YIF1A

{{Short description|Protein-coding gene in the species Homo sapiens}}

Protein YIF1A is a Yip1 domain family proteins that in humans is encoded by the YIF1A gene.{{cite journal | vauthors = Vitale G, Alexandrov K, Ullrich O, Horiuchi H, Giner A, Dobson C, Baykova O, Gournier H, Stenmark H, Zerial M | display-authors = 6 | title = The GDP/GTP cycle of Rab5 in the regulation of endocytotic membrane traffic | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 60 | pages = 211–20 | date = Jan 1997 | pmid = 8824393 | doi = 10.1101/SQB.1995.060.01.024 }}{{cite journal | vauthors = Matern H, Yang X, Andrulis E, Sternglanz R, Trepte HH, Gallwitz D | title = A novel Golgi membrane protein is part of a GTPase-binding protein complex involved in vesicle targeting | journal = The EMBO Journal | volume = 19 | issue = 17 | pages = 4485–92 | date = September 2000 | pmid = 10970842 | pmc = 302084 | doi = 10.1093/emboj/19.17.4485 }}{{cite journal | vauthors = Yoshida Y, Suzuki K, Yamamoto A, Sakai N, Bando M, Tanimoto K, Yamaguchi Y, Sakaguchi T, Akhter H, Fujii G, Yoshimura S, Ogata S, Sohda M, Misumi Y, Nakamura N | display-authors = 6 | title = YIPF5 and YIF1A recycle between the ER and the Golgi apparatus and are involved in the maintenance of the Golgi structure | journal = Experimental Cell Research | volume = 314 | issue = 19 | pages = 3427–43 | date = November 2008 | pmid = 18718466 | doi = 10.1016/j.yexcr.2008.07.023 }}{{cite web | title = Entrez Gene: YIF1A Yip1 interacting factor homolog A (S. cerevisiae)| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=10897}}

Gene

YIF1A (Yip1 interacting factor homolog A) is also known as YIF1, YIF1P, FinGER7, and 54TM.{{Cite web|title=YIF1A related genes - GeneCards Search Results|url=https://www.genecards.org/Search/Keyword?queryString=YIF1A|access-date=2020-06-21|website=www.genecards.org}} It has 4,591 base pairs with 8 exons, and it is located on the minus strand of chromosome 11, at 11q13.2, in humans.{{Cite web|title=YIF1A - Gene - NCBI|url=https://www.ncbi.nlm.nih.gov/gene/?term=YIF1A|access-date=2020-06-21|website=www.ncbi.nlm.nih.gov}}

= Promoters =

There are four predicted promoter for YIIF1A.{{Cite web|title=Genomatix: Genome Annotation and Browser: Query Input|url=https://www.genomatix.de/cgi-bin/eldorado/eldorado.pl?s=60bc9d9a3ed5be4c2c5871e63042a971|access-date=2020-07-30|website=www.genomatix.de}}{{Dead link|date=March 2024 |bot=InternetArchiveBot |fix-attempted=yes }} The predicted promoter region with highest confidence is GXP_50494 and has 1252 base pairs long; it extends past the first exon of YIF1A. This promoter is located on the minus strand of chromosome 11.

= Transcription factors =

The promoter of YIF1A transcript variant 1 contains numerous transcription factor binding sites.{{Cite web|title=Genomatix: MatInspector Input|url=https://www.genomatix.de/cgi-bin/matinspector_prof/mat_fam.pl?s=ce6f229bfa4b14d36729a0ccecac8d6f|access-date=2020-08-03|website=www.genomatix.de}}{{Dead link|date=March 2024 |bot=InternetArchiveBot |fix-attempted=yes }} Transcription factors predicted to bind to the promoter region include the following.

