FAM98A

Last updated
FAM98A
Identifiers
Aliases FAM98A , family with sequence similarity 98 member A
External IDs MGI: 1919972 HomoloGene: 41042 GeneCards: FAM98A
Orthologs
SpeciesHumanMouse
Entrez

25940

72722

Ensembl

ENSG00000119812

ENSMUSG00000002017

UniProt

Q8NCA5

Q3TJZ6

RefSeq (mRNA)

NM_015475
NM_001304538

NM_133747
NM_001357860

RefSeq (protein)

NP_001291467
NP_056290
NP_001291467.1
NP_056290.3

NP_598508
NP_001344789

Location (UCSC) Chr 2: 33.53 – 33.6 Mb Chr 17: 75.84 – 75.86 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Family with sequence similarity 98, member A, or FAM98A, is a gene that in the human genome encodes the FAM98A protein. FAM98A has two paralogs in humans, FAM98B and FAM98C. All three are characterized by DUF2465, a conserved domain shown to bind to RNA. [5] FAM98A is also characterized by a glycine-rich C-terminal domain. [6] FAM98A also has homologs in vertebrates and invertebrates and has distant homologs in choanoflagellates and green algae.

Contents

Gene

Locus

The FAM98A gene is located on 2p22.3 in humans on the "-" (minus) strand. Including the 5' and 3' UTR, the gene spans 15,634 bases and contains 8 exons. [7]

mRNA

The mRNA is 2745bp, comprising the 8 exons. The coding sequence starts at base 75 and continues until base 1631. The polyA tail signal sequence is a six-nucleotide sequence 20 bases from the 3' end of the transcript at base 2725-2730, and the polyA site is at base 2745. [8]

Protein

Primary Sequence

FAM98A is 518 amino acids in length with a molecular weight of 55.3 kDa, without modifications. Residues 10-329 comprise the DUF2465, and the remainder of the protein is a diglycine-rich C terminus. Glycine makes up approximately 20% of the protein, with the majority of these in the last 200 residues. [9]

Post-Translational Modifications

FAM98A has six strongly predicted phosphorylation sites in DUF2465. These sites are predicted to phosphorylate S169, T178, S236, T243, S276, and S285 by protein kinase C. [10] GPS also predicts phosphorylation by protein kinase C at S285 and T178. [11] FAM98A is likely sumoylated at K183 and K195. [12] Sumoylation may allow the cell to re-localize FAM98A between the nucleus and the cytoplasm. [13] The glycine-rich C terminus has repeat GRG sequences, which has been shown to be susceptible to methylation of the arginine, either symmetrically or asymmetrically. [14] Another paper explains the effects of arginine methylation on biochemical functions such as transcription activation and repression, mRNA splicing, nuclear-cytosolic shuttling, and DNA repair. [15]

Secondary Structure

The N terminus is predicted to have multiple alpha helices, though the C terminus likely is only coiled. [16] The alpha helices do not form any channel, and FAM98A is not a transmembrane protein.

Tertiary and Quaternary Structure

The structure of FAM98A was predicted with the program Phyre2. The N-terminal region contains several alpha helices, and a C-terminal coiled region corresponding to the glycine-rich C terminus. These two regions of the protein are connected by an alpha helix approximately 50 residues long from the residues 200-256. Phyre2 found the most similar protein to be the human protein NDC80 kinetochore complex component, a nuclear protein that binds to microtubules. [17]

Domains and Motifs

FAM98A has a domain of unknown function 2465 (DUF2465) from the amino acids 10-329. Within the DUF2465, there is a heptide (VPDRGGR) near the C-terminal end that is conserved in all species tested. The C-terminal end is a glycine-rich domain (glycine makes up about 40% of the C terminus) with GGRGGR repeats. [9] At residues 149-155, there is a predicted nuclear export signal, with the sequence ICIALGM (generally [LIVFM]-X-[LIVFM]-X-[LIVFM]-X-[LIVFM]). [18] Residues 173-176 are predicted to be a nuclear localization signal KKLK (K-[K/R]-X-[K/R]). [19]

Homology

Paralogs

FAM98A has two paralogs: FAM98B and FAM98C. FAM98A is longest of the three paralogous protein products with 518 amino acids. It is more similar to FAM98B, whose glycine-rich C terminus is much shorter than FAM98A. FAM98C less similar than FAM98B to FAM98A, all but lacking in a C terminus after DUF2465, as well as containing more differences in the amino acid sequence within the DUF2465. All three protein products have been shown experimentally to associate non-specifically with RNA: FAM98A binds to mRNA and FAM98B is incorporated into a tRNA-splicing complex. [5]

