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Protein isoform

(Redirected fromIsoforms)

Aprotein isoform,or "protein variant",[1]is a member of a set of highly similarproteinsthat originate from a singlegeneand are the result of genetic differences.[2]While many perform the same or similar biological roles, some isoforms have unique functions. A set of protein isoforms may be formed fromalternative splicings,variablepromoterusage, or otherpost-transcriptional modificationsof a single gene;post-translational modificationsare generally not considered. (For that, seeProteoforms.) ThroughRNA splicingmechanisms,mRNAhas the ability to select different protein-coding segments (exons) of a gene, or even different parts of exons from RNA to form different mRNA sequences. Each unique sequence produces a specific form of a protein.

Protein A, B and C are isoforms encoded from the same gene throughalternative splicing.

The discovery of isoforms could explain the discrepancy between the small number of protein coding regions of genes revealed by thehuman genome projectand the large diversity of proteins seen in an organism: different proteins encoded by the same gene could increase the diversity of theproteome.Isoforms at the RNA level are readily characterized bycDNAtranscript studies. Many human genes possess confirmedalternative splicingisoforms. It has been estimated that ~100,000 expressed sequence tags (ESTs) can be identified in humans.[1]Isoforms at the protein level can manifest in the deletion of whole domains or shorter loops, usually located on the surface of the protein.[3]

Definition

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One single gene has the ability to produce multiple proteins that differ both in structure and composition;[4][5]this process is regulated by thealternative splicingof mRNA, though it is not clear to what extent such a process affects the diversity of the human proteome, as the abundance of mRNA transcript isoforms does not necessarily correlate with the abundance of protein isoforms.[6]Three-dimensional protein structure comparisons can be used to help determine which, if any, isoforms represent functional protein products, and the structure of most isoforms in the human proteome has been predicted byAlphaFoldand publicly released atisoform.io.[7]The specificity of translated isoforms is derived by the protein's structure/function, as well as the cell type and developmental stage during which they are produced.[4][5]Determining specificity becomes more complicated when a protein has multiple subunits and each subunit has multiple isoforms.

For example, the5' AMP-activated protein kinase(AMPK), an enzyme, which performs different roles in human cells, has 3 subunits:[8]

  • α, catalytic domain, has two isoforms: α1 and α2 which are encoded fromPRKAA1andPRKAA2
  • β, regulatory domain, has two isoforms: β1 and β2 which are encoded fromPRKAB1andPRKAB2
  • γ, regulatory domain, has three isoforms: γ1, γ2, and γ3 which are encoded fromPRKAG1,PRKAG2,andPRKAG3

In human skeletal muscle, the preferred form is α2β2γ1.[8]But in the human liver, the most abundant form is α1β2γ1.[8]

Mechanism

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Main article:Alternative splicing
Different mechanisms ofRNA splicing

The primary mechanisms that produce protein isoforms are alternative splicing and variable promoter usage, though modifications due to genetic changes, such asmutationsandpolymorphismsare sometimes also considered distinct isoforms.[9]

Alternative splicing is the mainpost-transcriptional modificationprocess that produces mRNA transcript isoforms, and is a major molecular mechanism that may contribute to protein diversity.[5]Thespliceosome,a largeribonucleoprotein,is the molecular machine inside the nucleus responsible for RNA cleavage andligation,removing non-protein coding segments (introns).[10]

Because splicing is a process that occurs betweentranscriptionandtranslation,its primary effects have mainly been studied throughgenomicstechniques—for example,microarrayanalyses andRNA sequencinghave been used to identify alternatively spliced transcripts and measure their abundances.[9]Transcript abundance is often used as a proxy for the abundance of protein isoforms, thoughproteomicsexperiments using gel electrophoresis and mass spectrometry have demonstrated that the correlation between transcript and protein counts is often low, and that one protein isoform is usually dominant.[11]One 2015 study states that the cause of this discrepancy likely occurs after translation, though the mechanism is essentially unknown.[12]Consequently, although alternative splicing has been implicated as an important link between variation and disease, there is no conclusive evidence that it acts primarily by producing novel protein isoforms.[11]

Alternative splicing generally describes a tightly regulated process in which alternative transcripts are intentionally generated by the splicing machinery. However, such transcripts are also produced by splicing errors in a process called "noisy splicing," and are also potentially translated into protein isoforms. Although ~95% of multi-exonic genes are thought to be alternatively spliced, one study on noisy splicing observed that most of the different low-abundance transcripts are noise, and predicts that most alternative transcript and protein isoforms present in a cell are not functionally relevant.[13]

Other transcriptional and post-transcriptional regulatory steps can also produce different protein isoforms.[14]Variable promoter usage occurs when the transcriptional machinery of a cell (RNA polymerase,transcription factors,and otherenzymes) begin transcription at different promoters—the region of DNA near a gene that serves as an initial binding site—resulting in slightly modified transcripts and protein isoforms.

