9 Protein Secretion and Export Protein Secretion Systems in Bacteria with an Outer Membrane Protein Secretion in Bacteria That Lack an Outer Membrane Sortases
10 Regulation of Gene Expression Transcriptional Regulation Posttranscriptional Regulation
11 What You Need To Know Open Reading Frames Transcriptional and Translational Fusions
12 BOX 2.1 Antibiotic Inhibitors of Transcription
13 BOX 2.2 Molecular Phylogeny
14 BOX 2.3 Antibiotic Inhibitors of Translation
15 BOX 2.4 Mimicry in Translation
16 BOX 2.5 Exceptions to the Code
Fluorescence of transformants expressing MBP-GFP hybrid proteins. MC4100 transformed with the following: 1, pMGP2; 2, pMGC2; 8, MM52 [secA(Ts)] transformed with pMGP2; 3, pMGC2; 7, CK2163 (secB) transformed with pMGP2; 4, pMGC2; 6, IQ85 [secY(Ts)] transformed with pMGP2; and 5, pMGC2. From Feilmeier et al. 2000 (see Suggested Reading).
UNCOVERING THE MECHANISM OF PROTEIN SYNTHESIS, and therefore of gene expression, was one of the most significant accomplishments in the history of science. The process of gene expression is called the central dogma of molecular biology, which states that information stored in DNA is copied into RNA and then translated into protein. We now know of many exceptions to the central dogma. For example, information can sometimes flow in the reverse direction, from RNA to DNA. The information in RNA also can be changed after it has been copied from the DNA. Moreover, the information in DNA may be expressed differently depending on where it is in the genome. Despite these exceptions, however, the basic principles of the central dogma remain sound.
This chapter outlines the process of gene expression and protein synthesis, with a brief discussion of how proteins can be differentially localized after synthesis. The discussion is meant to be only a broad overview, with special emphasis on topics essential to an understanding of the chapters that follow and on subjects unique to bacteria. For more detailed treatments, consult any modern biochemistry textbook.
Overview
DNA carries the information for the synthesis of RNA and proteins in regions called genes. The first step in expressing a gene is to transcribe an RNA copy from one strand in that region. The word “transcription” is descriptive, because the information in RNA is copied from DNA in the same language, which is written in a sequence of nucleotides. If the gene carries information for a protein, this RNA transcript is called messenger RNA (mRNA). An mRNA is a messenger because it carries the information encoded in a gene to a ribosome, which is the main machinery for protein synthesis. Once on the ribosome, the information in the mRNA can be translated into the protein. Translation is another descriptive word, because one language—a sequence of nucleotides in DNA and RNA—is translated into a different language—a sequence of amino acids in a protein. The mRNA is translated as it moves through the ribosome, 3 nucleotides at a time. Each 3-nucleotide sequence, called a codon, carries information for a specific amino acid. The assignment of each of the possible codons to an amino acid is called the genetic code.
The actual translation from the language of nucleotide sequences to the language of amino acid sequences is performed by small RNAs called tRNAs and enzymes called aminoacyl-tRNA synthetases (aaRSs). The aaRS enzymes attach specific amino acids to their matching tRNAs. Each aminoacylated tRNA (aa-tRNA) specifically pairs with a codon in the mRNA as it moves through the ribosome, and the amino acid carried by the tRNA is added to the growing protein. The tRNA pairs with the codon in the mRNA through a 3-nucleotide sequence in the tRNA called the anticodon that is complementary to the codon in the mRNA. The base-pairing rules for codons and anticodons are basically the same as the base-pairing rules for DNA replication, and the pairing is antiparallel. The only major differences are that RNA has uracil (U) rather than thymine (T) and that the pairing between the last of the 3 bases in the codon and the first base in the anticodon is less stringent.
This basic outline of gene expression leaves many important questions unanswered. How does mRNA synthesis begin and end at the correct places and on the correct strand in the DNA? Similarly, how does translation start and stop at the correct places on the mRNA? What actually happens to the tRNA and ribosomes during translation? What happens to the mRNA and proteins after they are made? The answers to these questions and many others are important for the interpretation of genetic experiments, so we will discuss the structure of RNA and proteins and the processes by which they are synthesized in more detail.
The Structure and Function of RNA
In this section, we review the basic components of RNA and how it is synthesized. We also review how structure varies among different types of cellular RNAs and the role each type plays in cellular processes.
Types of RNA
There are several different classes of RNA in cells. Some of these, including mRNA, rRNA, and tRNA, are involved in protein synthesis. Each of these types of RNA has special properties, which are discussed below. Others are involved in regulation, replication, and protein secretion.
RNA Precursors
RNA is similar to DNA in that it is composed of a chain of nucleotides. However, RNA nucleotides contain the sugar ribose instead of deoxyribose. These five-carbon sugars differ in the second carbon, which is attached to a hydroxyl group in ribose rather than the hydrogen found in deoxyribose (see Figure 1.2). Figure 2.1A shows the structure of