Orthologs

Orthologs for FAM98A have been found in vertebrates. In insects and molluscs, there are predicted proteins for a FAM98A gene. Because there are three paralogs of FAM98 in humans, there is a common ancestor of these genes. A strict ortholog, a gene that is orthologous to FAM98A and not the entire FAM98 family, is less clear. FAM98A has not yet been thoroughly studied, compounded with the fact that many genomes are yet to be recorded, makes it more difficult to determine if the predicted FAM98A gene in mosquitoes is a strict ortholog (the split of FAM98 into FAM98A,B,C occurred before the species diverged) or if it is a homolog ("FAM98A" in mosquitoes is the ancestral FAM98 gene).

A graph of the data at the left relating the percent identity of the protein sequence between animals and humans. FAM98A Orthologs Graph.png
A graph of the data at the left relating the percent identity of the protein sequence between animals and humans.
Sequence NumberGenus species (Gsp)Common NameDate of Divergence (MYA) (from Time Tree)Accession # (from NCBI)Sequence Length (AA)IdentitySimilarity
1Homo sapiens (Hsa)Human0

NM_015475.3

518100100
2Mus musculus (Mmu)Mouse92.3

NP_598508.2

5159596
3Camelus ferus (Cfe)Bactrian Camel94.2

XP_006192455.1

5179798
4Pantholops hodgsonii (Pho)Tibetan Antelope94.2

XP_005963883.1

5219697
5Elephantulus edwardii (Eed)Cage Elephant Shrew98.7

XP_006882420.1

5179496
6Geospiza fortis (Gfo)Medium Ground Finch296

XP_005416400.1

6488488
7Pseudopodoces humilis (Phu)Ground Tit296

XP_005526966.1

5458488
8Alligator mississippiensis (Ami)American Alligator296

XP_006273242.1

5568186
9Pelodiscus sinensis (Psi)Chinese Soft-shelled Turtle296

XP_006131385.1

5498588
10Chrysemys picta bellii (Cpi)Western Painted Turtle296

XP_005296336.1

5498588
11Xenopus tropicalis (Xtr)Western Clawed Frog371.2

XP_002934502.2

5207986
12Anoplopoma fimbria (Afi)Sablefish400.1

BT082651.1

3533148
13Ictalurus punctatus (Ipu)Channel Catfish400.1

AHH38396.1

5436775
14Camponotus floridanus (Cfl)Florida Carpenter Ant782.7

EFN74857.1

5164153
15Culex quinquefasciatus (Cqu)Mosquito782.7

XM_001846602.1

4983852
16Ceratitis capitata (Cca)Medfly782.7

JAC03102.1

4543551
17Lepeophtheirus salmonis (Lsa)Salmon Louse782.7

BT078155.1

4672945
18Crassotrea gigas (Cgi)Pacific Oyster782.7

EKC33026.1

4224559
19Clonorchis sinensis (Csi)Chinese Liver Fluke792.4

GAA34581.2

3783547
20Echinococcus granulosus (Egr)Dog Tapeworm792.4

CDJ19758.1

11773956

Distant Homologs

Genes homologous to FAM98A are predicted to occur in many taxa within Animalia, but there are other taxa outside of Animalia that may have homologous FAM98 genes in their genomes. Eukaryotes such as the opisthokonts Monosiga brevicollis (XP_00174505.1) and Capraspora owczarzaki (XP_004346371.1), and even the protist Chlorella variabilis (XP_005845167.1), a green alga, may contain FAM98 in their genomes. [20]

Homologous Domains

The homologous domain in FAM98A is the DUF2465 (Domain of Unknown Function 2465) domain. The function of this domain, like the gene itself, is largely unknown, though it has been reported that it preferentially binds to RNA, targeting mRNA in FAM98A and tRNA in FAM98B. [5]

Expression

Promoter

The promoter (GXP_90934) assigned to the human FAM98A transcript (GXT_24436545) [21] is 915 bp long, and it overlaps with the transcript to include 243 bp of mRNA transcript. Nuclear respiratory factor 1 (NRF1) is a transcription factor that had seven sites predicted to bind on the promoter, four of which had a Matrix similarity - optimum score of greater than or equal to 0.085 and the two highest scoring transcription factors predicted were NRF1 with scores of 0.204 and 0.199. [22]