Acute myeloid leukemia 1 protein, RUNX1 (runt-related transcription factor 1)
Zinc finger protein 263, ZKSCAN12 (zinc finger protein with KRAB and SCAN domains 12)
E2F transcription factor 1
EGR1, early growth response 1
GATA-binding factor 1
Transcription factor CP2-like 1 (LBP-9)
X-box binding protein RFX1
Estrogen response elements (ER alpha), IR3 sites
Lactotransferrin and deltalactoferrin, growth-inhibiting protein 12
TGFB-inducible early growth response protein 1 (KLF10)

= Expression =

The expression of YIF1A is highest in the duodenum and liver. It is also expressed at moderate levels in tissues including the colon, ovary, pancreases, spleen, and esophagus, and expressed at lower levels in a variety of other tissues.{{cite journal | vauthors = Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto CA, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M | display-authors = 6 | title = Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics | journal = Molecular & Cellular Proteomics | volume = 13 | issue = 2 | pages = 397–406 | date = February 2014 | pmid = 24309898 | pmc = 3916642 | doi = 10.1074/mcp.M113.035600 | doi-access = free }}{{cite journal | vauthors = Duff MO, Olson S, Wei X, Garrett SC, Osman A, Bolisetty M, Plocik A, Celniker SE, Graveley BR | display-authors = 6 | title = Genome-wide identification of zero nucleotide recursive splicing in Drosophila | journal = Nature | volume = 521 | issue = 7552 | pages = 376–9 | date = May 2015 | pmid = 25970244 | pmc = 4529404 | doi = 10.1038/nature14475 | bibcode = 2015Natur.521..376D }}{{cite journal | vauthors = Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J | display-authors = 6 | title = Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development | journal = Genome Biology | volume = 16 | pages = 126 | date = June 2015 | issue = 1 | pmid = 26076956 | pmc = 4506483 | doi = 10.1186/s13059-015-0690-5 | doi-access = free }} NCBI GeoProfile data provide the tissue expression graph for YIF1A in humans; it also indicates that YIF1A is expressed at moderately to moderately low across all other tissues.{{Cite web|title=GDS596 / 202418_at|url=https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS596:202418_at|access-date=2020-08-02|website=www.ncbi.nlm.nih.gov}}

mRNA

File:Schematic_illustration_of_YIF1A.pngYIF1A has isoforms 1 and 2, with exons 8 and 7 respectively. The two transcripts undergo alternate splicing and are translated into proteins with 293 and 241 amino acids, respectively.{{Cite web|title=protein YIF1A isoform 2 [Homo sapiens] - Protein - NCBI|url=https://www.ncbi.nlm.nih.gov/protein/NP_001287790.1|access-date=2020-07-28|website=www.ncbi.nlm.nih.gov}}{{Cite web|title=protein YIF1A isoform 1 [Homo sapiens] - Protein - NCBI|url=https://www.ncbi.nlm.nih.gov/protein/NP_065203.2|access-date=2020-07-28|website=www.ncbi.nlm.nih.gov}}

= RNA-binding proteins =

The 5' untranslated region has predicted sites for binding by RBXM, EIF4B, and FUS. The 3' untranslated region has predicted sites for binding by ELAVL1, which is AU rich elements and regulate mRNA stability.{{Cite web|title=RBPDB: The database of RNA-binding specificities|url=http://rbpdb.ccbr.utoronto.ca/|access-date=2020-08-01|website=rbpdb.ccbr.utoronto.ca}}

Protein

The longest protein isoform of YIF1A is 293 amino acids in length. It has an observed molecular weight of approximately 32.0 kDa with a predicted isoelectric point of approximately 8.98.{{Cite web|title=SAPS < Sequence Statistics < EMBL-EBI|url=https://www.ebi.ac.uk/Tools/seqstats/saps/|access-date=2020-07-28|website=www.ebi.ac.uk}}{{Cite web|title=ExPASy - Compute pI/Mw tool|url=https://web.expasy.org/compute_pi/|access-date=2020-07-28|website=web.expasy.org}}

= Composition =

YIF1 is a very normal protein in terms of the amino acid quantities it contains. The composition of each amino acid residue is similar to its average relative composition among human proteins. There are no charge clusters, runs, or patterns. There is a repetitive structure for protein YIF1A at [ 201- 204 and 288- 291 ] TFHL.

