DNAJC28

File:DNAJC28_Gene_Neighborhood.jpg

The DNAJC28 gene is located on the negative strand of Chromosome 21 (21q22.11), spanning 3,784 base pairs.{{Cite web |title=AceView: Gene:DNAJC28, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView. |url=https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&term=DNAJC28&submit=Go |access-date=2024-09-26 |website=www.ncbi.nlm.nih.gov}} Also known as C21orf78 or (previously) C21orf55 in humans, this gene has orthologs in animals, plants, and fungi.{{Cite web |title=DNAJC28 orthologs |url=https://www.ncbi.nlm.nih.gov/gene/54943/ortholog/?scope=7776 |access-date=2024-09-26 |website=NCBI |language=en}} DNAJC28 has only 2 exons, the first of which is the only one that differs between transcript variants.

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.{{Cite web |date=2024-08-05 |title=Homo sapiens DnaJ heat shock protein family (Hsp40) member C28 (DNAJC28), transcript variant 1, mRNA |url=https://www.ncbi.nlm.nih.gov/nuccore/NM_017833.5 |access-date=2024-12-12 |website=National Center of Biotechnology Information}}

File:DNAJC28Exons.jpg

The protein DNAJC28 is 388 amino acids long and contains a conserved N-terminal J (DnaJ) domain, which is critical for interaction with Hsp70s.{{Cite journal |last=Morano |first=Kevin A. |date=2007-05-18 |title=New Tricks for an Old Dog: The Evolving World of Hsp70 |url=https://nyaspubs.onlinelibrary.wiley.com/doi/10.1196/annals.1391.018 |journal=Annals of the New York Academy of Sciences |language=en |volume=1113 |issue=1 |pages=1–14 |doi=10.1196/annals.1391.018 |pmid=17513460 |issn=0077-8923}} Molecular weight and isoelectric point of human DNAJC28 without post-translational modification are 45.8 kDal and 9.57 pI, respectively.{{Cite web |title=SAPS Sequence Statistics |url=https://www.ebi.ac.uk/jdispatcher/seqstats/saps |access-date=2024-12-05 |website=www.ebi.ac.uk}}{{Cite web |title=Expasy - Compute pI/Mw tool |url=https://web.expasy.org/compute_pi/ |access-date=2024-12-05 |website=web.expasy.org}} DNAJC28 has no isoforms. No pattern was found across orthologs for amino acid composition.

DNAJC28 contains a J 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.{{Cite web |title=CDD Conserved Protein Domain Family: DnaJ |url=https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=99751 |access-date=2024-12-05 |website=www.ncbi.nlm.nih.gov}} 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.{{Cite journal |last1=Kampinga |first1=Harm H. |last2=Craig |first2=Elizabeth A. |date=2010-08-01 |title=The HSP70 chaperone machinery: J proteins as drivers of functional specificity |journal=Nature Reviews Molecular Cell Biology |language=en |volume=11 |issue=8 |pages=579–592 |doi=10.1038/nrm2941 |issn=1471-0072 |pmc=3003299 |pmid=20651708}}{{Cite journal |last1=Alderson |first1=Thomas Reid |last2=Kim |first2=Jin Hae |last3=Markley |first3=John Lute |date=2016-07-06 |title=Dynamical Structures of Hsp70 and Hsp70-Hsp40 Complexes |journal=Structure |language=en |volume=24 |issue=7 |pages=1014–1030 |doi=10.1016/j.str.2016.05.011 |pmc=4938735 |pmid=27345933}}

There is a conserved domain of unknown function (DUF1992) from amino acids 203-272.{{Cite web |title=CDD Conserved Protein Domain Family: DJC28_CD |url=https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?ascbin=8&maxaln=10&seltype=2&uid=pfam09350 |access-date=2024-12-05 |website=www.ncbi.nlm.nih.gov}}

