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With our fermentations we're noticing that it takes anappreciable amount of time for E. coli (K12 variant) tochange from being metabolically streamlined on amino acids to beingmetabolically streamlined to glucose.

How long does it take for such microorganisms to adjust to a newfeedstock?

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Jean Keeling
Jean KeelingLv2
18 Jun 2019

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Related questions

Case Study:

Bacteria are everywhere—on our skin, in our food, suspended in our drinking water. Although the
microbial majority is benign, a few bacterial species can make us sick. To safeguard against food- and
water-borne disease, microbiologists routinely screen our drinking water for bacterial pathogens.
Animal feces contain coliform bacteria, microorganisms that inhabit the intestines of warm-blooded
animals. Many coliform bacteria are also found on plants and in soil and water. Coliform bacteria are
not pathogens themselves, but their presence indicates the possibility of finding pathogens. In contrast,
fecal coliform bacteria such as Escherichia coli are found in feces, and their presence in drinking water
indicates fecal contamination. E. coli can also be a pathogen itself, so if E. coli is found in drinking
water there is a good chance that other pathogens are present, too.1
To detect E. coli and other coliform bacteria, microbiologists filter water samples and place the filter in
a Petri dish containing growth medium such as Endo agar. Microorganisms from the water grow and
form colonies, giving an estimate of the number of bacteria in each milliliter of water.
While E. coli forms colored, shiny colonies on Endo agar, other coliforms grow as white or clear
colonies.

Dark colonies = E. coli
White/clear colonies = coliform bacteria
White + Dark colonies = total coliform
bacteria.

The guidelines of maximum allowable limits for total coliforms in drinking and recreational waters vary
by state. Representative limits appear in the table below.2, 3, 4

Table 1. Maximum allowable limits of fecal coliform bacteria
(cells/100 ml)
Total Coliforms E. Coli
Drinking Water 0 0
Recreational Waters 400 235

Questions
1. Why would we want to count the number of fecal coliforms in a water sample?
2. Do 400 coliforms per 100 milliliters strike you as very many?
3. How many other types of bacteria might be present in a normal water sample?
4. What problems might Mary encounter when she uses these techniques in Antarctica?

1) This question is a modification of Question 2.3, page 134, in a textbook Introduction to Bioinformatics by Arthur Lesk.

It is estimated that the human immune system can produce 1015 antibodies. Would it be feasible for such a large number of proteins each to be encoded entirely by a separate gene, with the diversity arising from gene duplication and divergence? A typical gene for an immune system biomolecule is ~2000 bp long. Show calculations to justify your answer.

To answer the question above you will need to find the size of the human genome. Do this using the databases at either NCBI or Ensembl. Use your chosen database's most recent reference assembly for the human genome. Give the size, and the URL (at either NCBI, Ensembl, or EBI) at which you found the size.

2) This is a modification of Question 2.1, page 132, in a textbook by Arthur Lesk.

According to the NCBI database, the size of the E. coli strain K12 substrain MG1655 reference genome is 4,641,652 bp. The overall base composition of the genome is A/T=49.2%, G/C=50.8%. In a random sequence of 4,641,652 nucleotides with these properties, what is the expected number of occurrences of the sequence CTAG? I.e. how many times would we expect to see the sequence CTAG in the E. coli genome due to random chance alone? Give your answer to the nearest integer.

5. The SH3 domain is about 60 amino acids long. It recognizes and binds to structural motifs in other proteins. The motif recognized by SH3 domains was found by constructing a fusion protein between an SH3 domain and glutathione-S-transferase (GST). GST fusions allow for easy purification fusing a glutathione affinity column that binds GST specifically. After tagging the purified GST-SH3 protein with biotin to make it easy to detect it was used to screen filters containing E. coli colonies expressing a cDNA library. Two different clones were found to bind to the SH3 domain: in both cases binding was shown to occur at short proline-rich sequences.

a. Could you use biotin tagged GST-SHE proteins in the same way to find cDNA domains? Why? Explain.

b. Many proteins bind to short strings of amino acids in other proteins. How do you think these kinds of interactions differ from the binds of interactions found between protein subunits of multi-subunit enzymes?

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