This is a critical homework essay in my subject; please be aware of the timeline and the following instructions.
1- I have uploaded part 1 of my research paper (part 1 – Uptake of essential ions by Bacillus subtilis). You can use it as a base and expand it.
2- Most of the reference files you may need I already uploaded; please use them, and you can use other references (regarding the limit of uploaded files), but they should be a paper or a review.
3- these are the area and questions I want my research paper to talk about and answer them
Area to include and questions to answer
Bacillus subtilis ions uptake system
Define metal ion homeostasis
What are the Origins of metal ion selectivity in the DtxR/MntR family of metalloregulators
General background about each ion ( Iron, Magnesium, Manganese, copper, calcium, sodium)
How metal ions, especially those in low abundance, are depleted from the culture medium as the bacterial culture grows (previous study finding)?
Characterization of mutations that result in a loss of efficient metal uptake
In Bacillus subtilis
Iron:
Define Iron upsorbtion by Bacillus subtilis
The iron uptake system depends on the type of uptake system and on which wave that system is
Give detail about ABC transporters, siderophores, and elemental iron uptake system.
How does each system work (how they help in iron uptake)
Ex. give details about ABC transporter component (the Permease, Binding proteins, and ATP binding protein)
A brief overview of siderophores, their synthesis mechanisms, iron capture, and iron efflux
Determine the functional role of the siderophores, bacillibactin, and pulcherrimin in iron uptake. Can the growth medium composition affect their expression (previous study finding)?
Compare and contrast Bacillibactin (by B. subtilis) and Enterobactin (by E.coli) ( iron uptake by Bacillus subtilis)
Defined and characterize Fur, PerR, and FsrA iron regulons
Define and characterize the first (immediate), second, and third waves. In action, their role of action in iron limiting condition
Based on the Bacillus subtilis bacterial strain; explain each of the following iron uptake systems in detail, and describe how each system works, emphasising any functional residency between them. It would require a substantial section in the research paper.
The first wave (efeUOB) elemental uptake system, (fecCDEF) ferric citrate uptake system, and (fpbNOPQ) induce petrobactin to prevent iron deficiency
The second wave: (dhbACEBF) these are bacillibactin siderophores produced by B.S, (feuABC) these are bacillibactin which turned on by BS,(fhuBCGD) are hydroxamate siderophores uptake systems to scavenge iron from environment, and (ykuNOP) these are flavodoxins that can replace ferredoxins
The third wave: Called iron-sparing “responses” (fsrA), (fbpAB), and (fbpC)
Define What does iron sparing mean?
If applicable (is there any phenotypic characteristic for the mutant strains regarding iron uptake (previous studies)?
Provide information on pulcherimin, including its synthesis, pigment, iron limitation, and excess
Defined Redox Sensing and its role in regulating iron homeostasis?
Growth medium and iron
What is the baseline for metal uptake for the wild-type strain Bacillus subtilis
Is Fe limiting for growth in normal conditions?
Defined the bacterial growth in iron limiting and riching medium
How does Mg solve iron limitation – is it acting to displace Fe out of non-specific chelation complexes
Give information about the cellular requirements for iron uptake systems under defined conditions where Fe is supplied in different forms Fe(II), Fe(III), iron citrate, and iron chloride
Does glucose metabolism require higher Fe levels, resulting in the cell having to reprogram metabolic pathways?
Dose malate (another form of carbohydrate) metabolism do butter regarding iron uptake?
Manganese:
The details should be based on Bacillus subtilis gram-positive bacteria
Give detail about the Manganese uptake system
(mntABCDHR) and (mnePS) uptake systems
Defined and characterize MntR manganese regulon
Growth medium and Manganese
Bacterial growth in Manganese limiting and riching medium
Magnesium:
The details should be based on Bacillus subtilis gram-positive bacteria
Give detail on each Magnesium uptake system
(citM), (mgtE), (mpfA), and (yfjQ)
Growth medium and Magnesium
Bacterial growth in Magnesium limiting and riching medium
Bacillus subtilis cell wall composition and metal uptake
Give information about gram-positive cell wall components (synthesis and function)
Give information about the role of the cell wall in metal iron uptake
Ex: the cell wall charge, Lipoteichoic acids (LTA), and wall teichoic acids (WTA)
Provide information on these mutant strains. Are there any phenotypic characteristics for the mutant strains regarding iron uptake (study findings)
(yfnI) biosynthesis of lipoteichoic acid, (ItaS) major lipoteichoic acid synthase, (dltA)biosynthesis of teichoic acid, (pbpX)Penicillin-binding protein X, and (yqgS)biosynthesis of lipoteichoic acid
Compare  Bacillus subtilis, Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus in:
Provide information about each strain
Phenotypic characterization, metal uptake, and essential ions for growth
What is the best medium composition for the Bacillus subtilis growth (we have Liquid broth(LB), Nutrient agar(NA), Nutrient broth(NB), and minimal medium which it’s ingredients can differ from one study to another)
Is adding iron, Mn, and Mg to these mediums positively affect growth?
How do those effects on the iron uptake system in Bacillus subtilis
Sigma factors
Relate sigma factor to iron uptake – cell wall composition (general background – study finding will  be good )
Riboflavin strain
It seems like in iron limitation, Riboflavin can solve how this can work. Give general background about Riboflavin and iron limitation.
Reference can be used: Overview of the Bacterial Iron-Riboflavin Metabolic Axis.