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At2G37120: A Gene Exploration

At2G37120: A Gene Exploration. An Arabidopsis Journey Through Experimental Questioning By Jeremy Ziskind. 112011. DNA Pool 5. What is the structure of AT2G37120?. 123257. 118631. -887 -823. -201 -180 -53 1 146 173 509 713 855 932 1212 1241.

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At2G37120: A Gene Exploration

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  1. At2G37120: A Gene Exploration An Arabidopsis Journey Through Experimental Questioning By Jeremy Ziskind

  2. 112011 DNA Pool 5 What is the structure of AT2G37120? 123257 118631 -887 -823 -201 -180 -53 1 146 173 509 713 855 932 1212 1241 • Expressed in Suspensor of Scarlet Runner Bean • Chromosome 2 of Arabidopsis -932 base pairs in length -2 exons -5’ and 3’ UTRs • What organisms is a potential ortholog found in? -Oryza sativa, Japanese rice Madison Insert SALK Inserts

  3. What is the Gene’s Possible Function? • Codes for S1Fa which is most likely a nuclear DNA binding protein • S1Fa important for the binding specificity of a small protein that binds to DNA • Protein only has 70 amino acids (Smallest DNA binding protein ever reported) • Has no homology to any known DNA binding modules • Conclusion: S1Fa belong to a NOVEL CLASS OF DNA BINDING PROTEINS!!!

  4. SRB EST vs Arabidopsis • EST: PCSC16872 (42125) Length = 408 Score = 39.6 bits (80), Expect(3) = 2e-09 Identities = 15/21 (71%), Positives = 15/21 (71%) Frame = +2 / -2 • Query: 353 MRNVTSRPPITSSTINPGFNP 415 • MRNV S PP TS TI PG NP • Sbjct: 146 MRNVNSNPPTTSRTIKPGLNP 84 • CONCLUSIONS: SRB EST has 71% region of amino acid homology to Arabidopsis protein sequence Comparing AT2G37120 gene expression (protein sequence) in Arabidopsis to Scarlet Runner Bean expression

  5. Where is S1FA mRNA present in Arabidopsis and SRB? Conclusions: S1Fa is affected by lec1 because expression patterns are different in the absence of lec1 PcL1L Control mRNA accumulation patterns in Scarlet Runner Bean 100 Kb Ladder S1FA Bands Primer Dimerazation

  6. Is there a knockout in Madison Lines? Rounds 1 and 2 Superpool 28 DNA Pool 5 Superpool 28 Control -201 -180 -53 1 146 173 509 713 855 932 1212 1241 DNA Pool #5 with a size of about 1400 base pairs Sequencing results verify that the insert is in DNA Pool #5! DNA Pool Screen

  7. What is the genotype of Arabidopsis plants with SALK insert #118631? Negative Water Control Wild-type Allele Amplification Mutant Allele Amplification WT 9 8 7 6 5 4 3 2 1 Tubulin Conclusions: SALK plants 1-9 are homozygous for the wild-type allele and have no T-DNA insertions Extremely faint Tubulin

  8. Further Experiments • Further SALK genotyping must be performed to determine whether At2G37120 is important for seed development • Phenotyping must be done on SALK #118631 plants to determine if the knockouts affect seed development or any other aspect of plant development • DNA Pool #5 must be narrowed down to find the individual line with a knockout in At2G37120

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