User:Nzimm: Difference between revisions
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'''Email:''' nzimm (at) mit (dot) edu | '''Email:''' nzimm (at) mit (dot) edu | ||
====SAGA subunits, <i> S. cerevisiae </i>==== | |||
{| border="1" | |||
! Ada subunits | |||
! size,chromosome,null p-type | |||
! notes | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA1 Ada1] (aka HFI1, SUP110, SRM12, GAN1) | |||
| 1.467 kb/489 aa, Chr. XVI, <br>viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA2 Ada2] (aka SWI8) | |||
| 1.305 kb/434aa, Chr. IV, <br>viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ADA3 Ada3](aka NGG1, SWI7) | |||
| 2.109 kb/702aa, Chr. IV, <br>viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=GCN5 Gcn5] (aka ADA4, SWI9) | |||
| 1.32 kb/439aa, Chr. VII, <br>viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Ada5 Ada5] (aka SPT20) | |||
| 1.815 kb/604aa, Chr. XV, <br>viable | |||
| | |||
|} | |||
{| border="1" | |||
! Spt subunits | |||
! size, chromosome, null p-type | |||
! notes | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=spt3 Spt3] | |||
| 1.014 kb/337aa, Chr. IV, <br> viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Spt7 Spt7](aka GIT2) | |||
| 3.999 kb/1332aa, Chr. II, <br> viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Spt8 Spt8] | |||
| 1.809 kb/602aa, Chr. XII, <br> viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=SPT20 Spt20] (aka Ada5) | |||
| 1.815 kb/604aa, Chr. XV, <br> viable | |||
| | |||
|} | |||
{| border="1" | |||
! TAF subunits | |||
! size, chromosome, null p-type | |||
! notes | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=TAF5 TAF5] (aka TAF90) | |||
| 2.397 kb/798aa, Chr. II, <font color = red>inviable</font color> | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=TAF6 TAF6] (aka TAF60) | |||
| 1.551 kb/516aa, Chr. VII, <font color = red>inviable</font color> | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=TAF9 TAF9] (aka TAF17) | |||
| 0.474 kb/157aa, Chr. XIII, <font color = red>inviable</font color> | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=TAF10 TAF10] (aka TAF23, TAF25) | |||
| 0.621 kb/206aa, Chr. IV, <font color = red>inviable</font color> | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=TAF12 TAF12](aka TAF61, TAF68) | |||
| 1.620 kb/539aa, Chr. IV, <font color = red>inviable</font color> | |||
| | |||
|} | |||
{| border="1" | |||
! Tra1 subunit | |||
! size, chromosome, null p-type | |||
! notes | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=TRA1 Tra1] | |||
| 11.235 kb/3744aa, Chr. VIII, <font color = red>inviable</font color> | |||
| | |||
|} | |||
{| border="1" | |||
! other subunits | |||
! size, chromosome, null p-type | |||
! notes | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf73 Sgf73] | |||
| 1.974 kb/657aa, Chr. VII , <br> viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf29 Sgf29] | |||
| 0.779 kb/259aa, Chr. III, <br> viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf11 Sgf11] | |||
| 0.3 kb/99aa, Chr.XVI, <br> viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=ubp8 Ubp8] | |||
| 1.416 kb/471aa, Chr. XIII, <br> viable | |||
| | |||
|- | |||
| [http://db.yeastgenome.org/cgi-bin/locus.pl?locus=Sus1 Sus1] | |||
| gene with intron, Chr. II, <br> viable | |||
| | |||
|} |
Revision as of 10:41, 3 April 2007
Neil Zimmerman
Bio
- MIT Class of 2009
- Major: Biological Engineering
- Minors: Management and Music
- Varsity Soccer
- Wind Ensemble (Clarinet)
20.109
M13K07 Genome Engineering Plans:
Gene | Plans |
---|---|
I | Change # of protein copies expressed to experiment with different sized channels |
II | Modify residues to allow deactivation of p2 under certain conditions so that replication of + strand can be regulated |
III | Insert myc to allow detection with an antibody |
IV | Change # of protein copies expressed to experiment with different sized channels |
V | Add fluorescent tag to monitor levels of p5-ssDNA complex |
VI | Modify residues to help p3 bind more effectively to the ToIA protein on the E. coli F pilus |
VII | Minimize the bulk of the protein to allow more room for modifications on p9 |
VIII | Insert myc (as in III) or another tag to serve as a “hook” for attaching constructs to M13 |
IX | Add residues to N-terminus to present on the outside of the phage coat |
X | Add sensitivity to different stimulus than that of p2 in order to regulate replication of + strand in another fashion |
XI | Modify residues to allow proteins other than p8 to embed in the membrane and serve as the phage filament coat |
M13K07 Genome Refactoring:
In refactoring the M13K07 genome between the HpaI site in gene II and the BamHI site in gene III, I separated all overlapping elements across the region by copying overlapping sequences and placing the elements adjacent to one another on the refactored sequence. As a result, the refactored region is 1,000 bp larger than the original sequence. I also added annotation for & refactored the open reading frames of genes 2, 5, 7, and 10, which are not annotated in the M1307 part in the registry. I inserted the sequence encoding the myc protein into g3. I intend to separate each element with two unique restriction sites, so that the elements can be isolated & manipulated more easily. I initially proposed to add a fluorescent tag like GFP to g5, but seeing as how GFP is nearly 3 times the size of the protein product of g5, I chose to leave g5 unaltered. Below is a table describing the overlaps that were refactored.