Expression

In a GEO large-scale human transcriptome, FAM98A was ubiquitously expressed, though not uniformly expressed. Cell types that were most highly expressed were many parts of the brain (cortex, amygdala, thalamus, corpus callosum, and pituitary gland), the testis, uterus, and smooth muscle. [23] According to Aceview, FAM98A is expressed at 3.9 times the expression of the average gene. Eleven transcripts have been identified by AceView, five of which were "good", complete (both N and C termini fully translated) proteins. From the transcripts, there are apparently two main parts of FAM98A: the first four exons and the second four exons, and these parts correspond roughly to the tertiary structure of the protein - the N-terminal alpha-helices to exons 1-4, and the long alpha-helical arm and C terminus coils to exons 5-8. [24]

Function and Biochemistry

The function of FAM98A has not been experimentally determined, though it has been shown to bind its DUF2465 with mRNA. [5] Kiraga et al. have noted that basic proteins bind with nucleic acids. [25] In fact, FAM98A (and it orthologs) have an unmodified isoelectric point of approximately 9. [26]

Known Interactions

FAM98A has been experimentally shown to interact with UBC, DDX1, C14orf166, and SUMO3, and it is coexpressed with DDX1, C14orf166, and RBM25. [27] These latter three proteins interact with mRNA, as FAM98A is also predicted to do. DDX1 is a putative ATP-dependent RNA helicase in a spliceosome, likely releasing the RNA from the splicing complex. [28] C14orf166 is a polymerase II binding factor, [29] and RBM25 regulates alternative splicing. [30] All of these interactions suggest that FAM98A is a nuclear protein. FAM98A also interacts with SUMO3, which sumoylates lysines in the protein to facilitate transport across the nuclear membrane between the nucleus and cytosol. [13] FAM98A also binds nonspecific mRNA indicating a potential mRNA shuttle out of the nucleus to the ribosomes. [5]

Clinical Significance

In a study that looked at differences in expression levels of certain genes (including FAM98A) in both young and old men with high or low protein diets, the expression levels were measured as a ratio of low/high protein diets in each group of men (young and old). FAM98A had increased expression in low protein diets in both young and old men, 1.01 and 1.20, respectively. Only one other gene in the study had the same trend of increased expression in lower protein diets in both groups: THOC4. [31] THOC4, THO Complex 4 or Aly/REF export factor, dimerizes to form a larger complex and chaperones spliced mRNA, assisting with processing and export of the mRNA. [32] The paper mentions that up-regulation of mRNA in older individuals is associated with RNA binding/splicing, signaling proteins, and protein degradation; in fact, the older group has the higher expression of FAM98A in low protein diets than the younger men. [31]

Disease Association

Research on a population in Taiwan has found an association between young onset hypertension and two SNPs upstream of four genes at the locus 2p22.3. One of these four genes was FAM98A, though more research must be done to verify that it was FAM98A that was the gene responsible for the hypertension. [33] Indeed, FAM98A is expressed moderately high (roughly the 75th percentile) in smooth muscle and cardiac myocytes. [23]

Related Research Articles

<span class="mw-page-title-main">Alternative splicing</span> Process by which a gene can code for multiple proteins

Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. This means the exons are joined in different combinations, leading to different (alternative) mRNA strands. Consequently, the proteins translated from alternatively spliced mRNAs usually contain differences in their amino acid sequence and, often, in their biological functions.

<span class="mw-page-title-main">SR protein</span>

SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are "S" and "R" respectively. SR proteins are ~200-600 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm.

<span class="mw-page-title-main">YIF1A</span> 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.

<span class="mw-page-title-main">C11orf49</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">C20orf27</span> Protein-coding gene in the species Homo sapiens

UPF0687 protein C20orf27 is a protein that in humans is encoded by the C20orf27 gene. It is expressed in the majority of the human tissues. One study on this protein revealed its role in regulating cell cycle, apoptosis, and tumorigenesis via promoting the activation of NFĸB pathway.

<span class="mw-page-title-main">Proline-rich 12</span> Protein-coding gene in the species Homo sapiens

Proline-rich 12 (PRR12) is a protein of unknown function encoded by the gene PRR12.

<span class="mw-page-title-main">ARMH3</span> Protein-coding gene in the species Homo sapiens

ARMH3 or Armadillo Like Helical Domain Containing 3, also known as UPF0668 and c10orf76, is a protein that in humans is encoded by the ARMH3 gene. Its function is not currently known, but experimental evidence has suggested that it may be involved in transcriptional regulation. The protein contains a conserved proline-rich motif, suggesting that it may participate in protein-protein interactions via an SH3-binding domain, although no such interactions have been experimentally verified. The well-conserved gene appears to have emerged in Fungi approximately 1.2 billion years ago. The locus is alternatively spliced and predicted to yield five protein variants, three of which contain a protein domain of unknown function, DUF1741.

