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In addition to the mechanisms previously described, there are other ways to regulate the transcription of messenger RNA. One is to control the ef ciency of various processes. For example, we know that the promoter sequence of different genes in E. coli differs. Since the af nity for RNA polymerase is different for the different sequences, the rate of initiation of transcription for these genes also varies. The more ef cient promoters are transcribed at a greater rate than the less ef cient promoters. An example is the promoter of the i gene of the lac operon. This promoter is for a constitutive gene that usually produces only about one messenger RNA per cell cycle. However, mutants of the promoter sequence are known that produce up to fty messenger RNAs per cell cycle. Here, then, the transcriptional rate is controlled by the ef ciency of the promoter in binding RNA polymerase. Ef ciency can be controlled by the direct sequence of nucleotides (i.e., differences from the consensus sequence) or by the distance between consensus regions. For example, promoters vary in the number of bases between the 35 and 10 sequences. Seventeen seems to be the optimal number of bases separating the two. Presumably, more or fewer than seventeen reduces the ef ciency of transcription.
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Phage T4
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Phage T4, a relatively large phage with seventy-three genes, has transcription controlled by particular RNA polymerase speci city factors. Like phage , phage T4 has early, middle, and late genes, genes that need to be expressed in a particular order. Early T4 genes have promoters whose speci city of recognition depends on the sigma factor of the host ( 70 of E. coli). Two products of early phage genes are the AsiA and MotA proteins. AsiA binds to the 35 recognition region of 70, preventing transcription from both host genes and early phage genes. AsiA is thus called an anti-sigma factor, a protein that interferes with a sigma factor. Middle phage promoters do not have 35 recognition regions but do bind MotA. Host RNA polymerase bound with the 70-AsiA complex recognizes these promoters. Finally, late phage genes have promoters that depend on the phage-encoded sigma factor gp55 . Some proteins are needed both early and late in the infection process; they are speci ed by genes that have promoters recognized by different speci city factors.
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When considering control of gene expression, it is important to remember that all control mechanisms are aimed at exerting an in uence on either the amount, or the activity, of the gene product.Therefore, in addition to transcriptional controls, which in uence the amount of messenger RNA produced, there are also translational controls affecting how ef ciently the messenger RNA is translated. (Attenuator control see g. 14.16 can also be viewed as translational control because the environment is tested by translation even though attenuation results in the cessation of transcription.) In prokaryotes, translational control is of lesser importance than transcriptional control for two reasons. First, messenger RNAs are extremely unstable; with a lifetime of only
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Heat Shock Proteins
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A response to elevated temperature, found in both prokaryotes and eukaryotes, is the production of heat shock proteins (see chapter 10). In E. coli, elevated temperatures cause the general shutdown of protein synthesis concomitant with the appearance of at least seventeen heat shock proteins. These proteins help protect the cell against the consequences of elevated temperature; some are molecular chaperones (see chapter 11). The production of these
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Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
14. Gene Expression: Control in Prokaryotes and Phages
The McGraw Hill Companies, 2001
Translational Control
about two minutes, there is little room for controlling the rates of translation of existing messenger RNAs because they simply do not last very long. Second, although there are some indications of translational control in prokaryotes, such control is inef cient energy is wasted synthesizing messenger RNAs that may never be used. Translational control can be exerted on a gene if the gene occurs distally from the promoter in a polycistronic operon. The genes that are transcribed last appear to be translated at a lower rate than the genes transcribed rst. The three lac operon genes, for instance, are translated roughly in a ratio of 10:5:2. This ratio is due to the polarity of the translation process. That is, in prokaryotes, translation is directly tied to transcription a messenger RNA can have ribosomes attached to it well before transcription ends. Thus, genes at the beginning of the operon are available for translation before genes at the end. In addition, exonucleases seem to degrade messenger RNA more ef ciently from the 3 end. Presumably, natural selection has ordered the genes within operons so that those producing enzymes needed in greater quantities will be at the beginning of an operon. Translation can also be regulated by RNA-RNA hybridization. RNA complementary to the 5 end of a messenger RNA can prevent the translation of that messenger RNA. The regulating RNA is called antisense RNA. In gure 14.36, the messenger RNA from the ompF gene in E. coli is prevented from being translated by complementary base pair binding with an antisense RNA called micF RNA (mic stands for mRNA-interfering complementary RNA). The ompF gene codes for a membrane component called a porin, which, as the name suggests, provides pores in the cell membrane for transport of materials. Surprisingly, a second porin gene, ompC, seems to be the source of the micF RNA. Transcription of the opposite DNA strand (the one not normally transcribed) near the promoter of the ompC gene yields the antisense
RNA. One porin gene thus seems to regulate the expression of another porin gene, for reasons that are not completely understood. Antisense RNA has also been implicated in such phenomena as the control of plasmid number and the control of transposon Tn10 transposition. Control by antisense RNA is a fertile eld for gene therapy because antisense RNA can be arti cially synthesized and then injected into eukaryotic cells. A third translational control mechanism consists of the ef ciency with which the messenger RNA binds to the ribosome. This is related to some extent to the sequence of nucleotides at the 5 end of the messenger RNA that is complementary to the 3 end of the 16S ribosomal RNA segment in the ribosome (the Shine-Dalgarno sequence). Variations from the consensus sequences demonstrate different ef ciencies of binding and, therefore, the initiation of translation occurs at different rates. The redundancy in the genetic code can also play a part in translational control of some proteins since different transfer RNAs occur in the cell in different quantities. Genes with abundant protein products may have codons that specify the more common transfer RNAs, a concept called codon preference. In other words, certain codons are preferred; they specify transfer RNAs that are abundant. Genes that code for proteins not needed in abundance could have several codons specifying the rarer transfer RNAs, which would slow down the rate of translation for these genes. The codon distribution of the phage MS2 in table 14.2 shows that every codon is used except the UGA stop codon. (The numbers in the table refer to the incidence of a particular codon in the phage genome.) However, the distribution is not random for all amino acids. For example, the amino acid glycine has two common codons and two rarer codons. The same holds for arginine but not, for example, valine. Finally, translational control can be exerted at the ribosome. When an uncharged transfer RNA nds its way into
Complementarity between the RNA of the ompF gene and antisense RNA, or micF RNA. The region of overlap includes the Shine-Dalgarno sequence and the initiation codon, effectively preventing ribosome binding and translation of the ompF RNA. Notice the stem-loops on each side of the overlap. (Reproduced, with permission, from the Annual Review of Biochemistry, Volume 55,
1986 by Annual Reviews, Inc.)
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