Ubiquitin-mediated proteolysis
From Purdue Genomics Database Facility
Contents |
Related enzymes in Selaginella moellendorffii
Ying Li (li23@purdue.edu) and Michael Gribskov (gribskov@purdue.edu)
Ubiquitin-activating enzyme (UBAs, or E1s), Ubiquitin-conjugating enzymes (UBCs, or E2s) and Ubiquitin-protein ligases (E3s) are the three types of enzymes involved in the ubiquitin-mediated proteolysis process in plants/animals. Proteins destined to be degraded are multi-ubiquitinated through a process catalyzed by the above enzymes, then are recognized and degraded by the 26S proteasome.
There are fewer E1 isoforms compared to E2 isoforms and the much more complicated E3 isoforms in plants (see Table 1, Table 2 and Table 4). Eighteen E2s are identified based on protein sequences comparison with other plant species. Table 2 shows the grouping based on sequence similarity (Kraft, et al., 2005) and comparison of UBCs among Arabidopsis thaliana, Oryza sativa , Selaginella moellendorffii and Physcomitrella Patens. Table 3 lists the number of putative E3s (ordered by E3 subfamilies) in Selaginella moellendorffii.
Table 1. Comparison of E1s
| E1 | Number of putative orthologs* | |||
|---|---|---|---|---|
| Arabidopsis | Oryza | Selaginella | Physcometrella | |
| UBA1/UBA2 | 2 | 4 | 1 (2) | 2 |
Table 2. Grouping and comparison of E2s
| Group | E2 | Number of putative orthologs* | |||
|---|---|---|---|---|---|
| Arabidopsis | Oryza | Selaginella | Physcomitrella | ||
| I | SCE1a | 1 | 1 | 1 | 1 |
| II | RCE1 | 1 | 0 | 0 | 0 |
| II | RCE2 | 1 | 1 (3) | 2 (2,2) | 2 (2,3) |
| III | UBC1 | 1 | 1 (3) | 2 (2,2) | 1 (2) |
| III | UBC2 | 1 | 0 | 0 | 0 |
| III | UBC3 | 1 | 0 | 0 | 0 |
| IV | UBC4 | 1 | 1 (1) | 0 | 1 (1) |
| IV | UBC5 | 1 | 0 | 2 (2,2) | 1 (1) |
| IV | UBC6 | 1 | 0 | 0 | 0 |
| V | UBC7 | 1 | 1 (1) | 0 | 0 |
| V | UBC13 | 1 | 1 (1) | 1 (2) | 1 (3) |
| V | UBC14 | 1 | 0 | 0 | 1 (1) |
| VI | UBC8 | 1 | 1 (1) | 1 (2) | 0 |
| VI | UBC9 | 1 | 1 (1) | 0 | 1 (1) |
| VI | UBC10 | 1 | 1 (3) | 0 | 0 |
| VI | UBC11 | 1 | 1 (1) | 1 (2) | 0 |
| VI | UBC12 | 1 | 0 | 0 | 0 |
| VI | UBC28 | 1 | 1 (1) | 1 (4) | 1 (3) |
| VI | UBC29 | 1 | 0 | 0 | 0 |
| VI | UBC30 | 1 | 0 | 0 | 1 (2) |
| VII | UBC15 | 1 | 1 (1) | 1 (2) | 1 (2) |
| VII | UBC16 | 1 | 0 | 1 (2) | 1 (2) |
| VII | UBC17 | 1 | 0 | 0 | 0 |
| VII | UBC18 | 1 | 1 (1) | 0 | 0 |
| VIII | UBC19 | 1 | 0 | 1 (2) | 0 |
| VIII | UBC20 | 1 | 1 (1) | 0 | 1 (1) |
| IX | UBC21 | 1 | 1 (1) | 0 | 1 (1) |
| X | UBC22 | 1 | 1 (1) | 1 (2) | 1 (1) |
| XI | UBC23 | 1 | 1 (2) | 0 | 1 (1) |
| XI | UBC24 | 1 | 1 (1) | 0 | 0 |
| XI | UBC25 | 1 | 1 (5) | 0 | 0 |
| XI | UBC26 | 1 | 1 (1) | 0 | 0 |
| XII | UBC27 | 1 | 1 (1) | 1 (2) | 1 (1) |
| XIII | UBC31 | 1 | 0 | 0 | 0 |
| XIV | UBC32 | 1 | 1 (1) | 1 (2) | 1 (1) |
| XIV | UBC33 | 1 | 1 (1) | 1 (2) | 1 (1) |
| XIV | UBC34 | 1 | 0 | 0 | 0 |
| XV | UBC35 | 1 | 1 (1) | 1 (2) | 1 (1) |
| XV | UBC36 | 1 | 0 | 0 | 1 (1) |
| XVI | UBC37 | 1 | 1 (1) | 1 (2) | 1 (1) |
| Total | 37 | 23 | 17 | 21 | |
footnote: number of putative loci( number of putative alleles detected, separated by comma if there are more than one group of alleles).