There is a coiled-coil region from approximately amino acids 288 to 318 that is conserved throughout all listed orthologs (through fungi and plants).{{Cite journal |last1=Zimmermann |first1=Lukas |last2=Stephens |first2=Andrew |last3=Nam |first3=Seung-Zin |last4=Rau |first4=David |last5=Kübler |first5=Jonas |last6=Lozajic |first6=Marko |last7=Gabler |first7=Felix |last8=Söding |first8=Johannes |last9=Lupas |first9=Andrei N. |last10=Alva |first10=Vikram |date=2018-07-20 |title=A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core |url=https://linkinghub.elsevier.com/retrieve/pii/S0022283617305879 |journal=Journal of Molecular Biology |language=en |volume=430 |issue=15 |pages=2237–2243 |doi=10.1016/j.jmb.2017.12.007|pmid=29258817 }}{{Cite journal |last1=Paysan-Lafosse |first1=Typhaine |last2=Blum |first2=Matthias |last3=Chuguransky |first3=Sara |last4=Grego |first4=Tiago |last5=Pinto |first5=Beatriz Lázaro |last6=Salazar |first6=Gustavo |last7=Bileschi |first7=Maxwell |last8=Bork |first8=Peer |last9=Bridge |first9=Alan |last10=Colwell |first10=Lucy |last11=Gough |first11=Julian |last12=Haft |first12=Daniel |last13=Letunić |first13=Ivica |last14=Marchler-Bauer |first14=Aron |last15=Mi |first15=Huaiyu |date=2023-01-06 |title=InterPro in 2022 |url=https://academic.oup.com/nar/article/51/D1/D418/6814474 |journal=Nucleic Acids Research |language=en |volume=51 |issue=D1 |pages=D418–D427 |doi=10.1093/nar/gkac993 |issn=0305-1048 |pmc=9825450 |pmid=36350672}}

File:Predicted_DNAJC28_J_domain.png

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.{{Citation |last1=Faust |first1=Ofrah |title=Structural and Biochemical Properties of Hsp40/Hsp70 Chaperone System |date=2020 |work=HSF1 and Molecular Chaperones in Biology and Cancer |volume=1243 |pages=3–20 |editor-last=Mendillo |editor-first=Marc Laurence |url=https://link.springer.com/10.1007/978-3-030-40204-4_1 |access-date=2024-12-05 |place=Cham |publisher=Springer International Publishing |language=en |doi=10.1007/978-3-030-40204-4_1 |isbn=978-3-030-40203-7 |last2=Rosenzweig |first2=Rina |pmid=32297208 |editor2-last=Pincus |editor2-first=David |editor3-last=Scherz-Shouval |editor3-first=Ruth}} DNAJC28's J domain tertiary structure was predicted and annotated based on the characteristics of other J domains.

DNAJC28 was found to mostly interact with proteins involved with the mitochondria and mitochondrial ATP synthase. Mitochondrial Hsp70 is also known to control F₁F₀ ATP synthase assembly and control the quality of F₁F₀ ATP synthase components.{{Cite journal |last1=Song |first1=Jiyao |last2=Steidle |first2=Liesa |last3=Steymans |first3=Isabelle |last4=Singh |first4=Jasjot |last5=Sanner |first5=Anne |last6=Böttinger |first6=Lena |last7=Winter |first7=Dominic |last8=Becker |first8=Thomas |date=2023-01-03 |title=The mitochondrial Hsp70 controls the assembly of the F1FO-ATP synthase |journal=Nature Communications |language=en |volume=14 |issue=1 |pages=39 |doi=10.1038/s41467-022-35720-5 |issn=2041-1723 |pmc=9810599 |pmid=36596815}}{{Cite journal |last1=Papathanassiu |first1=Adonia E. |last2=MacDonald |first2=Nicholas J. |last3=Bencsura |first3=Akos |last4=Vu |first4=Hong A. |date=2006-06-23 |title=F1F0-ATP synthase functions as a co-chaperone of Hsp90–substrate protein complexes |url=https://linkinghub.elsevier.com/retrieve/pii/S0006291X06009582 |journal=Biochemical and Biophysical Research Communications |language=en |volume=345 |issue=1 |pages=419–429 |doi=10.1016/j.bbrc.2006.04.104}} Other mitochondrial protein interactions were found on BioGrid.{{Cite journal |last1=Piette |first1=Benjamin L. |last2=Alerasool |first2=Nader |last3=Lin |first3=Zhen-Yuan |last4=Lacoste |first4=Jessica |last5=Lam |first5=Mandy Hiu Yi |last6=Qian |first6=Wesley Wei |last7=Tran |first7=Stephanie |last8=Larsen |first8=Brett |last9=Campos |first9=Eric |last10=Peng |first10=Jian |last11=Gingras |first11=Anne-Claude |last12=Taipale |first12=Mikko |date=2021-06-17 |title=Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains |url=https://linkinghub.elsevier.com/retrieve/pii/S1097276521003178 |journal=Molecular Cell |language=English |volume=81 |issue=12 |pages=2549–2565.e8 |doi=10.1016/j.molcel.2021.04.012 |issn=1097-2765 |pmid=33957083}}{{Cite web |title=Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains. {{!}} BioGRID |url=https://thebiogrid.org/228319/publication/comprehensive-interactome-profiling-of-the-human-hsp70-network-highlights-functional-differentiation-of-j-domains.html |access-date=2024-12-12 |website=thebiogrid.org}}

