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Cooper GM. The Cell: A Molecular Approach. 2nd edition. Sunderland (MA): Sinauer Associates; 2000.

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Although transcription proceeds by the exact same fundamental mechanisms in all cells, it is substantially even more facility in eukaryotic cells than in bacteria. This is reflected in two unique distinctions in between the prokaryotic and also eukaryotic devices. First, whereas all genes are transcribed by a single RNA polymerase in bacteria, eukaryotic cells contain multiple various RNA polymerases that transcribe distinctive classes of genes. Second, rather than binding straight to promoter sequences, eukaryotic RNA polymerases should interact through a range of extra proteins to especially initiate transcription. This boosted intricacy of eukaryotic transcription presumably facilitates the sophisticated regulation of gene expression essential to straight the activities of the many type of different cell forms of multicellular organisms.

Eukaryotic RNA Polymerases

Eukaryotic cells contain 3 distinct nuclear RNA polymerases that transcribe various classes of genes (Table 6.1). Protein-coding genes are transcribed by RNA polymerase II to yield mRNAs; ribosomal RNAs (rRNAs) and carry RNAs (tRNAs) are transcribed by RNA polymerases I and III. RNA polymerase I is specifically devoted to transcription of the three biggest species of rRNAs, which are designated 28S, 18S, and also 5.8S according to their prices of sedimentation in the time of velocity centrifugation. RNA polymerase III transcribes the genes for tRNAs and also for the smallest species of ribosomal RNA (5S rRNA). A few of the tiny RNAs affiliated in splicing and also protein deliver (snRNAs and scRNAs) are also transcribed by RNA polymerase III, while others are polymerase II transcripts. In enhancement, sepaprice RNA polymerases (which are similar to bacterial RNA polymerases) are found in chloroplasts and mitochondria, wright here they particularly transcribe the DNAs of those organelles.


All 3 of the nuclear RNA polymerases are facility enzymes, consisting of 8 to 14 various subunits each. Although they acknowledge various promoters and transcribe unique classes of genes, they share a number of widespread features. The 2 biggest subunits of all 3 eukaryotic RNA polymerases are related to the β and β′subdevices of the single E. coli RNA polymerase. In enhancement, 5 subunits of the eukaryotic RNA polymerases are widespread to all 3 various enzymes. Consistent via these structural similarities, the various eukaryotic polymerases share several practical properties, consisting of the have to communicate through other proteins to as necessary initiate transcription.

General Transcription Factors and also Initiation of Transcription by RNA Polymerase II

Since RNA polymerase II is responsible for the synthesis of mRNA from protein-coding genes, it has been the focus of a lot of studies of transcription in eukaryotes. Early attempts at researching this enzyme indicated that its activity is different from that of prokaryotic RNA polymerase. The specific transcription of bacterial genes that deserve to be accomplished in vitro ssuggest by the enhancement of purified RNA polymerase to DNA containing a promoter is not possible in eukaryotic systems. The basis of this distinction was elucidated in 1979, as soon as Robert Roeder and also his colleagues discovered that RNA polymerase II is able to initiate transcription only if added proteins are included to the reaction. Hence, transcription in the eukaryotic mechanism showed up to require unique initiation determinants that (in contrast to bacterial σ factors) were not associated with the polymerase.

Biochemical fractiocountry of nuclear extracts has actually now caused the identification of certain proteins (dubbed transcription factors) that are forced for RNA polymerase II to initiate transcription. Certainly, the identification and characterization of these determinants represents a significant part of continuous initiatives to understand also transcription in eukaryotic cells. Two general types of transcription components have been defined. General transcription determinants are associated in transcription from all polymerase II promoters and therefore constitute component of the standard transcription machinery. Additional transcription components (debated later in the chapter) bind to DNA sequences that regulate the expression of individual genes and also are for this reason responsible for regulating gene expression.

