What are the transcription start and stop signals in eukaryotes and prokaryotes?
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How do bacteria and other prokaryotes convert DNA into RNA and protein? Show
One of the characteristics that distinguish prokaryotes from eukaryotes is that their DNA is not found in a membrane-bound nucleus; instead, it is found in the nucleoid region of the cytoplasm. How does this distinction make transcription and translation different between prokaryotes and eukaryotes? Here, we will discuss each step of the two processes and elaborate on similarities and differences in how these take place in prokaryotes and eukaryotes. Recap: Transcription and translationGene expression is the process of converting instructions in our DNA into RNA and protein. It takes place in two major stages:
When, where, and how many genes are expressed are determined by a process called gene regulation. Difference between transcription and translation in prokaryotes and eukaryotesLike eukaryotic cells, prokaryotic cells undergo gene expression and regulation. Prokaryotic cellsare simple, unicellular organisms that do not have a nucleus or any other membrane-bound organelles. This distinguishing feature of prokaryotic cells makes the transcription and translation process of prokaryotic cells different from those of eukaryotic cells. Stages of transcription in prokaryotesAs with eukaryotes, prokaryotic transcription takes place in three steps: initiation, elongation, and termination. The major differences between prokaryotic and eukaryotic transcription can be found in the initiation and termination stages. We'll go through each stage and identify where these differences lie. 1st stage of transcription in prokaryotes: initiationInitiation of transcription begins with the enzyme RNA polymerasebinding to a specific sequence on the DNA double-strand known as the promoter, which represents the start of the gene. Unlike eukaryotes which have three types of polymerase (I, II, and III), prokaryotes have only one type of polymerase. The DNA then unwinds at the promoter region, and the RNA polymerase binds to the transcription start site. Now, the RNA polymerase is ready to “read” the bases in the sequence of the unwound DNA strand and produce RNA with a complementary base sequence. Prokaryotic cells have operators, repressors, and activator proteins that participate in the initiation stage.
Transcription factors in prokaryotesTranscription factors are proteins that regulate the activity of a gene by sending a signal to the cell that transcription is needed. As such, they play an important role in regulating prokaryotic gene expression. Prokaryotes such as bacteria use a transcription factor called sigma which loosely binds the DNA and assists the RNA polymerase in searching for a promoter during the initiation stage. 2nd stage of transcription in prokaryotes: elongationThe RNA polymerase “reads” the bases by traveling through the DNA strand from 3′ → 5’. As it travels through the strand, it “copies” the strand by adding complementary base pairs from the opposite direction. Because the end-product of transcription is RNA, the base adenine (A) is encoded as uracil (U) instead of thymine (T) when the complementary bases are added. During elongation, a DNA sequence GCATGG would be encoded as CGUACC in the growing RNA strand. It is also in this stage that the sugar-phosphate backbone of the RNA is created by the RNA polymerase. Whereas the pentose sugar in DNA is deoxyribose, the resulting RNA strand will have ribose. 3rd stage of transcription in prokaryotes: terminationElongation continues until the RNA polymerase encounters a termination sequence in the gene which signals the end of transcription. Prokaryotic termination can follow two possible paths:
In this stage, the hydrogen bonds that bring together the RNA and DNA helices break, releasing the newly formed RNA. In prokaryotic cells, the transcription process ends here, but in eukaryotic cells, the mRNA undergoes further processing. Palindromic sequence: a short DNA segment (consisting of 3 to 5 bases) where the bases are identical when its complementary strand is read in the opposite direction. Stem-loop structure: a single-stranded nucleic acid molecule coils on itself, creating a complementary double helix "stem" with a "loop" on top. Its appearance is similar to a lollipop. Stages of translation in prokaryotesAs with eukaryotes, prokaryotic translation takes place in three steps: initiation, elongation, and termination. In both eukaryotes and prokaryotes, translation takes place in ribosomes. The major difference between prokaryotic and eukaryotic translation is in the initiation stage, while the elongation and termination stages are very similar. Again, we'll discuss the entire prokaryotic translation process and identify where these differences lie. 1st stage of translation in prokaryotes: initiationRibosomes can be broken down into large and small ribosomal subunits.