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<span class="mw-page-title-main">C3orf70</span> Protein-coding gene in the species Homo sapiens

C3orf70 also known as Chromosome 3 Open Reading Frame 70, is a 250aa protein in humans that is encoded by the C3orf70 gene. The protein encoded is predicted to be a nuclear protein; however, its exact function is currently unknown. C3orf70 can be identified with known aliases: Chromosome 3 Open Reading Frame 70, AK091454, UPF0524, and LOC285382.

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<span class="mw-page-title-main">TMEM171</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">Small integral membrane protein 14</span>

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<span class="mw-page-title-main">C7orf50</span> Mammalian protein found in Homo sapiens

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<span class="mw-page-title-main">LSMEM2</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">FAM98C</span> Gene

Family with sequence 98, member C or FAM98C is a gene that encodes for FAM98C has two aliases FLJ44669 and hypothetical protein LOC147965. FAM98C has two paralogs in humans FAM98A and FAM98B. FAM98C can be characterized for being a Leucine-rich protein. The function of FAM98C is still not defined. FAM98C has orthologs in mammals, reptiles, and amphibians and has a distant orhtologs in Rhinatrema bivittatum and Nanorana parkeri.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000119812 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000002017 - Ensembl, May 2017
  3. ↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. 1 2 3 4 5 Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J (July 2013). "Experimental characterization of the human non-sequence-specific nucleic acid interactome". Genome Biology. 14 (7): R81. doi: 10.1186/gb-2013-14-7-r81 . PMC   4053969 . PMID   23902751.
  6. ↑ "Pfam: Family: DUF2465 (PF10239)". Pfam. EMBL-EBI. Retrieved 5 May 2014.
  7. ↑ "Human Gene FAM98A (uc002rpa.1)". Genome. NCBI. Retrieved 5 May 2014.
  8. ↑ NCBI (National Center for Biotechnology Information) mRNA sequence FAM98A NM_015475.3 https://www.ncbi.nlm.nih.gov/nuccore/NM_015475.3
  9. 1 2 Brendel, V.; Bucher, P.; Nourbakhsh, I.R.; Blaisdell, B.E.; Karlin, S. (1992). "Methods and algorithms for statistical analysis of protein sequences". Proc. Natl. Acad. Sci. U.S.A. 89 (6): 2002–2006. Bibcode:1992PNAS...89.2002B. doi: 10.1073/pnas.89.6.2002 . PMC   48584 . PMID   1549558.
  10. ↑ Blom N, Sicheritz-Pontén T, Gupta R, Gammeltoft S, Brunak S (June 2004). "Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence". Proteomics. 4 (6): 1633–49. doi:10.1002/pmic.200300771. PMID   15174133. S2CID   18810164.
  11. ↑ Xue Y, Ren J, Gao X, Jin C, Wen L, Yao X (September 2008). "GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy". Molecular & Cellular Proteomics. 7 (9): 1598–608. doi:10.1074/mcp.m700574-mcp200. PMC   2528073 . PMID   18463090.
  12. ↑ Abgent, a WuXi App Tec company. SUMOplotTM Analysis Program. 2013. http://www.abgent.com/tools
  13. 1 2 Matunis MJ, Coutavas E, Blobel G (December 1996). "A novel ubiquitin-like modification modulates the partitioning of the Ran-GTPase-activating protein RanGAP1 between the cytosol and the nuclear pore complex". The Journal of Cell Biology. 135 (6 Pt 1): 1457–70. doi:10.1083/jcb.135.6.1457. PMC   2133973 . PMID   8978815.
  14. ↑ Hyun YL, Lew DB, Park SH, Kim CW, Paik WK, Kim S (June 2000). "Enzymic methylation of arginyl residues in -gly-arg-gly- peptides". The Biochemical Journal. 348 (3): 573–8. doi:10.1042/0264-6021:3480573. PMC   1221099 . PMID   10839988.
