GENE20001: Speciata Pretendus is a Haploid Fungus - Science Assignment Help

Assignment Task:

Task:

General background information and overview.
Speciata pretendus is a haploid fungus with a life-cycle similar to that of baker’s yeast Saccharomyces cerevisiae. It is used for the production of rare medicinal compounds; however, a harmless by-product (By-product B) is often produced, and this is readily converted to a toxin (Compound C), via a biochemical pathway involving ‘Enzyme P’. An alternative, but less active, pathway involving Enzyme W can convert By-product B into a harmless compound (Compound D). These two biochemical pathways are shown below.

A previously cloned gene called repX codes for a C6 zinc cluster transcription factor called ‘Repressor X’ which acts as a negative regulator of enzP gene expression. A new research lab is investigating a number of strategies to try to reduce the production of the toxic compound C.
Outlined below are four approaches that are being used to investigate how they can manipulate repX and other regulatory genes to reduce Compound C and/or increase Compound D production in S. pretendus and related species. Each of these approaches will correspond to a section of the assignment for which you will need to analyse data and explain your rationale.

Section 1. They want to introduce specific mutations to increase the activity of RepX. Your task is to evaluate the consequences of different mutations on the ability of RepX to regulate Enzyme P.
Section 2. A related species, Speciata hypothetica, does not appear to produce Compound C under laboratory conditions. They have cloned and sequenced a molecule of DNA that they think may contain a gene related to the repX gene of Speciata pretendus. Your task is to confirm the annotation of the facA gene from S. hypothetica.

Section 3. They have found two additional genes, repY and repZ, in S. pretendus that contribute to Compound C production and they want to determine how these interact with repX. Your task is to study the data from genetic crosses to determine the genetic interaction and linkage between genes regulating the expression of the gene for Enzyme P

Section 4. They wish to explore how to manipulate the expression of Enzyme W so that By-product B is broken down via the alternate pathway. This will in turn reduce the amount of By-product B that can be converted to Compound C. Your task will be to predict how mutations in regulatory genes will affect gene expression and Compound C production. Instructions for completing the assignment

• In each section you are provided with the relevant information and appropriate data to complete the analysis.
• The questions to be addressed for each section are provided at the end of the document.
• The total word count should not exceed 1000 words in total. Approximate word counts included in square brackets next to the questions have been indicated as a guide only.

Section 1: Evaluating the consequences of mutations on RepX
The Repressor X protein contains multiple regions that are important for its function. Each of these regions is shown on the annotated DNA sequence provided on pages 3 and 4.
• The C6 zinc cluster domain which is required for zinc binding and binding to DNA is shown in yellow underlined text. The characteristic sequence of the domain is represented as CysX2CysX6CysX5-12CysX2CysX6-8Cys (where X may denote any amino acid). The specific C residues involved in co-ordination of the zinc atoms are highlighted in green.

• A linked region adjacent to the zinc finger that is required for recognising specific target DNA sequences is underlined in red.
• A region required for dimerization, through which Rep X forms both homo- and heterodimers that enable DNA binding, is indicated in grey text.
• A C-terminal region of the protein that allows it to function as an activator for some target genes (but not for enzP) is shown in the yellow highlighted text. The acidic and hydrophobic residues are particularly important for this activity.

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