Overlapping elements | Action |
---|---|
rbs g7 & g5 ORF | copied overlapping sequence & placed rbs g7 adjacent to the 3' end of the g5 ORF |
promoter g8 & rbs g9 | copied overlapping sequence & placed rbs g9 adjacent to the 3' end of promoter g8 |
promoter g3 & g8 ORF | copied overlapping sqeuence & placed promoter g3 adjacent to the 3' end of g8 ORF |
g10 ORF, g10 rbs, g10 promoter, g5 promoter, & g2 ORF | copied g2 ORF & placed adjacent to 5' end of other (non-overlapping) elements |
inserted the sequence encoding the myc protein into the BamHI site of g3 |
Current Courses
Other
Email: nzimm (at) mit (dot) edu
SAGA subunits, S. cerevisiae
Ada subunits | size,chromosome,null p-type | notes |
---|---|---|
Ada1 (aka HFI1, SUP110, SRM12, GAN1) | 1.467 kb/489 aa, Chr. XVI, viable |
|
Ada2 (aka SWI8) | 1.305 kb/434aa, Chr. IV, viable |
|
Ada3(aka NGG1, SWI7) | 2.109 kb/702aa, Chr. IV, viable |
|
Gcn5 (aka ADA4, SWI9) | 1.32 kb/439aa, Chr. VII, viable |
|
Ada5 (aka SPT20) | 1.815 kb/604aa, Chr. XV, viable |
Spt subunits | size, chromosome, null p-type | notes |
---|---|---|
Spt3 | 1.014 kb/337aa, Chr. IV, viable |
|
Spt7(aka GIT2) | 3.999 kb/1332aa, Chr. II, viable |
|
Spt8 | 1.809 kb/602aa, Chr. XII, viable |
|
Spt20 (aka Ada5) | 1.815 kb/604aa, Chr. XV, viable |
TAF subunits | size, chromosome, null p-type | notes |
---|---|---|
TAF5 (aka TAF90) | 2.397 kb/798aa, Chr. II, inviable | |
TAF6 (aka TAF60) | 1.551 kb/516aa, Chr. VII, inviable | |
TAF9 (aka TAF17) | 0.474 kb/157aa, Chr. XIII, inviable | |
TAF10 (aka TAF23, TAF25) | 0.621 kb/206aa, Chr. IV, inviable | |
TAF12(aka TAF61, TAF68) | 1.620 kb/539aa, Chr. IV, inviable |
Tra1 subunit | size, chromosome, null p-type | notes |
---|---|---|
Tra1 | 11.235 kb/3744aa, Chr. VIII, inviable |
other subunits | size, chromosome, null p-type | notes |
---|---|---|
Sgf73 | 1.974 kb/657aa, Chr. VII , viable |
|
Sgf29 | 0.779 kb/259aa, Chr. III, viable |
|
Sgf11 | 0.3 kb/99aa, Chr.XVI, viable |
|
Ubp8 | 1.416 kb/471aa, Chr. XIII, viable |
|
Sus1 | gene with intron, Chr. II, viable |