- ID: EG10665.
- Name: nusA
- Organism: E. coli
- UniProt ID: P0A7Z4
NusA, a gene which was included in the final JCVI-syn3.0 genome, is also found in E. coli within an operon that encodes at least four proteins.  In E. coli, it has been studied extensively; such research has shown that nusA is highly involved in the transcription process. Specifically, nusA is involved in termination and antitermination by RNA polymerase. Termination is the process where further elongation of RNA transcripts by RNA polymerase ceases; antitermination, however, is a process where RNA polymerase continues to elongate an RNA transcript even after it has reached a termination region or signal.
The nusA protein is a monomeric protein comprised of 584 amino acids. The tertiary structure of the protein results in a number of regions that have now been characterized. The S1 and KH regions are known for conferring the functional activity to the protein. There are also two additional domains that are RNA polymerase binding domains.  The RNA polymerase binding domains are extremely important for nusA’s termination activity, as it is essential that nusA bind with RNA polymerase’s C-terminus. Given that RNA polymerase is actually a complex of smaller proteins, nusA actually binds specifically with the C-terminus of the RpoA monomer within the RNA polymerase complex. The nusA and RpoA binding event results in a conformational change within the protein. This change prevents RNA polymerase from being able to continue binding RNA, thereby effectively terminating RNA elongation. nusA can also allow RNA to form hairpins, which are also biological termination motifs. 
nusA has been associated with other proteins and specifically targeted operons. For example, nusA can terminate, or simply pause, transcription of the rrnB operon and also of the tr2 operon.  Furthermore, nusA has been documented to work in concert with many other intracellular proteins to obtain its termination activity. Specifically, nusA works with rho protein in some termination instances. It also works with phage lambda N termination protein in other instances. 
Though nusA appears to be best known for its transcriptional regulation role in termination and antitermination, it also is involved in ribosomal RNA synthesis and DNA repair. Regarding DNA repair, nusA plays a role in regulating processes such as nucleotide excision and translesion synthesis.  These processes are highly related. Nucleotide excision as a cellular quality control process where mismatched nucleotides in dsDNA get excised from the strand. Translesion synthesis plays a role in nucleotide excision in that it is a process where standard DNA polymerases are swapped for specialized DNA polymerases that engage in DNA repair, such as remedying thymidine dimers.
- DNA Length: 1488 base pairs.
- DNA sequence:
ATG AAC AAG GAA ATT TTG GCT GTT GTG GAG GCA GTC TCT AAT GAG AAA GCA TTA CCC CGT GAA AAA ATT TTT GAG GCG TTA GAG TCA GCG TTA GCG ACC GCT ACC AAA AAA AAA TAC GAG CAA GAA ATC GAT GTC CGT GTG CAA ATC GAT CGT AAG TCG GGC GAC TTT GAT ACT TTT CGC CGC TGG CTT GTA GTG GAC GAG GTA ACG CAA CCC ACC AAG GAA ATT ACG TTA GAA GCA GCC CGT TAC GAA GAT GAA TCA CTT AAC CTG GGA GAT TAC GTG GAG GAC CAA ATT GAG TCC GTG ACA TTT GAT CGC ATT ACA ACG CAG ACA GCC AAG CAA GTG ATT GTG CAG AAG GTC CGT GAG GCA GAG CGT GCA ATG GTG GTA GAC CAG TTT CGC GAG CAT GAA GGT GAG ATC ATT ACC GGC GTG GTA