= Domain and motifs =

YIF1A has a conserved domain, pfam03878 (AA 57 →287). Within the domain, there are 5 transmembrane domains, 3 non-cytosolic domains, and 3 cytosolic domains. It has been hypothesized that there is a possible role in transport between the endoplasmic reticulum and Golgi.

= Structure =

File:YIF1A_tertiary_structure.png

The structure of YIF1A consist of approximately 59% alpha-helices, with TM helix and disordered regions making up the rest of the structure; no beta- strand was predicted.{{Cite web|title=NPS@ : GOR4 secondary structure prediction|url=https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html|access-date=2020-07-28|website=npsa-prabi.ibcp.fr}}

= Localization =

YIF1A's predicted location is in the endoplasmic reticulum, with intracellular N-terminus and an extracellular C-terminus.{{Cite web|title=PredictProtein - Protein Sequence Analysis, Prediction of Structural and Functional Features|url=https://www.predictprotein.org/|access-date=2020-07-28|website=www.predictprotein.org}}{{Cite web|title=Phobius|url=http://phobius.sbc.su.se/|access-date=2020-07-28|website=phobius.sbc.su.se}}

= Post-translational modifications =

YIF1A undergoes methionine cleavage and N-terminal acetylation, which is one of the most common post translation modifications of eukaryotic proteins.{{Cite web|title=TERMINUS - Welcome to terminus|url=http://terminus.unige.ch/|access-date=2020-07-28|website=terminus.unige.ch}} It also phosphorylated by unspecified kinases at several sites.{{Cite web|title=NetPhosK 1.0 Server|url=http://www.cbs.dtu.dk/services/NetPhosK/|access-date=2020-07-28|website=www.cbs.dtu.dk|archive-date=2021-07-09|archive-url=https://web.archive.org/web/20210709183544/http://www.cbs.dtu.dk/services/NetPhosK/|url-status=dead}} Three glycation site is predicted in lysine residue(lys 104,161, and 211).{{Cite web|title=NetGlycate 1.0 Server - prediction results|url=http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5F24B43C000072EE69610765&wait=20|access-date=2020-08-01|website=www.cbs.dtu.dk}} YIF1A undergoes O-ß-GlcNAc modification at 5 sites, 1 of them being Yin-Yang sites.{{Cite web|title=YinOYang 1.2 Server|url=http://www.cbs.dtu.dk/services/YinOYang/|access-date=2020-07-28|website=www.cbs.dtu.dk}}

= Interacting protein =

Based on fluorescence microscopy, validated two hybrid, and anti tag coimmunoprecipitation, the protein that is most likely to interact with YIF1A are GPR37, SEC23IP, REEP2, and YIPF5. Studies suggest that interaction between VAPB and YIF1A control membrane delivery into dendrites.{{cite journal|author6-link=Casper Hoogenraad | vauthors = Kuijpers M, Yu KL, Teuling E, Akhmanova A, Jaarsma D, Hoogenraad CC | title = The ALS8 protein VAPB interacts with the ER-Golgi recycling protein YIF1A and regulates membrane delivery into dendrites | journal = The EMBO Journal | volume = 32 | issue = 14 | pages = 2056–72 | date = July 2013 | pmid = 23736259 | pmc = 3715857 | doi = 10.1038/emboj.2013.131 }} It also participates in ER unfolded protein response (UPR) by inducing ERN1/IRE1.{{Cite web|title=YIF1A protein (human) - STRING interaction network|url=https://string-db.org/cgi/network.pl?taskId=hUHSbeqPGLU8|access-date=2020-07-29|website=string-db.org}} Additionally, the YIF1A protein interacts with the M protein of SARS-Cov-2.{{Cite journal|last=Mahen|first=Robert|date=2020-04-09|title=A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing|url=http://dx.doi.org/10.1242/prelights.18355|access-date=2020-08-05|doi=10.1242/prelights.18355|s2cid=243418486 }}

