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Ch. 16 - Genomics: Genetics from a Whole-Genome Perspective
Sanders - Genetic Analysis: An Integrated Approach 3rd Edition
Sanders3rd EditionGenetic Analysis: An Integrated ApproachISBN: 9780135564172Not the one you use?Change textbook
All textbooksSanders 3rd EditionCh. 16 - Genomics: Genetics from a Whole-Genome PerspectiveProblem 25b
Chapter 16, Problem 25b

In conducting the study described in Problem 24, you have noted that a set of S. cerevisiae genes are repressed when yeast are grown under high-salt conditions. How might you approach this question if genome sequences for the related Saccharomyces species S. paradoxus, S. mikatae, and S. bayanus were also available?

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Step 1: Begin by identifying the genes in S. cerevisiae that are repressed under high-salt conditions. Use transcriptomic data or gene expression profiling to pinpoint these genes.
Step 2: Obtain the genome sequences for the related Saccharomyces species (S. paradoxus, S. mikatae, and S. bayanus). Ensure the sequences are properly annotated to facilitate comparative analysis.
Step 3: Perform a comparative genomic analysis to identify orthologous genes in the related species. Use sequence alignment tools such as BLAST or Clustal Omega to find homologous genes across the species.
Step 4: Analyze the regulatory regions (promoters and enhancers) of the orthologous genes in all species. Look for conserved motifs or transcription factor binding sites that might be involved in salt-induced repression. Tools like MEME or FIMO can help identify these motifs.
Step 5: Investigate whether the repression mechanism is conserved across species by conducting functional assays, such as reporter gene experiments or mutational analysis, to test the activity of regulatory elements under high-salt conditions.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

Gene Regulation

Gene regulation refers to the mechanisms that control the expression of genes, determining when and how much of a gene product is produced. In the context of S. cerevisiae, understanding how high-salt conditions repress certain genes is crucial for exploring adaptive responses and metabolic pathways. This concept is fundamental for analyzing the effects of environmental stressors on gene expression.
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Review of Regulation

Comparative Genomics

Comparative genomics involves comparing the genomic features of different organisms to understand evolutionary relationships and functional similarities. By examining the genome sequences of S. paradoxus, S. mikatae, and S. bayanus alongside S. cerevisiae, researchers can identify conserved regulatory elements and gene functions that may contribute to salt tolerance or stress responses across species.
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Phylogenetic Analysis

Phylogenetic analysis is the study of evolutionary relationships among biological entities, often using genetic data to construct evolutionary trees. In this scenario, analyzing the phylogenetic relationships among the Saccharomyces species can provide insights into how gene repression mechanisms have evolved in response to high-salt environments, revealing potential adaptive strategies that may differ among species.
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Related Practice
Textbook Question

In the globin gene family (shown in the below diagram), which pair of genes would exhibit a higher level of sequence similarity, the human δ-globin and human β-globin genes or the human β-globin and chimpanzee β-globin genes? Can you explain your answer in terms of the timing of gene duplications?

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Textbook Question

You are studying similarities and differences in how organisms respond to high salt concentrations and high temperatures. You begin your investigation by using microarrays to compare gene expression patterns of S. cerevisiae in normal growth conditions, in high salt concentrations, and at high temperatures. The results are shown here, with the values of red and green representing the extent of increase and decrease, respectively, of expression for genes a–s in the experimental conditions versus the control (normal growth) conditions. What is the first step you will take to analyze your data?

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Textbook Question
In conducting the study described in Problem 24, you have noted that a set of S. cerevisiae genes are repressed when yeast are grown under high-salt conditions.How might you determine whether this set of genes is regulated by a common transcription factor?
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Textbook Question

PEG10 (paternally expressed gene 10) is a paternally expressed gene (meaning only the paternal allele is expressed) that has an essential role in the formation of the placenta of the mouse. In the mouse genome, the PEG10 gene is flanked by the SGCE and PPP1R9A genes. To study the origin of PEG10, you examine syntenic regions spanning the SGCE and PPP1R9A loci in the genomes of several vertebrates, and you note that the PEG10 gene is present in the genomes of placental and marsupial mammals but not in the platypus, chicken, or fugu genomes.

The green bars in the figure indicate the exons of each gene. The gray bars represent LINEs and SINEs, and the blue bars represent long terminal repeat (LTR) elements of retrotransposons. Solid black diagonal lines link introns, and dashed black lines connect orthologous exons. Arrowheads indicate the direction of transcription.

Using the predicted protein sequence of PEG10, you perform a tblastn search for homologous genes and find that the most similar sequences are in a class of retrotransposons (the sushi-ichi retrotransposons). Propose an evolutionary scenario for the origin of the PEG10 gene, and relate its origin to its biological function.

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Textbook Question

What is the difference between biochemical and biological function?

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Textbook Question

Using the two-hybrid system to detect interactions between proteins, you obtained the following results: A clone encoding gene A gave positive results with clones B and C; clone B gave positive results with clones A, D, and E but not C; and clone E gave positive results only with clone B. Another clone F gave positive results with clone G but not with any of A–E. Can you explain these results? To follow up your two-hybrid results, you isolate null loss-of-function mutations in each of the genes A–G. Mutants of genes A, B, C, D, and E grow at only 80% of the rate of the wild type, whereas mutants of genes F and G are phenotypically indistinguishable from the wild type. You construct several double-mutant strains: The ab, ac, ad, and ae double mutants all grow at about 80% of the rate of the wild type, but af and ag double mutants exhibit lethality. Explain these results. How do the two-hybrid system and genetic interaction results complement one another? Can you reconcile your two-hybrid system and genetic interaction results in a single model?

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