  15. ↑ Bedford MT, Clarke SG (January 2009). "Protein arginine methylation in mammals: who, what, and why" (PDF). Molecular Cell. 33 (1): 1–13. doi:10.1016/j.molcel.2008.12.013. PMC   3372459 . PMID   19150423.
  16. ↑ PELE (BPS, D_R, DSC, GGR, GOR, G_G, H_K, K_S, L_G, Q_S, JOI). SDSC Workbench. Board of Trustees of the University of Illinois, 1999.
  17. ↑ Kelley LA, Sternberg MJ (2009). "Protein structure prediction on the Web: a case study using the Phyre server" (PDF). Nature Protocols. 4 (3): 363–71. doi:10.1038/nprot.2009.2. hdl: 10044/1/18157 . PMID   19247286. S2CID   12497300.
  18. ↑ Fu SC, Imai K, Horton P (September 2011). "Prediction of leucine-rich nuclear export signal containing proteins with NESsential". Nucleic Acids Research. 39 (16): e111. doi:10.1093/nar/gkr493. PMC   3167595 . PMID   21705415.
  19. ↑ Timmers AC, Stuger R, Schaap PJ, van 't Riet J, Raué HA (June 1999). "Nuclear and nucleolar localization of Saccharomyces cerevisiae ribosomal proteins S22 and S25". FEBS Letters. 452 (3): 335–40. doi: 10.1016/s0014-5793(99)00669-9 . PMID   10386617. S2CID   1933493.
  20. ↑ Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 (17): 3389–402. doi:10.1093/nar/25.17.3389. PMC   146917 . PMID   9254694.
  21. ↑ Transcript GXT_2827489. Genomatix software. 2014. http://www.genomatix.de/cgi-bin/%5B%5D/eldorado/eldorado.pl?s=2ab9d4751cbd873358acdd746c629f61;TRANS=1;TRANSCRIPTID=2827489;ELDORADO_VERSION=E28R1306
  22. ↑ GXP_90934. Genomatix software. 2014. http://www.genomatix.de/cgi-bin/%5B%5D/eldorado/eldorado.pl?s=99a7e4da5d3118fa8a93fb9a283d710f;PROM_ID=GXP_90934;GROUP=vertebrates;GROUP=others;ELDORADO_VERSION=E28R1306
  23. 1 2 National Center for Biotechnology Information, US National Library of Medicine. Gene Expression Omnibus (GEO) Profiles. "Large-scale analysis of the human transcriptome (HG-U133A)". https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS596:212333_at
  24. ↑ "Homo sapiens complex locus FAM98A, encoding family with sequence similarity 98, member A." AceView. NCBI.
  25. ↑ Kiraga J, Mackiewicz P, Mackiewicz D, Kowalczuk M, Biecek P, Polak N, Smolarczyk K, Dudek MR, Cebrat S (June 2007). "The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms". BMC Genomics. 8: 163. doi: 10.1186/1471-2164-8-163 . PMC   1905920 . PMID   17565672.
  26. ↑ Program by Dr. Luca Toldo, developed at http://www.embl-heidelberg.de. Changed by Bjoern Kindler to print also the lowest found net charge. Available at EMBL WWW Gateway to Isoelectric Point Service "EMBL WWW Gateway to Isoelectric Point Service". Archived from the original on 2008-10-26. Retrieved 2014-05-10.
  27. ↑ STRING 9.1. FAM98A. http://string-db.org/newstring_cgi/show_network_section.pl
  28. ↑ "DEAD (Asp-Glu-Ala-Asp) Box Helicase 1". GeneCards.
  29. ↑ "Chromosome 14 Open Reading Frame 166". GeneCards.
  30. ↑ "RNA Binding Motif Protein 25". GeneCards.
  31. 1 2 Thalacker-Mercer AE, Fleet JC, Craig BA, Campbell WW (November 2010). "The skeletal muscle transcript profile reflects accommodative responses to inadequate protein intake in younger and older males". The Journal of Nutritional Biochemistry. 21 (11): 1076–82. doi:10.1016/j.jnutbio.2009.09.004. PMC   2891367 . PMID   20149619.
  32. ↑ "Aly/REF Export Factor". GeneCards.
  33. ↑ Yang HC, Liang YJ, Wu YL, Chung CM, Chiang KM, Ho HY, Ting CT, Lin TH, Sheu SH, Tsai WC, Chen JH, Leu HB, Yin WH, Chiu TY, Chen CI, Fann CS, Wu JY, Lin TN, Lin SJ, Chen YT, Chen JW, Pan WH (2009). "Genome-wide association study of young-onset hypertension in the Han Chinese population of Taiwan". PLOS ONE. 4 (5): e5459. Bibcode:2009PLoSO...4.5459Y. doi: 10.1371/journal.pone.0005459 . PMC   2674219 . PMID   19421330.
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