AAA AAG GTC AAC CGT GAC AAT ATT TCT TTG GAT TTA GGT AAC AAT GCC GAG GCG GTA ATC TTG CGC GAA GAT ATG TTG CCA CGC GAA AAT TTC CGT CCA GGG GAT CGT GTA CGC GGT GTG TTA TAT AGT GTC CGC CCC GAG GCC CGC GGT GCA CAA CTG TTT GTG ACT CGT TCG AAA CCG GAA ATG CTT ATT GAA TTG TTC CGT ATC GAG GTC CCG GAG ATC GGT GAG GAG GTC ATT GAG ATC AAA GCC GCG GCT CGT GAT CCG GGG TCT CGT GCA AAG ATT GCT GTG AAA ACG AAC GAC AAA CGC ATT GAT CCC GTT GGC GCC TGC GTT GGG ATG CGC GGT GCC CGT GTA CAA GCC GTT AGC ACT GAG CTG GGA GGG GAA CGT ATT GAT ATC GTT CTG TGG GAC GAT AAT CCC GCC CAG TTC GTG ATC AAC GCT ATG GCC CCT GCA GAC GTT GCG TCG ATT GTC GTC GAC GAA GAC AAG CAT ACG ATG GAT ATC GCA GTG GAA GCT GGC AAT CTT GCA CAA GCT ATT GGA CGC AAC GGC CAA AAT GTA CGC CTT GCA AGC CAG TTA AGC GGA TGG GAA TTG AAC GTG ATG ACA GTA GAT GAT TTA CAA GCA AAG CAT CAA GCC GAA GCA CAC GCC GCG ATC GAT ACG TTC ACA AAA TAT TTG GAT ATC GAC GAG GAC TTC GCT ACT GTC TTA GTA GAG GAA GGA TTT TCG ACG TTA GAA GAG TTG GCT TAC GTG CCT ATG AAG GAA CTT TTG GAG ATT GAG GGA TTA GAC GAG CCC ACG GTA GAG GCT TTG CGC GAA CGT GCG AAA AAC GCG CTG GCA ACC ATT GCT CAG GCA CAA GAA GAA AGC CTT GGA GAC AAC AAA CCC GCA GAT GAT TTA TTA AAC TTA GAA GGG GTG GAC CGT GAC CTG GCC TTT AAG TTA GCC GCC CGC GGA GTA TGC ACC CTT GAG GAC CTT GCG GAG CAA GGG ATC GAT GAC CTT GCT GAC ATT GAG GGC CTT ACC GAC GAG AAA GCC GGA GCA CTG ATC ATG GCT GCC CGC AAC ATT TGC TGG TTT GGG GAT GAG GCA TAA
- Amino Acid length: 495 amino acids.
- Amino Acid sequence:
Function and Homologs
- Functional Category: Transcription.
- Product: transcription termination/antitermination L factor
- Module: transcriptional termination and antitermination.
- Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
- Equivalent JCVI functional protein: MMSYN1 0300.
- Expression Level: High.
- Expression Level Hypothesis: Given that nusA is involved in transcriptional processes, it is likely that it should be expressed at high levels because transcription is a ubiquitous cellular process. Interestingly, nusA is only expressed at medium levels in mycoplasma genitalium (and likely also in mycoplasma mycoides), but the difference may be that nusA is involved in transcriptional termination and elongation for more genes in E. coli than it is in mycoplasma species.
- Expression Level References and Description: Expression level data is from the provided E. coli proteome dataset.
- Expression Time: Immediate.
- Expression Time Hypothesis: Since nusA is involved in transcription and is expressed at high levels in E. coli, which suggests it is involved in many transcription events, it should be expressed immediately. For accurate transcription, nusA is a necessary component of the transcription machinery.
- Expression Time References and Description: Expression timing data was not available. However, I considered nusA's expression levels, its cellular functions, and how it compares to its mycoplasma genitalium homolog; these considerations informed my hypothesis of nusA's expression timing in the absence of experimental data.
- Other Components: EG10893, RNA polymerase subunit rpoA
- Possible Dependencies: Nucleotide Synthesis, nusA's termination and antitermination activity can only be effective with available ribonucleotides.
- Process: RNA synthesis termination
- Inputs: RNA polymerase + mRNA (with hairpin)
- Outputs: RNA polymerase, mRNA (free)
- 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