Five general transcription factors are compelled for initiation of transcription by RNA polymerase II in reconstituted in vitro systems (Figure 6.12). The promoters of many kind of genes transcribed by polymerase II contain a sequence comparable to TATAA 25 to 30 nucleotides upstream of the transcription start website. This sequence (called the TATA box) resembles the -10 sequence element of bacterial promoters, and the outcomes of presenting mutations into TATAA sequences have demonstrated their duty in the initiation of transcription. The first action in formation of a transcription complicated is the binding of a general transcription variable called TFIID to the TATA box (TF indicates transcription factor; II indicates polymerase II). TFIID is itself composed of multiple subsystems, including the TATA-binding protein (TBP), which binds particularly to the TATAA consensus sequence, and also 10-12 other polypeptides, called TBP-connected factors (TAFs). TBP then binds a 2nd general transcription element (TFIIB) forming a TBP-TFIIB facility at the promoter (Figure 6.13). TFIIB in turn serves as a bridge to RNA polymerase, which binds to the TBP-TFIIB complex in association with a third element, TFIIF.


Figure 6.12

Formation of a polymerase II transcription complex. Many kind of polymerase II promoters have actually a TATA box (consensus sequence TATAA) 25 to 30 nucleotides upstream of the transcription begin site. This sequence is well-known by transcription factor TFIID, which (even more...)


Figure 6.13

Model of the TBP-TFIIB facility bound to DNA. The DNA is shown as a stick figure consisting of yellow and also green strands, via the site of transcription initiation designated +1. TBP consists of two repeats, colored light blue and also dark blue. TFIIB repeats (more...)

Following recruitment of RNA polymerase II to the promoter, the binding of two additional factors (TFIIE and also TFIIH) is compelled for initiation of transcription. TFIIH is a multisubunit factor that appears to play at leastern 2 important functions. First, 2 subdevices of TFIIH are helicases, which might unwind DNA approximately the initiation site. (These subunits of TFIIH are likewise required for nucleotide excision repair, as debated in Chapter 5.) Anvarious other subunit of TFIIH is a protein kinase that phosphorylates repeated sequences existing in the C-terminal domain of the biggest subunit of RNA polymerase II. Phosphorylation of these sequences is thshould release the polymerase from its association through the initiation complex, permitting it to proceed alengthy the layout as it elongates the growing RNA chain.

In addition to a TATA box, the promoters of many genes transcribed by RNA polymerase II contain a second essential sequence facet (an initiator, or Inr, sequence) that spans the transcription start site. In addition, some RNA polymerase II promoters contain only an Inr aspect, through no TATA box. Initiation at these promoters still requires TFIID (and TBP), also though TBP obviously does not identify these promoters by binding straight to the TATA sequence. Instead, various other subunits of TFIID (TAFs) appear to bind to the Inr sequences. This binding recruits TBP to the promoter, and TFIIB, polymerase II, and added transcription components then assemble as already described. TBP for this reason plays a central function in initiating polymerase II transcription, also on promoters that absence a TATA box.

Regardless of the development of in vitro devices and also the characterization of a number of general transcription components, much continues to be to be learned concerning the device of polymerase II transcription in eukaryotic cells. The sequential recruitment of transcription components explained below represents the minimal device compelled for transcription in vitro; additional components might be necessary within the cell. Furthermore, RNA polymerase II appears to be able to associate through some transcription components in vivo before the assembly of a transcription facility on DNA. In particular, precreated complexes of RNA polymerase II with TFIIB, TFIIE, TFIIF, TFIIH, and other transcriptional regulatory proteins have been detected in both yeast and also mammalian cells. These large complexes (called polymerase II holoenzymes) have the right to be recruited to a promoter using straight interactivity with TFIID (Figure 6.14). The loved one contributions of stepwise assembly of individual determinants versus recruitment of the RNA polymerase II holoenzyme to promoters within the cell therefore remain to be determined.


