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The flood of information on gene and protein sequences from the genome projects has revolutionised molecular and evolutionary biology and has led to the rapid development of the science called genomics. Reliable prediction of the function of a novel gene/protein requires complex computational analysis of genomic and protein sequence information which exploit the principles governing the evolution of protein structure and function. This book aims to provide an up-to-date summary of the principles of protein evolution and discusses both the methods available to analyse the evolutionary history of proteins as well as those for predicting their structure-function relationships. Protein Evolution is intended for senior undergraduates and graduate students taking courses in protein structure and evolution, as well as bioinformatics. it will also be a useful supplement for students taking wider courses in molecular evolution, as well as a valuable resource for professionals in the area of functional genomics.
9781405151665_4_003.qxd 10/08/2007 10:07 AM Page 57 MUTATIONS 57 Table 3.1 (Continued) (c) BLOSUM62 substitution matrix from conserved protein blocks. (From Henikoff & Henikoff, 1992.) (c) C S T P A G N D E Q H R K M I L V F Y W 9 −1 −1 −3 0 −3 −3 −3 −4 −3 −3 −3 −3 −1 −1 −1 −1 −2 −2 −2 4 1 −1 1 0 1 0 0 0 −1 −1 0 −1 −2 −2 −2 −2 −2 −3 5 −1 0 −2 0 −1 −1 −1 −2 −1 −1 −1 −1 −1 0 −2 −2 −2 7 −1 −2 −2 −1 −1 −1 −2 −2 −1 −2 −3 −3 −2 −4 −3 −4 4 0 −2 −2 −1 −1 −2 −1 −1 −1 −1 −1 0 −2 −2 −3 6 0 −1 −2
i.e. they can interact with promoter(s) on other chromosomes (Lomvardas et al., 2006; Savarese & Grosschedl, 2006). In a more conventional, narrower sense, the term gene is used to refer to structural genes, which are transcribed. The noncoding RNA genes, which are only transcribed, may yield stable RNA products such as ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), antisense RNA, ribozyme RNA etc. Small nucleolar RNAs (snoRNA) are involved in directing the processing and
A+T-richness of the genome of Dictyostelium discoideum was found to determine codon usage, 9781405151665_4_004.qxd 10/08/2007 02:07PM Page 78 78 CHAPTER 4 inasmuch as codons of the form NNT or NNA are favoured over their NNG or NNC synonyms (see Chapter 9). 4.5 Molecular phylogeny The purpose of this section is to explain how phylogenetic trees may be reconstructed from analysis of nucleotide and protein sequences of proteincoding genes, from analyses of protein structures and from analyses
of paralogs, lateral gene transfer (or horizontal gene transfer) between species can lead to the acquisition of novel genes (that have no homologs in the recipient) or to the acquisition of a ‘foreign’ homolog – a xenolog – of existing genes. There are several diagnostic signs of lateral gene transfer that indicate that its evolutionary history differs from those of vertically transmitted genes (for examples see Chapter 9): 1 Unrecognized xenology can cause taxon phylogenies that are in conflict
soluble, thereby facilitating their removal from the body in the urine or bile. The evolutionary diversification of UDPGTs reflects the constant selective pressure to get rid of a large variety of toxic compounds. One major source of toxic compounds for plant-eating animals is ingested plant phenolic metabolites. The appearance of a novel type of detoxifying enzyme (with a novel substrate specificity) could confer a selective advantage on an organism: it could enable the organism to utilize