Nuclear protein-coding genes

Their gene copy number is 10- to 100-fold higher than that of nuclear protein coding genes. 

In nuclear protein coding genes, mutations in third positions of codons of 4-codon families are not entirely silent. There is often a preference for usage of one codon over another. The strength of the codon bias varies among nuclear encoded proteins and is inversely related to rate of evolution of these genes (Sharp and Li 1989). 

Figure 8.2 Molecular evidence for vertebrate phylogeny. (a) Combined analysis of 10 nuclear protein-coding genes, (b) Combined analysis of seven nuclear protein-coding genes having representatives of hagfish and lamprey. Bootstrap confidence values are shown at nodes.

RNA polymerase II (RNA Pol II) is located in the nucleoplasm and transcribes protein-coding genes, to yield pre-mRNA, and also the genes encoding small nuclear RNAs (snRNAs) involved in mRNA processing (see Topic G8), except for U6 snRNA. 

In previous sections many of the eukaryotic proteins and DNA sequences that participate in transcription and its control have been introduced. In this section, we focus on assembly of transcription preinitiation complexes involving RNA polymerase II (Pol II). Recall that this eukaryotic RNA polymerase catalyzes synthesis of mRNAs and a few small nuclear RNAs (snRNAs). Mechanisms that control the assembly of Pol II transcription preinitiation complexes, and hence the rate of transcription of protein-coding genes, are considered in the next section. 

Different mechanisms of transcription termination are employed by each of the eukaryotic nuclear RNA polymerases. Transcription of most protein-coding genes is not... 

Nascent RNA transcripts from protein-coding genes and mRNA processing Intermediates, collectively referred to as pre-mRNA, do not exist as free RNA molecules in the nuclei of eukaryotic cells. From the time nascent transcripts first emerge from RNA polymerase II until mature mRNAs are transported into the cytoplasm, the RNA molecules are associated with an abundant set of nuclear proteins. These... 

There are four major classes of RNA in cells messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). The relative abundance, and complexity (number of distinct types), of these RNA molecules is quite different. About 80% of RNA in a cell consists of rRNA, the RNA component of ribosomes. There are only four types of eukaryotic rRNA (28S, 18S, 5.8S, and 5S) and, therefore, the sequence complexity of this class is actually quite low. In contrast, mRNA constitutes just 5% of total cellular RNA, yet it is the most diverse, with an estimated 104105 different species which correspond to the same number of protein coding genes. Both tRNA and snRNA (in eukaryotes) make up the remaining fraction of RNA in a cell (-15%), with -50 different types of tRNA and -10 different snRNAs. The total number of molecules per cell of each class of RNA is therefore based on the relationship between the total mass of each RNA class, the average length of RNA molecules in that class, and the sequence complexity. 

Eukaryotic RNA polymerases are less well-characterized than the bacterial enzyme. Biochemical studies have so far identified three distinct nuclear RNA polymerase activities in eukaryotic cell extracts prepared from both yeast and human cells. These RNA polymerases, referred to as RNA pol I, RNA pol II, and RNA pol HI, each contain a large number of subunits, some of which appeared to be shared between the different RNA polymerase subtypes. As shown in Table 24.1, RNA pol I transcribes ribosomal RNA genes, RNA pol II transcribes the majority of protein-coding genes, into mRNA, and RNA pol III transcribes tRNA, small nuclear RNAs (snRNAs), and ribosomal 5S genes. Note also that the mitochondrial genome is transcribed by a nuclear-encoded mitochondrial RNA polymerase. The yeast mitochondrial RNA polymerase holoenzyme consists of a 140-kd catalytic subunit and a 43-kd promoter-recognition protein similar to the bacterial s factor. 

Initiation complex - All of the protein-coding genes in eukaryotes are transcribed by RNA polymerase II (pol II) This enzyme also transcribes some of the small nuclear RNAs involved in splicing (see here). Like other RNA polymerases, pol II is a complex, multisubunit enzyme, but not even its numerous subunits are sufficient to allow pol II to initiate transcription on a eukaryotic promoter. To form a minimal complex capable of initiation, at least five additional protein factors are needed Figure 28.24 and listed in Table 28.4. The minimal unit involves the TATA binding protein, (TBP), but in vivo formation of the complex probably always uses TFllD, a multi-subunit structure incorporating both TBP and TATA binding associated factors (TAFs). 

Each mRNA molecule contains a nucleotide sequence that is converted into the amino acid sequence of a polypeptide chain in the process of translation. In eukaryotes, messenger RNA (mRNA) is transcribed from protein-coding genes as a long primary transcript that is processed in the nucleus to form mRNA. The various processing intermediates, which are mRNA precursors, are called pre-mRNA or hnRNA (heterogenous nuclear RNA). mRNA travels through nuclear pores to the cytoplasm, where it binds to ribosomes and tRNAs and directs the sequential insertion of the appropriate amino acids into a polypeptide chain. 

The TATA box-binding protein (TBP) is a basic transcription factor absolutely required for transcription by the three nuclear RNA polymerases (7). RNA polymerase II transcription of many protein coding genes requires direct contact of the DNA by TBP, at a sequence called the TATA box, which is located approximately 30 basepairs upstream of the transcription initiation site (2). This complex directs the assembly of the remaining basic transcription factors into a preinitiation complex (i). 

The code is not entirely universal there are minor differences between the codes used for synthesis of proteins encoded by nuclear versus mitochondrial genes of human cells. 

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