File:Conceptual_translation_~YIF1A.png

Homology

YIF1A has a single Paralog called YIF1B, which is located on human chromosome 19. YIF1A has 238 identified orthologs.{{Cite web|title=Nucleotide BLAST: Search nucleotide databases using a nucleotide query|url=https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome|access-date=2020-08-03|website=blast.ncbi.nlm.nih.gov}} The ortholog contains vertebrates such as mammals, amphibians, and reptiles. It also has invertebrates species such as Insecta, Anthozoa, and Ascidiacea. No ortholog was found in protists, bacteria, or archaea.

The following table provides a sample of the ortholog of YIF1A.

class="wikitable"

!Genus and species

!Accession Number

!Date of Divergence (MYA){{Cite web|title=TimeTree :: The Timescale of Life|url=http://www.timetree.org|access-date=2020-07-02|website=www.timetree.org}}

!Sequence Length(AA)

!Sequence Identity{{Cite web|title=Human BLAT Search|url=https://genome.ucsc.edu/cgi-bin/hgBlat?hgsid=847663723_MobOikzKAL9i7XZKke8yCj5cyz1Y&command=start|access-date=2020-07-02|website=genome.ucsc.edu}}

Homo sapiens (Human)

|[https://www.ncbi.nlm.nih.gov/gene/?term=NP_065203 NP_065203]

|293

|100

Aotus nancymaae (Ma's night monkey)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_012318344 XP_012318344]

|43

|317

|94

Mus musculus (Mouse)

|[https://www.ncbi.nlm.nih.gov/gene/?term=NP_080829 NP_080829]

|90

|293

|93

Sus scrofa (Wild Boar)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_013849519 XP_013849519]

|96

|311

|92

Delphinapterus leucas (White whale)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_022447094 XP_022447094]

|96

|306

|91

Phascolarctos cinereus (Koala)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_020823757 XP_020823757]

|159

|293

|88

Ornithorhynchus anatinus(Platypus)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_028915982 XP_028915982]

|177

|293

|88

Chelonia mydas(Green turtle)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_007056281 XP_007056281]

|312

|240

|78

Chrysemys picta bellii(Painted turtle)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_005305497 XP_005305497]

|312

|293

|73

Microcaecilia unicolor(Amph.)

|[https://www.ncbi.nlm.nih.gov/gene/?term=YIF1A+Microcaecilia+unicolor XP_029470520]

|352

|306

|72

Rhinatrema bivittatum(Two-lined caecilian)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_029470520 XP_029470520]

|352

|307

|71

Latimeria chalumnae (Gombessa)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_014345204 XP_014345204]

|413

|296

|71

Salmo trutta (Brown trou)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_029585843 XP_029585843]

|435

|309

|70

Echeneis naucrates (live sharksucker)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_029368074 XP_029368074]

|435

|308

|66

Danio rerio (Zebrafish)

|[https://www.ncbi.nlm.nih.gov/gene/?term=NP_956225 NP_956225]

|435

|307

|65

Maylandia zebra (zebra mbuna)

|[https://www.ncbi.nlm.nih.gov/gene/?term=XP_004545672 XP_004545672]

|435

|308

|63

Saccharomyces cerevisiae S288C (Baker's yeast)

|[https://www.ncbi.nlm.nih.gov/gene/?term=NP_014136 NP_014136]

|1017

|314

|33

Physcomitrium patens (moss)

|XP_024362517

|1275

|282

|30

YIF1A

Gene

= Promoters =

= Transcription factors =

= Expression =

mRNA

= RNA-binding proteins =

Protein

= Composition =

= Domain and motifs =

= Structure =

= Localization =

= Post-translational modifications =

= Interacting protein =

Homology

References

Further reading