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You will be compiling your bibliography and creating an outline of the changes you will make in this sandbox.

Bibliography

[edit]
  • UniProt entry[1]
    • UniProt is an open source database of protein sequences and function, so it should be a reliable source. It draws data from a number of peer reviewed sources, and its 5/5 reliability rating will help establish notability
  • Xiong, Ruyi, and Wang, Aiming. SCE1, the SUMO-Conjugating Enzyme in Plants That Interacts with NIb, the RNA-Dependent RNA Polymerase of Turnip Mosaic Virus, Is Required for Viral Infection.[2]
    • This peer reviewed article discusses this enzymes role in Potyvirus infection in Arabidopsis, but also brings in E. coli and tobacco plant genomics, showing how widespread this enzyme is. It goes into mechanisms as well.
  • Ghimire et al, SUMO conjugating enzyme: a vital player of SUMO pathway in plants[3]
    • This review goes into the broad strokes surrounding this family of enzymes. It has an excellent figure that will be included in my article as well, showing the pathway that SCE1 participates in.
  • Lois, M.L., Lima, C.D., and Chua, N.H. Small Ubiquitin-Like Modifier Modulates Abscisic Acid Signaling in Arabidopsis.[4]
    • This peer reviewed article suggests that SCE1 plays a part in stress response pathways in Arabidopsis. It also goes into how it interacts with other enzymes in the pathway and discusses its isozymes (right?) in yeast
  • Garcia-Dominguez, M., March-Diaz, R., and Reyes, J.C. The PHD Domain of Plant PIAS Proteins Mediates Sumoylation of Bromodomain GTE Proteins.[5]
    • This peer reviewed article discusses AtSCE1's binding ability with PIAS proteins, which is often required for sumoylation
  • Saracco, S.A., et al. Genetic Analysis of SUMOylation in Arabidopsis: Conjugation of SUMO1 and SUMO2 to Nuclear Proteins Is Essential.[6]
    • Discusses a few of the reasons why sumoylation is essential, shows how SCE1 mutants are embryonic lethal
  • Crozet, P. et al. SUMOylation represses SnRK1 signaling in Arabidopsis[7]
    • SCEI interacts with SnRK1, an important protein for the plant to determine which pathways to send carbon to in response to external conditions
  • Liu, B., Lois, M.L., and Reverter, D. Structural insights into SUMO E1-E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution.[8]
    • This article publishes the crystal structure of this enzyme and discusses how its active site differs from other organismal isozymes, explaining why it doesn't work in yeast mutation experiments that I believe are discussed in previous articles in this list
  • Huang et al. The Arabidopsis SUMO E3 ligase AtMMS21, a homologue of NSE2/MMS21, regulates cell proliferation in the root[9]
    • This article mentions that AtSCE1 interacts with AtMMS21, which is necessary for cell proliferation in root tissues.
  • Mazr et al. Arabidopsis TCP Transcription Factors Interact with the SUMO Conjugating Machinery in Nuclear Foci[10]
    • This article describes the transcription factors that interact with SCE1, and discusses the functions of these TFs in the plant
  • Kurepa et al. The Small Ubiquitin-like Modifier (SUMO) Protein Modification System in Arabidopsis[11]
    • The first characterization of the SUMO pathway in plants, first time it was confirmed to be present in plants
  • The Arabidopsis Information Resource (TAIR)[12]
    • This database maintains genomic data about model organism Arabidopsis thaliana.