Characteristics

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Generally, one protein isoform is labeled as the canonical sequence based on criteria such as its prevalence and similarity toorthologous—or functionally analogous—sequences in other species.[15]Isoforms are assumed to have similar functional properties, as most have similar sequences, and share some to most exons with the canonical sequence. However, some isoforms show much greater divergence (for example, throughtrans-splicing), and can share few to no exons with the canonical sequence. In addition, they can have different biological effects—for example, in an extreme case, the function of one isoform can promote cell survival, while another promotes cell death—or can have similar basic functions but differ in their sub-cellular localization.[16]A 2016 study, however, functionally characterized all the isoforms of 1,492 genes and determined that most isoforms behave as "functional alloforms." The authors came to the conclusion that isoforms behave like distinct proteins after observing that the functional of most isoforms did not overlap.[17]Because the study was conducted on cellsin vitro,it is not known if the isoforms in the expressed human proteome share these characteristics. Additionally, because the function of each isoform must generally be determined separately, most identified and predicted isoforms still have unknown functions.

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Glycoform

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Main article:Glycoprotein

Aglycoformis an isoform of a protein that differs only with respect to the number or type of attachedglycan.Glycoproteinsoften consist of a number of different glycoforms, with alterations in the attachedsaccharideoroligosaccharide.These modifications may result from differences inbiosynthesisduring the process ofglycosylation,or due to the action ofglycosidasesorglycosyltransferases.Glycoforms may be detected through detailed chemical analysis of separated glycoforms, but more conveniently detected through differential reaction withlectins,as inlectin affinity chromatographyandlectinaffinity electrophoresis.Typical examples of glycoproteins consisting of glycoforms are theblood proteinsasorosomucoid,antitrypsin,andhaptoglobin.An unusual glycoform variation is seen inneuronal cell adhesion molecule, NCAMinvolvingpolysialic acids, PSA.

Examples

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  • G-actin:despite its conserved nature, it has a varying number of isoforms (at least six in mammals).
  • Creatine kinase,the presence of which in the blood can be used as an aid in the diagnosis ofmyocardial infarction,exists in 3 isoforms.
  • Hyaluronan synthase,the enzyme responsible for the production of hyaluronan, has three isoforms in mammalian cells.
  • UDP-glucuronosyltransferase,an enzyme superfamily responsible for the detoxification pathway of many drugs, environmental pollutants, and toxic endogenous compounds has 16 known isoforms encoded in the human genome.[18]
  • G6PDA: normal ratio of active isoforms in cells of any tissue is 1:1 shared with G6PDG. This is precisely the normal isoform ratio in hyperplasia. Only one of these isoforms is found during neoplasia.[19]

Monoamine oxidase,a family of enzymes that catalyze the oxidation of monoamines, exists in two isoforms, MAO-A and MAO-B.

