- ID: MMSYN1-0300
- Name: nusA
- Organism: JCVI-Syn3.0
- UniProt ID: F4MPN0
MMSYN1-0300, also known as nusA, encodes the nusA protein in mycoplasma mycoides that plays a role in termination and antitermination of RNA synthesis. Termination is the process where RNA polymerase ceases elongating the nascent RNA transcript. Antitermination, on the other hand, is a process where RNA polymerase continues elongating the nascent RNA transcript even after it has encountered a termination signal.
nusA, a monomeric protein localized in the cytoplasm, derives it termination and antitermination activity via its ability to bind both RNA polymerase and RNA. In mycoplasma mycoides, much of NusA’s aforementioned function has been extrapolated from knowledge of homologous proteins in other organisms. 
nusA in mycoplasma mycoides has S1 and KH domains. The S1 domain confers nusA’s RNA-binding ability. Furthermore, the S1 domain is a conserved structure found in many other proteins that also have RNA-binding function. Similarly, the KH domain is also shared amongst all prokaryotic proteins that also participate in the transcription process of elongating RNA. 
- DNA Length: 1755 base pairs.
- DNA sequence:
ATG CTT AAC GGC ACT GAG CTT TTA GAA AGC ATT AAA CTT ATC GAA AAG GAG AAA GGG ATT TCT AAA GAG AGC ATC ATT AAC GGC TTA AAG GAG GGA TTA CAG AAG GCT TAT GAG CGC TTT TAT GAT ACC GAC GCA ATC ATT AAA ATT GAT ATT AAT GAG AAT ACC GGG CTG ATC ACC ATG CAC CAA GAA TTA AAA GTA GTA GAT GAC GAA CAG CTG GAT GAT GAC TGG CTG GAA ATT ACC CTG TCC AAG GCG AAG CTG AAG AAT CCT GAC ATC CAG ATC GGC GAC ACT ATC TAC AAA CCC ATC GAG TTT AGC GAG GAA TTT TCG CGC ATG GTA GTA AAT CAG GTG CGT CAA ATC TTC CAG CAG AAA ATC CGT GAA GCT GAG CGC GCA CGC ATC TAT GAG CAA TTT GTG AGT TTG GAA GGT GAG GTC GTT CAG GCG AAA GTA GTT GGG ATG AAT CGT GAA AAC AAT TAT GTG TTG GAC ATC AAT GGT ACT ACC GCC TAC CTG TGG AAG TCC AAA ACC ATC AAC AAT GAA ATC TTC CAA ATT AAC GAA ATT ATC GAT GTA TAT ATC GAG GTG GTG GAG AAA GAA TCT AAA CTG TCA CAA ATC TCC ATC TCT CGC ACT GCA CCT AAT TTT TTA ACG AAA CTT ATT GAG CGT GAA GTA CCC GAG GTT CGC ATG GGA ATC GTT GAA ATT AAG GCC GTT TCA CGT GAA CCT GGC AAA CGC TCC AAG GTC GCC GTC ATT ACT CAC AAC AAT AAT GTG GAA CCG ATC GGC GCG ATC ATC GGC GTT GGT GGA AAT CGC ATC AAC CGT ATT AGT GAC ATC TTA AAG GGG GAA AAG ATC GAC ATC ATT CGT TGG GAT GAG GAC CAG ATT ACA TAC CTT ATC AAC GCG ATG ACT CCG GTC AAA GTC ATT AGT ATT AAT AAA ATT GGA GAT GAA TAC GAT ATT GTA GTA CCC GAT ACG CAG CTG AGT TTG GCG ATT GGA AAG CAG GGC GTG GCG GCC AAG TTA ATT GCG AGT TTA TTG AAG ACC AAG ATC AAT ATC TTT TCA TAC TCT ACG GCG TTA AAA GAG AAT ATG GAT ATT TTG TGG AAT GGG GAT ACG ACG ATC CAA GAA GTA GAG ACG AAT ACA TAC ACG CCA AAG ACT AAA GCA ACC AAA AAG GAG GAG AAG CCG GTT ATC ACT ACA ACT AAG AAG CCA ATT AAG CAA ACT ACA AAG AAA GAG GAG AAC CAA ATC GAT GTT GAC GCC TTG ATC GCT TTC CAA GCC GAA GTT GAG CAC GAA CAG GAA CTG AAG GAC CAA GAG GAG CTG CTT AAA CAG GAG TCT ATG TAC AAA GAA TAC GAG AAT AAT TTT AAC GAC TTT GAA AAT GAA AAA GAA ATC CTG TTG GCG GAA AAG CAG CTG GAG ACG CAG AAT CAG ATT ATT AAG GAG CCT GTC GTG GAA GTA CAG GAA TTT GAG ATC GAG AAA CAA AGC AAG ATT GAG GAT CAG ATT ACT GAG AAT AAG CAG CCG GAA ATT AAG ACA GAG GTC GAA ACC AAA CCT AAT ATT GTG GAA CAG GTC AAT AAA TTG AAT ACA AAC AAG CCC AAT AAC AAA TTC GAA CAA AAT CGC TTC AAT TAC AAG AAA CAA AAG CAG AAA GAG GAG GAA CTG GAG CTG GAT TTT GAC ATT AAG AAC GAG CCG GAC ATC GAT GAA ATC GAC GCA AAT CTT AAG GCT TTT AAC GAT GCG ATT TTG AAA CAA GAA GAT GAC GAA GAC CTT GAT ATC GAC TTG GAT GAT TAC GAT AAG TAT TAT GAT TAA
- Amino Acid length: 584.
- Amino Acid sequence:
Function and Homologs
- Functional Category: Transcription.
- Product: Transcription termination/antitermination protein NusA
- Module: Transcriptional termination and antitermination.
- Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
- transcription termination/antitermination protein NusA [Mycoplasma feriruminatoris], 849/96%/0/79%, 
- transcription termination/antitermination protein NusA [Mycoplasma leachii], 835/100%/0/76%, 
- transcription termination/antitermination protein NusA [Mycoplasma capricolum], 818/100%/0/77%, 
- Equivalent E. coli functional protein: EG10665.
- Expression Level: Medium
- Expression Level Hypothesis: NusA likely is only expressed at medium levels because although it is involved in transcription processes, which are extremely important and ubiquitous, it is only involved in some termination and antitermination events. Thus, it is not necessary for every transcription process, and so it should only be expressed at a corresponding level to the number of genes for which it actually terminates or elongates.
- Expression Level References and Description: This expression level was gathered from data on Mycoplasma genitalium protein counts; given how closely related it is to Mycoplasma mycoides, it can be used to estimate expression levels in Mycoplasma mycoides as well.
- Expression Time: Early.
- Expression Time Hypothesis: Given that NusA is not necessary for all transcription events, it may not need to be expressed immediately. However, since it is still involved in transcription for some genes, it probably needs to still be expressed early so that it can help complete transcription for these genes. (It would be informative to know which genes NusA terminates or elongates to help determine timing -- e.g. if it is involved in transcription of very important genes, then it would need to be expressed earlier than if it is only necessary for less important genes -- but this information is very hard to come by, if it is known at all right now).
- Expression Time References and Description: I attempted to research the expression timing of NusA, as well as the genes for which it plays an active role in expression. My search attempts were not successful, so I hypothesized on my own by considering its function, whether the processes in which it participates are necessary early or late, and whether the genes it terminates or elongates are needed earlier or later in the cell life cycle.
- Other Components: MMSYN1 0645, 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