Uncovering the Prokaryotic Operon: A Key Component of Protein Synthesis - Essay Sample

Introduction

An operon is a segment of prokaryotic DNA consisting of adjacent genes which are functionally related and have a common promoter. The gene clusters forming an operon code functionally related proteins hence are transcribed together. An operon typically consists of structural genes, a promoter gene, and a regulator gene. Operons are an essential element of protein synthesis in many bacteria and bacteriophages (Zander et al. 2017).

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Other prokaryotes such as certain algae also utilize operons in their genetic control of protein synthesis. Operons provide these prokaryotes with an energy-efficient mechanism by which proteins are synthesized in a coordinated manner only when the organism requires the proteins to sustain its life processes (Tischer et al. 2019). An operon is described as inducible or repressible, depending on the default status of the operon. An inducible operon is inactive by default and is activated by the presence of an inducer molecule, while a repressible operon is active by default and is inactivated by the presence of a repressor molecule.

The arabinose operon (ara operon) is one of the essential operons utilized by Escherichia coli to sustain its life. The ara operon is used in the breakdown of the five-carbon aldose L-arabinose to generate D-xylulose-5-phosphate that is utilized by the pentose phosphate pathway (Ammar et al. 2018, p. 3). The ara operon consists of three structural genes which code for three different enzymes for the catabolism of L-arabinose.

Arabinose is a very essential molecule for the survival of the bacterial cell. In many bacterial cells, arabinose serves as the major carbon source for energy catabolism and biosynthesis. Most essentially, arabinose is broken down to D-xylulose-5-phosphate which is fed into the pentose phosphate pathway (Koirala et al. 2016, p. 389). This pathway is utilized further downstream by the bacterial for energy production via glycolysis.

The arabinose operon comprises of structural genes, inducer genes, catabolic active site, operator genes, promoter genes, and regulator gene, arranged in a linear structure. The structural genes encode enzymes involved in arabinose catabolism. These structural genes include araB coding for ribulokinase, araA coding for isomerase, and araD coding for epimerase. The inducer genes(araI1 and araI2) act as the initiator of the operon. AraI1 acts as a positive initiator while araI2 acts as a negative initiator. The catabolic active site, CAP (catabolite activator protein) binds cyclic adenosine monophosphate(cAMP) in the presence of high arabinose concentration to activate mRNA transcription.

The operator genes (O1 and O2) operate the ara operon through positive and negative regulation depending on the arabinose concentration (Ammar et al. 2018, p. 4). During high arabinose concentration, O1 activates the operon via positive regulation whereas O2 inactivates the operon in low arabinose concentration via negative regulation. Therefore, the operator genes act as the dual switch for the operon.

The two promoter genes PBAD and PC act as promoters for the three structural genes and the regulator gene, respectively. PBAD promotes the synthesis of the araBAD mRNA which transcribes the three catabolic enzymes of the araB, araA, and araD genes. PC promotes synthesis of the araC mRNA which transcribes araC protein, the ara operon repressor protein encoded by the regulator gene ara-C (Tischer et al. 2019). The diagram below shows a detailed structure of the arabinose operon.

Sigma factors are specific proteins required for the initiation of bacterial transcription during protein synthesis. Sigma factors are highly specific to their target sites and it is only in the presence of these factors, also called specificity factors, can bacterial transcription begin. Sigma factors exert their effect by enabling the specific binding of bacterial RNA polymerases to their promoter genes. Besides their specificity, the action of sigma factors in initiating transcription also depends on the environmental factors that signal transcription of various bacterial proteins.

As an essential pathway in the biochemistry of E. coli, the arabinose operon also operates through the action of sigma factors that regulate the two promoters (PBAD and PC) involved in this genetic pathway (Tischer et al. 2019). The sigma factors of the arabinose operon are signaled externally through substrate-level regulation depending on the environmental concentration of arabinose. PBAD is regulated by the binding of sigma factor-70 while sigma factor-38 binds to and regulates the promoter PC.

The arabinose operon is regulated by a dual control mechanism depending on the environmental signal available. The external environmental signals controlling this operon include substrate-level activation and metabolite repression. Substrate level regulation entails the expression of the operon only when the substrate arabinose is present in the environment. Catabolite repression occurs when there is a high environmental concentration of glucose, regardless of the presence of arabinose. In such a scenario, the bacterial cell preferentially catabolizes glucose as a more efficient source of metabolic energy than arabinose (Jenkins & Macauley, 2017). The dual nature of the arabinose operon makes it both an inducible and repressible operon. As such, the arabinose undergoes both positive control and negative control depending on the prevailing environmental signals.