File:DNAJC28_Evolutionary_History.png

There are three distinct subfamilies within the DnaJ family, 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.{{Cite web |title=DnaJ [Escherichia coli] - Protein - NCBI |url=https://www.ncbi.nlm.nih.gov/protein/AAA00009.1 |access-date=2024-12-12 |website=www.ncbi.nlm.nih.gov}} 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.{{Cite journal |last1=Kampinga |first1=Harm H. |last2=Hageman |first2=Jurre |last3=Vos |first3=Michel J. |last4=Kubota |first4=Hiroshi |last5=Tanguay |first5=Robert M. |last6=Bruford |first6=Elspeth A. |last7=Cheetham |first7=Michael E. |last8=Chen |first8=Bin |last9=Hightower |first9=Lawrence E. |date=2009-01-01 |title=Guidelines for the nomenclature of the human heat shock proteins |journal=Cell Stress and Chaperones |volume=14 |issue=1 |pages=105–111 |doi=10.1007/s12192-008-0068-7 |issn=1355-8145 |pmc=2673902 |pmid=18663603}}

DNAJC28 has one distant paralog, Component of Oligomeric Golgi Complex 4 (COG4).{{Cite web |last=Database |first=GeneCards Human Gene |title=DNAJC28 Gene - GeneCards {{!}} DJC28 Protein {{!}} DJC28 Antibody |url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=DNAJC28 |archive-url=http://web.archive.org/web/20221207232241/https://www.genecards.org/cgi-bin/carddisp.pl?gene=DNAJC28 |archive-date=2022-12-07 |access-date=2024-12-12 |website=www.genecards.org |language=en}}{{Cite web |title=Gene: COG4 (ENSG00000103051) - Paralogues - Homo_sapiens - Ensembl genome browser 113 |url=https://useast.ensembl.org/Homo_sapiens/Gene/Compara_Paralog?g=ENSG00000103051;r=16:70480568-70523560 |access-date=2024-12-12 |website=useast.ensembl.org}} 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.{{Cite web |title=conserved oligomeric Golgi complex subunit 4 isoform 1 [Homo sapiens] - Protein - NCBI |url=https://www.ncbi.nlm.nih.gov/protein/NP_056201.2 |access-date=2024-12-05 |website=www.ncbi.nlm.nih.gov}}

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.