References

[edit]
  1. ^ "UniProt". www.uniprot.org. Retrieved 2023-10-02.
  2. ^ Xiong, Ruyi; Wang, Aiming (2013-04-15). "SCE1, the SUMO-Conjugating Enzyme in Plants That Interacts with NIb, the RNA-Dependent RNA Polymerase of Turnip Mosaic Virus, Is Required for Viral Infection". Journal of Virology. 87 (8): 4704–4715. doi:10.1128/jvi.02828-12. PMC 3624346. PMID 23365455.{{cite journal}}: CS1 maint: PMC format (link)
  3. ^ Ghimire, Shantwana; Tang, Xun; Liu, Weigang; Fu, Xue; Zhang, Huanhuan; Zhang, Ning; Si, Huaijun (2021-10-01). "SUMO conjugating enzyme: a vital player of SUMO pathway in plants". Physiology and Molecular Biology of Plants. 27 (10): 2421–2431. doi:10.1007/s12298-021-01075-2. ISSN 0974-0430. PMC 8526628. PMID 34744375.{{cite journal}}: CS1 maint: PMC format (link)
  4. ^ Lois, Luisa Maria; Lima, Christopher D.; Chua, Nam-Hai (2003-05-16). "Small Ubiquitin-Like Modifier Modulates Abscisic Acid Signaling in Arabidopsis". The Plant Cell. 15 (6): 1347–1359. doi:10.1105/tpc.009902. ISSN 1040-4651. PMC 156371. PMID 12782728.{{cite journal}}: CS1 maint: PMC format (link)
  5. ^ Garcia-Dominguez, Mario; March-Diaz, Rosana; Reyes, Jose C. (2008-08). "The PHD Domain of Plant PIAS Proteins Mediates Sumoylation of Bromodomain GTE Proteins". Journal of Biological Chemistry. 283 (31): 21469–21477. doi:10.1074/jbc.m708176200. ISSN 0021-9258. {{cite journal}}: Check date values in: |date= (help)CS1 maint: unflagged free DOI (link)
  6. ^ Saracco, Scott A.; Miller, Marcus J.; Kurepa, Jasmina; Vierstra, Richard D. (2007-07-20). "Genetic Analysis of SUMOylation in Arabidopsis: Conjugation of SUMO1 and SUMO2 to Nuclear Proteins Is Essential". Plant Physiology. 145 (1): 119–134. doi:10.1104/pp.107.102285. ISSN 0032-0889. PMC 1976578. PMID 17644626.{{cite journal}}: CS1 maint: PMC format (link)
  7. ^ Crozet, Pierre; Margalha, Leonor; Butowt, Rafal; Fernandes, Noémia; Elias, Carlos A.; Orosa, Beatriz; Tomanov, Konstantin; Teige, Markus; Bachmair, Andreas; Sadanandom, Ari; Baena‐González, Elena (2016-01). "SUMO ylation represses Sn RK 1 signaling in Arabidopsis". The Plant Journal. 85 (1): 120–133. doi:10.1111/tpj.13096. ISSN 0960-7412. PMC 4817235. PMID 26662259. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  8. ^ Liu, B.; Lois, L.M.; Reverter, D. (2019-07-03). "Structure of the E2 conjugating enzyme, SCE1, from Arabidopsis thaliana". dx.doi.org. doi:10.2210/pdb6gv3/pdb. Retrieved 2023-10-03.
  9. ^ Huang, Lixia; Yang, Songguang; Zhang, Shengchun; Liu, Ming; Lai, Jianbin; Qi, Yanli; Shi, Songfeng; Wang, Jinxiang; Wang, Yaqin; Xie, Qi; Yang, Chengwei (2009-11). "The Arabidopsis SUMO E3 ligase AtMMS21, a homologue of NSE2/MMS21, regulates cell proliferation in the root". The Plant Journal. 60 (4): 666–678. doi:10.1111/j.1365-313X.2009.03992.x. {{cite journal}}: Check date values in: |date= (help)
  10. ^ Mazur, Magdalena J.; Spears, Benjamin J.; Djajasaputra, André; van der Gragt, Michelle; Vlachakis, Georgios; Beerens, Bas; Gassmann, Walter; van den Burg, Harrold A. (2017). "Arabidopsis TCP Transcription Factors Interact with the SUMO Conjugating Machinery in Nuclear Foci". Frontiers in Plant Science. 8. doi:10.3389/fpls.2017.02043. ISSN 1664-462X. PMC 5714883. PMID 29250092.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  11. ^ Kurepa, Jasmina; Walker, Joseph M.; Smalle, Jan; Gosink, Mark M.; Davis, Seth J.; Durham, Tessa L.; Sung, Dong-Yul; Vierstra, Richard D. (2003-02). "The Small Ubiquitin-like Modifier (SUMO) Protein Modification System in Arabidopsis". Journal of Biological Chemistry. 278 (9): 6862–6872. doi:10.1074/jbc.m209694200. ISSN 0021-9258. {{cite journal}}: Check date values in: |date= (help)CS1 maint: unflagged free DOI (link)
  12. ^ "TAIR - Home Page". www.arabidopsis.org. Retrieved 2023-10-03.

Outline of proposed changes

[edit]
  • An infobox nonhuman protein template[1]
    • One of those little boxes with a quick summary of important info, will include an image of the crystal structure (with caption), organsism, symbol, entrez, PDB,RefSeq, Uniprot, EC number, chromosome, start and end position
  • Introduction[2][3][1]
    • Quick definition of SCE1, that it is an E2 enzyme found in the sumoylation pathway in Arabidopsis, how many BP it has
  • Discovery[2][4]
    • Describe how the pathway is ubiquitous, first confirmation in plants in 2002
  • Structure[1][5]
    • Some basic discourse about motifs, active sites, etc
  • Function[6][7][8][9][10][11][12]
    • I think my bibliography goes these pretty well, there is a fair bit of knowledge surrounding what this bad boy does in the plant and how it interacts with everything
  • Pathway[3][2]
    • I'll likely include a nice reference image from source 3, go into detail about the pathway which is pretty well characterized
  1. ^ a b c Cite error: The named reference :0 was invoked but never defined (see the help page).
  2. ^ a b c Cite error: The named reference :10 was invoked but never defined (see the help page).
  3. ^ a b Cite error: The named reference :2 was invoked but never defined (see the help page).
  4. ^ Cite error: The named reference :11 was invoked but never defined (see the help page).
  5. ^ Cite error: The named reference :7 was invoked but never defined (see the help page).
  6. ^ Cite error: The named reference :1 was invoked but never defined (see the help page).
  7. ^ Cite error: The named reference :3 was invoked but never defined (see the help page).
  8. ^ Cite error: The named reference :4 was invoked but never defined (see the help page).
  9. ^ Cite error: The named reference :5 was invoked but never defined (see the help page).
  10. ^ Cite error: The named reference :6 was invoked but never defined (see the help page).
  11. ^ Cite error: The named reference :8 was invoked but never defined (see the help page).
  12. ^ Cite error: The named reference :9 was invoked but never defined (see the help page).
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