- ID: EG10415.
- Name: greA
- Organism: E. coli
- UniProt ID: P0A6W5
greA, also known as MMSYN1_0253 in the JCVI-syn3.0 genome, is a protein directly involved in regulating transcriptional processes through interacting with RNA polymerase. Specifically, greA is involved in alleviating issues arising when RNA polymerase and the nascent RNA transcript get “locked” into complexes that form during transcription. This happens when the RNA polymerase encounters “arresting sites” in the DNA sequence. To rescue the RNA polymerase from the complex and in order to resume elongation, GreA can dissolve the complex by cutting two or three ribonucleotides from the 3’-terminus of the RNA transcript. Once these ribonucleotides get released, RNA polymerase is free to continue elongating the RNA from the new 3’ end. 
greA derives its functionality from its basic N-terminus. This region of the protein both catalyzes and specifies the last few ribonucleotides which to release from the RNA transcript. Furthermore, greA activity requires greA and RNA polymerase to associate prior to when RNA polymerase stalls. Sometimes they associate even prior to beginning transcription. greA also allows RNA polymerase to backtrack to remedy incorrectly incorporated nucleotides. Lastly, greA has been shown to decrease “abortive initiation.” This is a process in which RNA polymerase never leaves the promoter sequence of a gene yet cycles through transcription initiation and releases short RNA transcripts. 
Beyond associating with RNA polymerase, greA also interacts with greB. greB has similar activity to greA, except it releases nine ribonucleotides from RNA transcripts rather than just two or three. Furthermore, greA and greB are involved together in regulatory pathways by DksA and ppGpp. 
- DNA Length: 477 base pairs.
- DNA sequence:
ATG CAA GCA ATT CCT ATG ACG CTT CGT GGT GCC GAA AAG CTG CGT GAA GAA CTG GAC TTT CTG AAG TCG GTA CGT CGT CCG GAA ATT ATT GCT GCT ATC GCT GAA GCC CGT GAG CAT GGC GAT CTT AAA GAG AAT GCG GAG TAT CAC GCT GCA CGC GAA CAG CAG GGA TTT TGT GAA GGT CGT ATT AAG GAC ATC GAA GCA AAA TTG AGT AAC GCC CAA GTC ATC GAT GTT ACG AAG ATG CCC AAT AAC GGT CGT GTT ATC TTT GGA GCA ACC GTG ACT GTG TTG AAC TTA GAC TCA GAT GAA GAG CAA ACC TAT CGC ATC GTT GGA GAC GAT GAG GCT GAT TTT AAG CAA AAC TTG ATT AGT GTC AAT AGC CCT ATT GCA CGC GGC TTG ATC GGG AAG GAA GAG GAT GAT GTG GTA GTT ATT AAA ACG CCA GGT GGC GAA GTT GAG TTC GAA GTG ATC AAA GTA GAG TAT TTG TAA
- Amino Acid length: 158 amino acids.
- Amino Acid sequence:
Function and Homologs
- Functional Category: Transcription.
- Product: Transcription elongation factor GreA
- Module: RNA elongation.
- Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
- Equivalent JCVI functional protein: MMSYN1 0253.
- Expression Level: High.
- Expression Level Hypothesis: greA is a necessary transcription factor. Given that transcription is constantly happening in the cell, transcription factors that are involved in all transcription events must be expressed at high levels to ensure effective transcription.
- Expression Level References and Description: The expression level data is from the provided E. coli dataset.
- Expression Time: Immediate.
- Expression Time Hypothesis: First, the high expression level of greA along with its cellular function as an important transcription factor indicate the likelihood of it being needed immediately. Furthermore, research in E. coli indicates that greA plays a role in inducing expression of the atp operon, which includes genes necessary for efficient cellular metabolism. As such, this supports the hypothesis that greA is expressed immediately.
- Expression Time References and Description: Specific expression timing data was unavailable. However, I was able to find which genes greA helps to upregulate , which helped inform my hypothesis regarding greA expression timing.
- Other Components: MMSYN1 0645, RNA polymerase subunit rpoA
- Possible Dependencies: Nucleotide Synthesis, greA functionality requires available ribonucleotides to be added to mRNA by RNA polymerase before it can cleave a few from the nascent mRNA chain.
- Process: transcription elongation
- Inputs: mRNA (n)
- Outputs: mRNA (n-2 or n-3), 2-3 ribonucleotides
- References: 
- Synthesis Score: The synthesis score of your construct: 1, 2,3
- Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
- Design Notes and Details: For example, had to use a rare codon to fix folding energy;
- GenBank File: A link to the GenBank file. file