File:DNAJC28_iTasser_Model_2_N-terminus.png

A mitochondrial presequence was predicted from amino acids 7-39. Amino acids 7-16 are a highly positively charged amphiphilicity region.{{Cite journal |last1=Fukasawa |first1=Yoshinori |last2=Tsuji |first2=Junko |last3=Fu |first3=Szu-Chin |last4=Tomii |first4=Kentaro |last5=Horton |first5=Paul |last6=Imai |first6=Kenichiro |date=April 2015 |title=MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites* |journal=Molecular & Cellular Proteomics |language=en |volume=14 |issue=4 |pages=1113–1126 |doi=10.1074/mcp.M114.043083 |doi-access=free |pmc=4390256 |pmid=25670805}} 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.{{Citation |last1=Nakai |first1=Kenta |title=Prediction of Protein Localization |date=2019 |encyclopedia=Encyclopedia of Bioinformatics and Computational Biology |pages=53–59 |url=https://linkinghub.elsevier.com/retrieve/pii/B9780128096338202707 |access-date=2024-12-05 |publisher=Elsevier |language=en |doi=10.1016/b978-0-12-809633-8.20270-7 |isbn=978-0-12-811432-2 |last2=Imai |first2=Kenichiro}}{{Cite journal |last1=Genge |first1=Marcel G. |last2=Mokranjac |first2=Dejana |date=2022-01-06 |title=Coordinated Translocation of Presequence-Containing Precursor Proteins Across Two Mitochondrial Membranes: Knowns and Unknowns of How TOM and TIM23 Complexes Cooperate With Each Other |journal=Frontiers in Physiology |language=English |volume=12 |doi=10.3389/fphys.2021.806426 |doi-access=free |issn=1664-042X |pmc=8770809 |pmid=35069261}} All of which are features of the DNAJC28 targeting presequence. The mitochondrial presequence cleavage site is predicted to be at amino acid 48.{{Cite web |title=PSORT II Prediction |url=https://psort.hgc.jp/form2.html |access-date=2024-12-05 |website=psort.hgc.jp}}

There is low, ubiquitous expression of DNAJC28 in all human tissues.{{Cite web |title=GDS3113 / 177128 |url=https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS3113:177128 |access-date=2024-12-05 |website=www.ncbi.nlm.nih.gov}} DNAJC28 is also expressed in almost all parts of the mouse brain, excluding the hypothalamus and pons.{{Cite web |title=Gene Detail :: Allen Brain Atlas: Mouse Brain |url=https://mouse.brain-map.org/gene/show/89904 |access-date=2024-12-05 |website=mouse.brain-map.org}}

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.{{Citation |last1=Musskopf |first1=Maiara K |title=HSP40 / DNAJ Chaperones |date=2018 |work=eLS |pages=1–11 |url=https://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0027633 |access-date=2024-12-12 |publisher=John Wiley & Sons, Ltd |language=en |doi=10.1002/9780470015902.a0027633 |isbn=978-0-470-01590-2 |last2=de Mattos |first2=Eduardo P |last3=Bergink |first3=Steven |last4=Kampinga |first4=Harm H}} Hsp40s bind misfolded polypeptides or protein aggregates and deliver them to Hsp70 substrate-binding domains, greatly stimulating ATPase activity in the Hsp70 nucleotide-binding domain. Heat Shock Protein genes are generally activated when the cell is exposed to stress, such as high temperature, infection, and low oxygen.{{Cite journal |last1=Song |first1=Lin |last2=Zhang |first2=Jiaren |last3=Li |first3=Chao |last4=Yao |first4=Jun |last5=Jiang |first5=Chen |last6=Li |first6=Yun |last7=Liu |first7=Shikai |last8=Liu |first8=Zhanjiang |date=2014-12-26 |title=Genome-Wide Identification of Hsp40 Genes in Channel Catfish and Their Regulated Expression after Bacterial Infection |journal=PLOS ONE |language=en |volume=9 |issue=12 |pages=e115752 |doi=10.1371/journal.pone.0115752 |doi-access=free |pmid=25542027 |pmc=4277396 |issn=1932-6203}} 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.

