The DnaJ/HSP40 family is one of the largest groups of molecular chaperones, characterized by their possession of a J domain (or DnaJ domain), which interacts with HSP70.[27] HSP40s bind misfolded polypeptides and deliver them to HSP70 substrate-binding domains, greatly stimulating ATPase activity in the HSP70 nucleotide-binding domain.[12] Heat Shock Protein genes are generally activated when the cell is exposed to stress, such as high temperature, infection, and low oxygen[28]. Subfamily C, which contains DNAJC28, is defined only by the presence of a J domain, not by the location of that J domain or specific-amino-acid rich sequences like the other two subfamilies. Members of subfamily C generally only interact with a limited number of substrates or do not bind directly to a substrate at all. Some HSP40 proteins, instead of working with HSP70, assist polypeptide movement through the mitochondrial translocon.[12]

The HPD tripeptide motif of the J domain interacts with key regions of HSP70 proteins, specifically the HSP70 linker and nucleotide-binding domain (NBD) crevice, which then restricts the HSP70 protein in an optimal position for ATP hydrolysis.[29] The J domain also interacts with the HSP70 substrate-binding domain β (SBDβ) to make more efficient signal transmission from the SBD to the NBD, greatly increasing affinity between the HSP70 ADP-bound equilibrium state and substrates.[30]

Orthologs

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DNAJC28 Evolutionary History comparing median Date of Divergence from Homo sapiens (millions of years) and Corrected Sequence Divergence for DNAJC28, Cytochrome C, Fibrinogen Alpha, and COG4. Corrected sequence divergence was calculated using the percent identity between the protein sequences of the different species to humans.

There are three distinct subfamilies within the DNAJ group, of which subfamily A has the most taxonomically distant homolog of E. coli DnaJ, suggesting that it evolved earlier in history than the other subfamilies.[31] DNAJC28 has its most distant orthologs in fungi. There are many DNAJ pseudogenes that are homologous only to part of the J-protein but tend to lack a majority of it[32].

DNAJC28 has one possible, distant paralog, Component of Oligomeric Golgi Complex 4 (COG4). COG4’s corresponding protein is a component of an oligomeric protein complex in the golgi apparatus that is involved in its structure and function, specifically retrograde transport.[33]

The gene DNAJC28 is evolving relatively slowly since it is not evolving much faster than Cytochrome C and is significantly slower than Fibrinogen Alpha, as shown by the dark blue trendline.

DNAJC28 Orthologs
Organism Type Species Name Common Name Taxonomic Group Date of Divergence % Identity % Similarity Accession Number Protein Length (Amino Acids)
Mammal Homo sapiens Human Primates 0 - - NP_060303.2 388
Mus musculus House mouse Rodentia 87 72.49% 79.70% NP_001093208.1 409
Pteropus vampyrus Large flying fox Chiroptera 94 86.49% 93.30% XP_011363977.1 384
Ornithorhynchus anatinus Platypus Monotremata 180 68.32% 79.40% XP_007667935.2 381
Reptile Alligator mississippiensis American alligator Crocodilia 319 64.72% 75.10% XP_059576706.1 378
Sphaerodactylus townsendi Townsend's least gecko Squamata 319 60.50% 73.10% XP_048348340.1 374
Bird Falco peregrinus Peregrin falcon Falconiformes 319 59.47% 73.30% XP_055657544.1 372
Gallus gallus Chicken Galliformes 319 59.09% 72.80% XP_004934562.2 373
Amphibian Bufo bufo Common toad Anura 352 58.70% 71.20% XP_040279093.1 384
Rhinatrema bivittatum Two-lined caecilians Gymnophiona 352 58.01% 71.90% XP_029459412.1 379
Fish Protopterus annectens West African lungfish Dipnoi 408 50.82% 67.40% XP_043928883.1 374
Latimeria chalumnae West Indian Ocean coelacanth Sarcopterygii 415 54.80% 74.50% XP_006001534.1 379
Danio rerio Zebrafish Cyprinidae 429 47.40% 66.00% NP_001017648.1 376
Callorhinchus milii Australian ghostshark Chondrichthyes 462 54.23% 64.30% XP_007904164.1 376
Invertebrate Drosophila melanogaster Fruit fly Insecta 686 39.27% 50.60% AAY55603.1 355
Fungi Rhizopus microsporus Fungal plant pathogen Mucoraceae 1275 46.67% 26.80% CEG77023.1 518
Dacryopinax primogenitus Jelly fungi Basidiomycota 1275 37.84% 33.80% XP_040633566.1 481
Rhizomucor pusillus Human disease fungi Lichtheimiaceae 1275 35.00% 34.50% KAL1929861.1 329
Plant Panicum virgatum Switchgrass Monocots 1530 40.00% 24.60% XP_039855031.1 221
Populus trichocarpa Black cottonwood Eudicots 1530 37.14% 26.20% XP_002322905.3 221
Sphagnum troendelagicum Norwegian peat moss Bryophyta 1530 36.50% 34.50% CAK9220607.1 261

