Page 55 - Genetics_From_Genes_to_Genomes_6th_FULL_Part3

10.2 Genome Architecture and Evolution 349

Figure 10.8 Domain architecture of transcription factors. Protein domains are indicated as colored icons labeled POZ, HD
(homeodomain), etc. Horizontal lines connect domains found in the same protein. The numbers and types of transcription factors vary
considerably between different species due to protein domain reshuffling during evolution. As an example, worms make about 143 different
transcription factors containing POZ domains, of which three are shown, while fruit flies make about 93 POZ-containing proteins, of which two
are shown. Some of the domains shown govern DNA binding, while others facilitate protein–protein interactions.
Worm Fly Human
POZ:~143 Homeodomain:~90 POZ:~95 Homeodomain:~92 POZ:~140 Homeodomain:~220
MATH POZ Paired HD HD POZ C2H2 C2H2 Paired HD HD POZ C2H2 C2H2 C2H2 C2H2 C2H2 C2H2 Paired HD HD
POZ K Pou HD Lim HD Pou HD Lim HD Pou HD Lim HD
POZ A POZ bZip
POZ
NHR:~230 C4DM:~80 SAZ (MYB-like):~35 Krab:~220 Scan:~50
Zn LB C4DM C2H2 C2H2 SAZ SAZ SAZ Krab C2H2 C2H2 C2H2 C2H2 C2H2 C2H2 Scan C2H2 C2H2 C2H2 C2H2 C2H2 C2H2
bHLH:~53 bHLH:~105
bHIH bHIH PAS PAS bHIH bHIH PAS PAS

Figure 10.9 Homeodomain consensus sequence. The consensus sequence of amino acids shows the most commonly found amino
acid at a given position within all known homeodomains in all organisms. Subsequent rows show matches to the consensus (purple) of
homeodomains in nine Drosophila proteins that dictate key aspects of the animal’s development. (These genes and proteins will be
discussed in Chapter 19.)
Consensus R R RKR TAYT RYQL LELE KE FHFNRYL T RRRR IE LAHS LNL TE RQVK IWFQNR RHKWK KEN
Ubx R R RGRQT YT RYQT LELE KE FHTNHYLT RRRR IEMAHA LSL TE RQ IKI WFQNRRMKLK KE I
Abd-A R RRGRQT YT RFQT LELE KE FHFNHYL T RRRR IE I AHA LSL TE RQ IKI WFQNRRMKLK KE L
Abd-B VRKKRKPY SK FQT LELE KE FLFNAVS KQKRWI LMRNAQSL TE RV IKI WFQNRRMKNK KNS
lab NNSGR TNFTNKQL T ELE KE FHFNRYL T RRRR IE IANT LQLNE TQVK IWFQNR RMKWK KEN
pb P R RLR TAY TNTQL LELE KE FHTNKYLCRPR RI EI AAS LDL TE RQVKVWFQNRRMKHK RQT
Dfd P K RQR TAYT LHQI LELE KE FHYNRYLT RRRR IE IAHT LVL SE RQ IKI WFQNRRMKWK KDN
Scr T K RQR TS YT RYQT LELE KE FHFNRYL T RRRR IE I AHA LSL TE RQ IKI WFQNRRMKWK KEN
Antp R K RGRQT YT RYQT LELE KE FHFNRYL T RRRR IE I AHA LSL TE RQ IKI WFQNRRMKWK EI N

different purposes. Similarly, many genes are composed of homeodomain-containing protein by comparing its puta-
multiple exons that encode discrete protein domains. The tive amino acid sequence to those of known homeodomains
shuffling, addition, or deletion of exons during evolution and searching for similarity (Fig. 10.9).
can create new genes whose protein products have novel The mechanism of RNA splicing facilitates this kind
domain architectures (different numbers and kinds of do- of exon rearrangement in eukaryotic genomes (and thus
mains in different orders) and thus can assume new roles in the creation of new genes) because the reshuffling does
cells and organisms. not have to be precise. Suppose, as shown in Fig. 10.10,
Figure 10.8 shows an example of the domains associ- that the exon of one gene plus its flanking introns is
ated with various transcription factors, proteins that bind moved to a new location in the intron of a different gene.
to regions of DNA such as enhancers that control the tran- This exon can now be spliced together with the second
scription of nearby genes. Exon shuffling over evolution gene’s exons to make a single mRNA molecule, regard-
has produced different transcription factors with differing less of where within the introns these pieces of DNA were
domains that enable these proteins to recognize particular brought together.
DNA sequences and also to interact uniquely with cofac-
tors such as other proteins.
Biologists may guess at the function of a new protein Gene families
(or the gene that encodes it) by analogy, if they find by Gene families are groups of genes closely related in se-
computerized analysis that it contains a domain known to quence and function; such gene families are abundant
play a specific role in other proteins. As an example, many throughout genomes. Examples of gene families include
proteins that include a homeodomain (a particular DNA- the genes that encode the hemoglobins that allow us to
binding motif) are transcription factors important for transport oxygen in our blood (Fig. 10.11), the immunoglo-
the development of multicellular organisms. Computer bins (antibodies) that help us ward off infections, and the
algorithms determine that a particular gene encodes a olfactory receptors critical for our sense of smell.