Figure 6.14

RNA polymerase II holoenzyme. The holoenzyme consists of a precreated complicated of RNA polymerase II, the general transcription determinants TFIIB, TFIIE, TFIIF, and TFIIH, and also a number of other proteins that activate transcription. This facility have the right to be recruited (even more...)

Transcription by RNA Polymerases I and III

As formerly questioned, distinct RNA polymerases are responsible for the transcription of genes encoding ribosomal and also carry RNAs in eukaryotic cells. All three RNA polymerases, however, need added transcription factors to associate via proper promoter sequences. In addition, although the three different polymerases in eukaryotic cells recognize distinct forms of promoters, a common transcription factor—the TATA-binding protein (TBP)—shows up to be forced for initiation of transcription by all 3 enzymes.

RNA polymerase I is devoted exclusively to the transcription of ribosomal RNA genes, which are present in tandem repeats. Transcription of these genes returns a big 45S pre-rRNA, which is then processed to yield the 28S, 18S, and 5.8S rRNAs (Figure 6.15). The promoter of ribosomal RNA genes spans around 150 base pairs simply upstream of the transcription initiation website. These promoter sequences are well-known by 2 transcription components, UBF (upstream binding factor) and SL1 (selectivity element 1), which bind cooperatively to the promoter and also then recruit polymerase I to create an initiation complex (Figure 6.16). The SL1 transcription element is written of four protein subdevices, among which, surprisingly, is TBP. The role of TBP has been demonstrated straight by the finding that yeasts transferring mutations in TBP are defective not just for transcription by polymerase II, however also for transcription by polymerases I and III. Therefore, TBP is a common transcription element required by all 3 classes of eukaryotic RNA polymerases. Because the promoter for ribosomal RNA genes does not contain a TATA box, TBP does not bind to certain promoter sequences. Instead, the association of TBP through ribosomal RNA genes is mediated by the binding of various other proteins in the SL1 complicated to the promoter, a instance similar to the association of TBP with the Inr sequences of polymerase II genes that lack TATA boxes.

Figure 6.15

The ribosomal RNA gene. The ribosomal DNA (rDNA) is transcribed to yield a large RNA molecule (45S pre-rRNA), which is then cleaved right into 28S, 18S, and also 5.8S rRNAs.

Figure 6.16

Initiation of rDNA transcription. Two transcription determinants, UBF and SL1, bind cooperatively to the rDNA promoter and recruit RNA polymerase I to create an initiation complex. One subunit of SL1 is the TATA-binding protein (TBP).

The genes for tRNAs, 5S rRNA, and also some of the small RNAs involved in splicing and also protein move are transcribed by polymerase III. These genes are identified by promoters that lie within, fairly than upstream of, the transcribed sequence (Figure 6.17). The most thoroughly stupassed away of the genes transcribed by polymerase III are the 5S rRNA genes of Xenopus. TFIIIA (which is the initially transcription factor to have actually been purified) initiates assembly of a transcription complicated by binding to particular DNA sequences in the 5S rRNA promoter. This binding is adhered to by the sequential binding of TFIIIC, TFIIIB, and the polymerase. The promoters for the tRNA genes differ from the 5S rRNA promoter in that they perform not contain the DNA sequence well-known by TFIIIA. Instead, TFIIIC binds directly to the promoter of tRNA genes, serving to recruit TFIIIB and also polymerase to create a transcription complicated. TFIIIB is written of multiple subsystems, one of which (as soon as again) is the TATA-binding protein, TBP. Therefore, although the three RNA polymerases of eukaryotic cells acknowledge various promoters, TBP shows up to be a common element that links promoter acknowledgment through polymerase recruitment to the transcription complicated.

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Figure 6.17

Transcription of polymerase III genes. The promoters of 5S rRNA and also tRNA genes are downstream of the transcrip-tion initiation website. Transcription of the 5S rRNA gene is initiated by the binding of TFIIIA, adhered to by the binding of TFIIIC, TFIIIB, and (more...)

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