Clinical significance

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The HSP70/HSP40 chaperone system works in proteostasis processes, which involves breaking down protein aggregations like a-synuclein which accumulates in Parkinson’s disease[34]. A study found that damaging missense variants of DNAJC28 are likely related to sporadic late-onset Parkinson’s disease.[35]

DNAJC28 was found to be excessively expressed in the hippocampus of the lupus-prone mice model MRL/lpr during TWEAK (TNF-like weak inducer of apoptosis) activation, which is associated with the neuropsychiatric impacts of lupus. That overexpression could either be damaging or a protective response to lupus.[36] Overexpression of other DNAJ genes has been shown to contribute to neuroprotective effects in multiple neurodegenerative disease models.[37] HSP70 are also know to be a crucial, suppressive part of the intrinsic apoptosis pathway.[38]

No SNPs were found to have clinical significance.[39]

References

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  20. ^ a b Piette, Benjamin L.; Alerasool, Nader; Lin, Zhen-Yuan; Lacoste, Jessica; Lam, Mandy Hiu Yi; Qian, Wesley Wei; Tran, Stephanie; Larsen, Brett; Campos, Eric; Peng, Jian; Gingras, Anne-Claude; Taipale, Mikko (2021-06-17). "Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains". Molecular Cell. 81 (12): 2549–2565.e8. doi:10.1016/j.molcel.2021.04.012. ISSN 1097-2765. PMID 33957083.
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  30. ^ De Los Rios, Paolo; Barducci, Alessandro (2014-05-27). Chakraborty, Arup K (ed.). "Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption". eLife. 3: e02218. doi:10.7554/eLife.02218. ISSN 2050-084X.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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  34. ^ Liu, Qinglian; Liang, Ce; Zhou, Lei (2019-10-07). "Structural and functional analysis of the Hsp70/Hsp40 chaperone system". Protein Science. 29 (2): 378–390. doi:10.1002/pro.3725. ISSN 0961-8368. PMC 6954727. PMID 31509306.{{cite journal}}: CS1 maint: PMC format (link)
  35. ^ Zhang, Kailin; Pan, Hongxu; Zhao, Yuwen; Wang, Yige; Zeng, Qian; Zhou, Xun; He, Runcheng; Zhou, Xiaoxia; Xiang, Yaqin; Zhou, Zhou; Li, Yu; Xu, Qian; Sun, Qiying; Tan, Jieqiong; Yan, Xinxiang (2022-09-01). "Genetic Analysis of HSP40/DNAJ Family Genes in Parkinson's Disease: a Large Case-Control Study". Molecular Neurobiology. 59 (9): 5443–5451. doi:10.1007/s12035-022-02920-5. ISSN 1559-1182.
  36. ^ Iacobas, Dumitru A.; Wen, Jing; Iacobas, Sanda; Putterman, Chaim; Schwartz, Noa (2021-07-29). "TWEAKing the Hippocampus: The Effects of TWEAK on the Genomic Fabric of the Hippocampus in a Neuropsychiatric Lupus Mouse Model". Genes. 12 (8): 1172. doi:10.3390/genes12081172. ISSN 2073-4425. PMC 8392718. PMID 34440346.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
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  39. ^ "Home - SNP - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2024-12-05.
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