See also

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References

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  1. ^abBrett D, Pospisil H, Valcárcel J, Reich J, Bork P (January 2002). "Alternative splicing and genome complexity".Nature Genetics.30(1):29–30.doi:10.1038/ng803.PMID11743582.S2CID2724843.
  2. ^Schlüter H, Apweiler R, Holzhütter HG, Jungblut PR (September 2009)."Finding one's way in proteomics: a protein species nomenclature".Chemistry Central Journal.3:11.doi:10.1186/1752-153X-3-11.PMC2758878.PMID19740416.
  3. ^Kozlowski, L.; Orlowski, J.; Bujnicki, J. M. (2012). "Structure Prediction for Alternatively Spliced Proteins".Alternative pre-mRNA Splicing.p. 582.doi:10.1002/9783527636778.ch54.ISBN9783527636778.
  4. ^abAndreadis A, Gallego ME, Nadal-Ginard B (1987-01-01). "Generation of protein isoform diversity by alternative splicing: mechanistic and biological implications".Annual Review of Cell Biology.3(1):207–42.doi:10.1146/annurev.cb.03.110187.001231.PMID2891362.
  5. ^abcBreitbart RE, Andreadis A, Nadal-Ginard B (1987-01-01). "Alternative splicing: a ubiquitous mechanism for the generation of multiple protein isoforms from single genes".Annual Review of Biochemistry.56(1):467–95.doi:10.1146/annurev.bi.56.070187.002343.PMID3304142.
  6. ^Liu Y, Beyer A, Aebersold R (April 2016)."On the Dependency of Cellular Protein Levels on mRNA Abundance".Cell.165(3):535–50.doi:10.1016/j.cell.2016.03.014.hdl:20.500.11850/116226.PMID27104977.
  7. ^Sommer, Markus J.; Cha, Sooyoung; Varabyou, Ales; Rincon, Natalia; Park, Sukhwan; Minkin, Ilia; Pertea, Mihaela; Steinegger, Martin; Salzberg, Steven L. (2022-12-15)."Structure-guided isoform identification for the human transcriptome".eLife.11:e82556.doi:10.7554/eLife.82556.PMC9812405.PMID36519529.
  8. ^abcDasgupta B, Chhipa RR (March 2016)."Evolving Lessons on the Complex Role of AMPK in Normal Physiology and Cancer".Trends in Pharmacological Sciences.37(3):192–206.doi:10.1016/j.tips.2015.11.007.PMC4764394.PMID26711141.
  9. ^abKornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz MJ (March 2013). "Alternative splicing: a pivotal step between eukaryotic transcription and translation".Nature Reviews Molecular Cell Biology.14(3):153–65.doi:10.1038/nrm3525.hdl:11336/21049.PMID23385723.S2CID54560052.
  10. ^Lee Y, Rio DC (2015-01-01)."Mechanisms and Regulation of Alternative Pre-mRNA Splicing".Annual Review of Biochemistry.84(1):291–323.doi:10.1146/annurev-biochem-060614-034316.PMC4526142.PMID25784052.
  11. ^abTress ML, Abascal F, Valencia A (February 2017)."Alternative Splicing May Not Be the Key to Proteome Complexity".Trends in Biochemical Sciences.42(2):98–110.doi:10.1016/j.tibs.2016.08.008.PMC6526280.PMID27712956.
  12. ^Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y (February 2015)."Genomic variation. Impact of regulatory variation from RNA to protein".Science.347(6222):664–7.doi:10.1126/science.1260793.PMC4507520.PMID25657249.
  13. ^Pickrell JK, Pai AA, Gilad Y, Pritchard JK (December 2010)."Noisy splicing drives mRNA isoform diversity in human cells".PLOS Genetics.6(12): e1001236.doi:10.1371/journal.pgen.1001236.PMC3000347.PMID21151575.
  14. ^Smith LM, Kelleher NL (March 2013)."Proteoform: a single term describing protein complexity".Nature Methods.10(3):186–7.doi:10.1038/nmeth.2369.PMC4114032.PMID23443629.
  15. ^Li HD, Menon R, Omenn GS, Guan Y (December 2014)."Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence"(PDF).Proteomics.14(23–24):2709–18.doi:10.1002/pmic.201400170.PMC4372202.PMID25265570.
  16. ^Sundvall M, Veikkolainen V, Kurppa K, Salah Z, Tvorogov D, van Zoelen EJ, Aqeilan R, Elenius K (December 2010)."Cell death or survival promoted by alternative isoforms of ErbB4".Molecular Biology of the Cell.21(23):4275–86.doi:10.1091/mbc.E10-04-0332.PMC2993754.PMID20943952.
  17. ^Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, et al. (February 2016)."Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing".Cell.164(4):805–17.doi:10.1016/j.cell.2016.01.029.PMC4882190.PMID26871637.
  18. ^Barre L, Fournel-Gigleux S, Finel M, Netter P, Magdalou J, Ouzzine M (March 2007)."Substrate specificity of the human UDP-glucuronosyltransferase UGT2B4 and UGT2B7. Identification of a critical aromatic amino acid residue at position 33".The FEBS Journal.274(5):1256–64.doi:10.1111/j.1742-4658.2007.05670.x.PMID17263731.
  19. ^Pathoma, Fundamentals of Pathology
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