Important human pathogen; causes syphilis; has not been cultured in vitro.

182 Chapter 7 The Blueprint of Life, from DNA to Protein bioinformatics, which has created the computer technology to store, retrieve, and analyze nucleotide sequence data.

Analyzing a Prokaryotic DNA Sequence

When analyzing a DNA sequence, the nucleotide sequence of the (+) strand is used to infer information contained in the corresponding RNA transcript. Because of this, terms like start codon, which actually refers to a sequence in mRNA, are used to describe sequences in DNA. For example, to locate the start codon AUG, which would be found in mRNA, one would look for the analogous sequence, ATG, in the (+) strand of the DNA molecule. In most cases it is not initially known which of the two strands is actually used as a template for RNA synthesis, so that both strands are potentially a (+) strand. Only after a promoter is located is it known which strand in a given region is actually the (+) strand.

To locate protein-encoding regions, computers are used to search for open reading frames (ORFs), stretches of DNA, generally longer than 300 bp, that begin with a start codon and end with a stop codon. An ORF potentially encodes a protein.

Other characteristics, such as the presence of an upstream sequence that can serve as a ribosome-binding site, also indicate that an ORF encodes a protein.

The nucleotide sequence of the ORF or deduced amino acid sequence of the encoded protein can be compared with other known sequences by searching computerized databases of published sequences. Not surprisingly, as genomes of more organisms are being sequenced, information contained in these databases is growing at a remarkable rate. If the encoded protein shows certain amino acid similarities, or homology, to characterized proteins, a putative function can sometimes be assigned. For example, proteins that bind DNA share amino acid sequences in certain regions. Likewise, regulatory regions in DNA such as promoters can sometimes be identified based on the nucleotide homologies to known sequences. ■ Regulatory proteins that bind DNA, p. 183

The 580,070-base-pair genome of Mycoplasma genitali-um is the smallest bacterial genome known. The predicted coding regions and the functional role of the genes are shown in figure 7.17.

Figure 7.17 Map of the Mycoplasma genitalium genome The wide arrows indicate the predicted protein-encoding regions.The orientation of the arrows indicates the direction of transcription; the color indicates the functional role.
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