In prokaryotes, the small ribosomal subunit binds to the Shine-Dalgarno sequenceon the mRNA template. The Shine-Dalgarno sequence “AGGAGG” is found just ahead of the “AUG” start codon. A codon is a nucleotide sequence in mRNA each consisting of three nucleotide bases. During translation, codons are “read” as words such that each three-letter codon represents one specific amino acid. Unlike in eukaryotes where translation takes place after transcription, in prokaryotes, the small ribosomal unit can bind to the mRNA even when transcription is still ongoing. This is called coupled transcription and translation. We'll discuss more of this later. The small ribosomal subunit then binds to the charged initiator tRNA molecule (tRNAi) and together these traverse the mRNA strand up to the start codon. This signals the start of translation. The anticodon on the tRNAi binds to the start codon through base pairing. The anticodon is a codon in the tRNA that is complementary to a codon in the mRNA. Then, the small ribosomal subunit, mRNA, and tRNAi attach to the large ribosomal subunit, forming what is known as the initiation complex. 2nd stage of translation in prokaryotes: elongationThe basics of the elongation and termination stages of prokaryotic and eukaryotic translation are similar. During elongation, the ribosome continues to translate codons and add amino acids to the growing amino acid chain. Elongation takes place in the three compartments of the large ribosomal subunit: A (aminoacyl) site, P (peptidyl) site, and E (exit) site. The process of elongation can be summarized as follows:
3rd stage of translation in prokaryotes: terminationTranslation ends when a nonsense or stop codon (UAA, UAG, or UGA) enters the A site. Release factors call for the tRNA and the polypeptide chain to be hydrolyzed, releasing the newly formed polypeptide chain. During and after translation, the polypeptide chain is “folded” into its specific three-dimensional structure in a process called protein folding. After termination, the nucleotides of the degraded mRNA can participate in another transcription reaction while the small and large ribosomal subunits dissociate from each other and from the mRNA, allowing them to participate in another translation process. Coupled transcription and translation in prokaryotesInstead of being enclosed in the nucleus, prokaryotic DNA is suspended in the cytoplasm in the central region of the cell called nucleoid.Because there is no membrane that separates prokaryotic DNA from ribosomes, transcription, and translation can take place almost simultaneously in prokaryotes (Fig. 1). Specifically, ribosomes can begin translation even when the transcription of mRNA has not yet ended, forming RNA polymerase-mRNA-ribosome complexes. On the other hand, eukaryotic DNA is enclosed in the membrane-bound nucleus, separating it from the ribosomes in the cytoplasm and endoplasmic reticulum. Because of this eukaryotic transcription and translation take place separately: the transcription of DNA into mRNA takes place inside the nucleus. From the nucleus, the mRNA moves to the ribosomes in the cytoplasm and endoplasmic reticulum where it is translated into protein (Fig. 2). Transcription and Translation in Prokaryotes - Key takeaways
References
What is the start signal for transcription in eukaryotes?Transcription Initiation. The first step in transcription is initiation, when the RNA pol binds to the DNA upstream (5′) of the gene at a specialized sequence called a promoter (Figure 2a). In bacteria, promoters are usually composed of three sequence elements, whereas in eukaryotes, there are as many as seven elements ...
What is the stop signal for transcription in prokaryotes?Termination in Prokaryotes
Depending on the gene being transcribed, there are two kinds of termination signals: one is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain.
What is the stop signal for transcription in eukaryotes?Thus for most pol II-transcribed mRNA genes the termination signal is the poly(A) addition site in the newly synthesized RNA which acts at a distance; its recognition by RNA-binding factors initiates a process that ends in termination at a downstream site.
What is the start signal for transcription in prokaryotes?Prokaryotic Promoters
A promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription.
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