MMSYN1 0026

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Author Information

Minku Lee

Basic Information

  • ID: MMSYN1_0026
  • Name: priB
  • Organism: Mycoplasma mycoides
  • Description: Binds single-stranded DNA at the primosome assembly site (PAS). During primosome assembly it facilitates the complex formation between PriA and DnaT. Plays critical roles in recognizing repaired replication forks and reloading the replisome onto the template to reinitiate DNA replication. Structural similarity of PriB to single-stranded DNA binding proteins reveals insights into its mechanisms of DNA binding. The structure further establishes a putative protein interaction surface that may contribute to the role of PriB in primosome assembly by facilitating interactions with PriA and DnaT. The gene encoding PriB protein appears to have arisen by duplication of the gene encoding single-stranded DNA binding protein (SSB) with subsequent evolution that led to its specialized function in replication. Furthermore, the priB gene is not well conserved among sequenced bacterial genomes as homologs have been identified only in the β- and γ-subdivisions of proteobacteria. At present, no priB homologs have been identified in eukaryotic genomes. While it is likely that most organisms have a requirement for restarting repaired replication forks following DNA damage, it is not yet clear if a PriB-like activity is uniformly utilized.

cited from https://www.ncbi.nlm.nih.gov/pubmed/15530361 and http://www.sciencedirect.com/science/article/pii/S0969212604003156

  • DNA Length: 441 base pairs.
  • DNA sequence:

ATG AAT CGT GTT AAT CTG GTT GGT CGT ATT ACC CGT GAT CTG GAA CTG CGT GTT GCA AAA AAT GGT AGC AAA TTT GTT TTT TTT ACC GTT GCA GTT AGCGAA TTT AGC ACC CGT GAA GAA AAA ACC AAT TAT ATT CCG TGT AGC GCA TTT GAT AAA ACC GCA GAA AAT ATG GTT AAA TAT CTG AGC AAA GGT AGC CTGATT AGC GTT GAA GGT CGT ATT ACC ACC CGT AAT AAT CAG ACC CCG GAT GGT AAA TTT GAA ACC ATT GTT AAT GTT CTG GCA GAA CGT GTT AAT TTT CTGGAA CCG AGC AAA AAT CGT AAT AAT ATG ACC ACC GAA CAG AAT GAT AAT TTT ACC CCG AAT CAG CCG ACC CAG CAG AAT AGC GAT AGC AGC TTT GAT GATCTG GTT GTT AGC GAT GAT GAT GAA CTG AGC ATT CTG TGG GAA TAA

  • Amino Acid length: 146 amino acids.
  • Amino Acid sequence:

MQNKSGLILLKEVFINNYSNKIDFLKTVFSDKQINELESITNIKELLTNLKELLDNQILIHQNKIKEYQLELKKTNKKILNKLWLWWLLPIIGMFIFFIIYNTRLQNPYYANQLVDIKVKITDLDIKNIYIDKLLEEINSSVKLKF*

Function and Homologs

  • Functional Category: DNA Replication
  • Product: Primosomal replication protein N
  • Module: Primosome
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • single-stranded DNA-binding protein [Catenibacterium mitsuokai] 101 101 95% 1e-24 39% WP_055232333.1
    • single-stranded DNA-binding protein [Gemella haemolysans] 101 101 99% 2e-24 39% WP_060913924.1
    • single-stranded DNA-binding protein [Gemella sanguinis] 100 100 73% 2e-24 50% WP_082147410.1

Expression

  • Expression Level: low
  • Expression Level Hypothesis: Expressed as low because although it's a necessary component for a primosome, which in turn is responsible for creating RNA primers used for DNA replication, this is not as frequent an occurrence as other necessary cell processes, so it would be low. Also, there are likely not a large amount of primosomes in a cell.
  • Expression Level References and Description: http://www.uniprot.org/uniprot/P07013
  • Expression Time: Middle
  • Expression Level Hypothesis: Expressed at this time to encourage DNA replication when the cell needs to prepare to split, a necessary component of a cell's life and therefore carries out necessary cell processes. Somewhat uncertain here.
  • Expression Time References and Description: Gathered information for cell processes descriptions and wikipedia. https://en.wikipedia.org/wiki/Primosome

Gene Context

  • Other Components in the functional module. Provide one other component in the functional module you selected. If you believe your module only has one component, say so.

I believe there is only one module.

  • Possible Dependencies: Other components on which the functional module depends, but that are not part of the module itself. Specify one possible dependency, if applicable.

DnaB Helicase, which is also part of the primosome.

  • Process: Identify one process that this functional module takes part in. Provide the inputs and outputs to the process.

Responsible for helping create RNA primers on single stranded DNA during replication by being necessary to construct the primosome. Inputs nucleotides to create primers.

    • Inputs: Comma separated list of inputs to the process

PriA, PriB, PriC, DnaB, DnaC, and DnaT

    • Outputs: Comma separated list out outputs from the process

Successfully constructed primosome

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file