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. The J domain also interacts with the Hsp70 substrate-binding domain β (SBDβ) to make signal transmission more efficient from the SBD to the NBD, greatly increasing affinity between the Hsp70 ADP-bound equilibrium state and substrates.{{Cite journal |last1=De Los Rios |first1=Paolo |last2=Barducci |first2=Alessandro |date=2014-05-27 |editor-last=Chakraborty |editor-first=Arup K |title=Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption |url=https://elifesciences.org/articles/02218#abstract |journal=eLife |volume=3 |pages=e02218 |doi=10.7554/eLife.02218 |doi-access=free |pmid=24867638 |issn=2050-084X|pmc=4030575 }}

The Hsp70/Hsp40 chaperone system works in proteostasis processes, which involves breaking down protein aggregations like a-synuclein which accumulates in Parkinson’s disease.{{Cite journal |last1=Liu |first1=Qinglian |last2=Liang |first2=Ce |last3=Zhou |first3=Lei |date=2019-10-07 |title=Structural and functional analysis of the Hsp70/Hsp40 chaperone system |journal=Protein Science |language=en |volume=29 |issue=2 |pages=378–390 |doi=10.1002/pro.3725 |issn=0961-8368 |pmc=6954727 |pmid=31509306}} A study found that damaging missense variants of DNAJC28 are likely related to sporadic late-onset Parkinson’s disease.{{Cite journal |last1=Zhang |first1=Kailin |last2=Pan |first2=Hongxu |last3=Zhao |first3=Yuwen |last4=Wang |first4=Yige |last5=Zeng |first5=Qian |last6=Zhou |first6=Xun |last7=He |first7=Runcheng |last8=Zhou |first8=Xiaoxia |last9=Xiang |first9=Yaqin |last10=Zhou |first10=Zhou |last11=Li |first11=Yu |last12=Xu |first12=Qian |last13=Sun |first13=Qiying |last14=Tan |first14=Jieqiong |last15=Yan |first15=Xinxiang |date=2022-09-01 |title=Genetic Analysis of HSP40/DNAJ Family Genes in Parkinson's Disease: a Large Case-Control Study |url=https://link.springer.com/article/10.1007/s12035-022-02920-5 |journal=Molecular Neurobiology |language=en |volume=59 |issue=9 |pages=5443–5451 |doi=10.1007/s12035-022-02920-5 |pmid=35715682 |issn=1559-1182}}

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.{{Cite journal |last1=Iacobas |first1=Dumitru A. |last2=Wen |first2=Jing |last3=Iacobas |first3=Sanda |last4=Putterman |first4=Chaim |last5=Schwartz |first5=Noa |date=2021-07-29 |title=TWEAKing the Hippocampus: The Effects of TWEAK on the Genomic Fabric of the Hippocampus in a Neuropsychiatric Lupus Mouse Model |journal=Genes |language=en |volume=12 |issue=8 |pages=1172 |doi=10.3390/genes12081172 |doi-access=free |issn=2073-4425 |pmc=8392718 |pmid=34440346}} Overexpression of other genes in the DnaJ family has been shown to contribute to neuroprotective effects in multiple neurodegenerative disease models.{{Cite journal |last1=Zarouchlioti |first1=Christina |last2=Parfitt |first2=David A. |last3=Li |first3=Wenwen |last4=Gittings |first4=Lauren M. |last5=Cheetham |first5=Michael E. |date=2018-01-19 |title=DNAJ Proteins in neurodegeneration: essential and protective factors |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |language=en |volume=373 |issue=1738 |pages=20160534 |doi=10.1098/rstb.2016.0534 |issn=0962-8436 |pmc=5717533 |pmid=29203718}} Hsp70 are also known to be a crucial, suppressive part of the intrinsic apoptosis pathway.{{Cite journal |last1=Lanneau |first1=D. |last2=Brunet |first2=M. |last3=Frisan |first3=E. |last4=Solary |first4=E. |last5=Fontenay |first5=M. |last6=Garrido |first6=C. |date=2008 |title=Heat shock proteins: essential proteins for apoptosis regulation |journal=Journal of Cellular and Molecular Medicine |language=en |volume=12 |issue=3 |pages=743–761 |doi=10.1111/j.1582-4934.2008.00273.x |issn=1582-4934 |pmc=4401125 |pmid=18266962}}

No DNAJC28 SNPs were found to have clinical significance.{{Cite web |title=Home - SNP - NCBI |url=https://www.ncbi.nlm.nih.gov/snp/ |access-date=2024-12-05 |website=www.ncbi.nlm.nih.gov}}

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