Table 3. Gene models in the assembly
| protein id | gene name | named by | model changes |
| 271478 | UBC1-1 | YING LI | no |
| 228869 | UBC1-2 | YING LI | no |
| 228475 | UBC1-3 | YING LI | no |
| 228312 | UBC1-4 | YING LI | no |
| 450658 | UBC5-1 | YING LI | yes |
| 450660 | UBC5-2 | YING LI | yes |
| 81550 | UBC5-3 | YING LI | no |
| 174924 | UBC5-4 | YING LI | no |
| 74865 | UBC13-1 | YING LI | no |
| 87352 | UBC13-2 | YING LI | no |
| 449723 | UBC8-1 | GRIBSKOV | yes |
| 450670 | UBC8-2 | YING LI | yes |
| 187468 | UBC11-1 | YING LI | yes |
| 233935 | UBC11-2 | YING LI | yes |
| 449724 | UBC28-1 | GRIBSKOV | yes |
| 228916 | UBC28-2 | YING LI | no |
| 270923 | UBC28-3 | YING LI | no |
| 270384 | UBC28-4 | YING LI | no |
| 270987 | UBC15-1 | YING LI | no |
| 159187 | UBC15-2 | YING LI | no |
| 268066 | UBC16-1 | YING LI | no |
| 172555 | UBC16-2 | YING LI | no |
| 181155 | UBC19-1 | YING LI | no |
| 450635 | UBC19-2 | YING LI | yes |
| 145850 | UBC22-1 | YING LI | no |
| 160563 | UBC22-2 | YING LI | no |
| 186167 | UBC27-1 | YING LI | no |
| 95808 | UBC27-2 | YING LI | no |
| 450643 | UBC32-1 | YING LI | yes |
| 450644 | UBC32-2 | YING LI | yes |
| 36529 | UBC33-1 | YING LI | no |
| 15877 | UBC33-2 | YING LI | no |
| 116003 | UBC35-1 | YING LI | no |
| 134879 | UBC35-2 | YING LI | no |
| 5749 | UBC37-like-1 | YING LI | no |
| 6339 | UBC37-like-2 | YING LI | no |
Table 4. Number of putative E3 Orthologs in Arabidopsis thalinana and Selaginella moellendorffii
| E3 subfamily | Number in ATH1 | Best Arabidopsis protein sequences match in Selmo1 | Best Selaginella protein sequences mathc in ATH1 | Arabidopsis-Selaginella sequence match combination |
| ASK | 21 | 4 | 4 | 8 |
| BTB | 80 | 33 | 40 | 66 |
| Cullin | 10 | 5 | 8 | 10 |
| HECT | 7 | 6 | 8 | 12 |
| UBOX | 60 | 19 | 25 | 36 |
| FBOX | 679 | 98 | 154 | 192 |
| RingFinger | 470 | 161 | 204 | 306 |
| PHD | 215 | 52 | 68 | 101 |
| DDB | 5 | 4 | 8 | 8 |
| RBX1 | 2 | 0 | 0 | 0 |
Note1: The matches include 1(arabidopsis gene)-to-2(selaginella alleles) and 2(arabidopsis genes)-to-1(selaginella allele) relationship, e.g., for ASK, each of the unique four arabidopsis protein sequences matched to two selaginella allele sequences, representing a 1-to-1 gene relationship; each of the selaginella allele matches to two candidate arabidopsis genes (which should be finalized to one eventually). The above relationship results in a combination of 8 matches.
Note2: Steps for obtaining the above results.
- Step 1: Run blastp using different queries and database (Blastp results are listed in tabular format)
- use Selmo1 protein sequences as the queries and ATH1 E3 protein sequences as the database
- use ATH1 E3 protein sequences as the queries and Selmo1 protein sequences as the database
- Step 2: Get common match sequences
- obtain common match sequences joined on Arabidopsis gene name (or AGI) and Selaginella protein ID.
- Step 3: Sort by E-values (smallest to biggest)
- Run a perl script that takes the common match sequences from step 2 and sorts E-values by Arabidopsis gene name and Selaginella protein ID, respectively. Output two corresponding lists.
- Step 4: Get the top two matches by selecting the smallest two E-values
- Join the two list by Arabidopsis gene name and Selaginella protein ID and filter the results using criteria (E-value rank = 1 or 2 for both ranks in the two lists).
Reference
Kraft,E., S.L. Stone, L. Ma, N. Su, Y. Gao, O. Lau, X. Deng, and J. Callis, Genome Analysis and Functional Characterization of the E2 and RING-Type E3 Ligase Ubiquitination Enzymes of Arabidopsis. Plant Physiol. 2005 December; 139(4): 1597–1611.