Arabinose acts as the inducer of the arabinose operon while araC protein acts as the repressor. In the absence of arabinose(that is, only the repressor araC protein present), negative control of the operon occurs hence no transcription occurs for the catabolic enzymes of the araBAD pathway (Tischer et al. 2019). The araC protein is homodimeric in structure. One monomer binds the operator O2 while the second monomer binds the inducer araI1. The binding of araC monomers to O2 and araI1 leads to the formation of a DNA loop which prevents the binding of RNA polymerase to the promoter PBAD. As a result, the structural genes araB, araA, and araD are not transcribed.

Positive control of the arabinose operon occurs in the presence of arabinose when the catabolic enzymes are required by the bacterial cell. In addition to the presence of arabinose, glucose levels in the environment must be sufficiently low or absent to warrant the utilization of arabinose as an alternative carbon source. The araC protein binds to the arabinose forming an arabinose-araC complex. The formation of the complex via a cAMP receptor protein(CRP) promotes the binding of the araC monomers to araI1 and araI2 (Tischer et al. 2019). The resulting conformation promotes the binding of RNA polymerase to the PBAD promoter hence allowing the transcription of the three catabolic enzymes by the three structural genes of the arabinose operon (Jenkins & Macauley, 2017).

Frameshift mutations occur due to the insertion or deletion of base pairs that are not multiples of three. Frameshift mutations lead to alterations of the reading frame by introducing premature stop codons and introducing non-related amino acids in the resulting proteins. As a result, the protein products of frameshift mutations are usually nonfunctional (Geyer & Mamlouk, 2018). As a result, frameshift mutations to the coding region of a control gene do not lead to stoppage of the gene transcription.

However, the gene is transcribed prematurely due to the premature stop codon introduced by the mutation. Additionally, the gene is translated but the protein product is nonfunctional. As a consequence of frameshift mutations in the control gene, the structural genes will be transcribed prematurely (Geyer & Mamlouk, 2018). However, the structural genes will not be translated due to alterations in the reading frame of the control gene by the frameshift mutation.

Both the arabinose operon and lac operon are essential pathways for the survival of E. coli. Whereas the arabinose operon is dual regulated (is both inducible and repressible), the lac operon is a purely inducible system. In the arabinose operon, arabinose acts as the true inducer of the operon. However, the lac operon does not use lactose as the true inducer of the system (Jenkins & Macauley, 2017). Instead, the lactose is first enzymatically converted to allolactose, the true inducer of the lac operon. Both operons have three structural genes (Zander et al. 2017). However, the lac operon has a terminator while the arabinose operon lacks a terminator.

Part B: Control of Eukaryotic Gene Expression – Effect of Mutation

Single nucleotide mutations (SNPs) are genetic variations that affect only a single nucleotide within a particular location of the genome. Single nucleotide polymorphisms occur either via deletions or insertions. SNPs are a rare type of mutation that leads to variations within the prokaryotic genome. The variations caused by SNPs occur with a frequency of about 1% member to member within an entire population (Wennmann et al. 2017). Single nucleotide deletions, one of the two types of SNPs, can affect both the coding or non-coding regions of the genome. These variations may also occur at the intergenic regions of the genome. Single nucleotide deletions are responsible for a variety of biological traits such as physical fitness levels and susceptibility to disease.

Genetic mutations are commonly associated with the alteration of the amino acid sequence of the resulting proteins of mutated genes. However, single-gene deletions and polymorphisms do not necessarily cause an alteration in the amino acid sequence of the resulting protein (Wennmann et al. 2017). This observation is as a result of the redundancy of the genetic code. By redundancy, it means that one amino acid can be encoded by more than one codon. Therefore, single nucleotide deletion may lead to the obsolescence of one codon for an amino acid without interfering with the other codon(s) of the same amino acid. For example, the codons AGA and AGG all code for arginine.

If a single nucleotide deletion affects the AGA codon, AGG will still encode arginine. However, the percentage of arginine in the resulting protein will be lower. A single nucleotide deletion at the polymerase A binding protein-coding region would not impact the transcription and translation of the gene. This is largely because the transcription and translational regulation of genes is majorly controlled by the non-coding regions of the genome. The impact of this mutation on the nature of the resulting protein depends on the type of single nucleotide deletion that occurs in the coding region (Wennmann et al. 2017). If the deletion is non-synonymous, the resulting protein becomes modified due to amino acid variations. However, the nature of the resulting protein does not change if the deletion is synonymous.

The Poly

A binding protein is an essential molecule in the regulation of gene activity within the eukaryotic cell. This protein is required during protein biosynthesis for the initiation of translation. Additionally, the protein plays a critical role in the coordination of RNA degradation. By binding to the polyA tail of the mRNA, polyA binding protein helps initiate protein translation. If a single-nucleotide deletion occurs at the coding region for polyA binding protein, other genes within the genome would still be transcribed.

However, these genes would not be translated due to codon obsolescence caused by the deletion. Consequently, the protein product of these genes would be functionally altered (Wennmann et al. 2017). Such a deletion would have an overall impact on the eukaryotic cell by altering the biosynthetic output of proteins by the cell. The mutation would...