Repeated sequences evolution

A New Mapping Procedure for Monitoring Repeat Sequence Evolution... 

Ornston LN, W-K Yeh (1982) Recurring themes and repeated sequences in metabolic evolution. In Biodegradation and Detoxification of Environmental Pollutants (Ed AM Chakrabarty), pp. 105-126. CRC Press Inc, Boca Raton. 

The malaria parasite Plasmodium has a complex life cycle with several forms and spends much of its life hiding within red blood cells.1 It may also suppress the immune system. The unicellular sporozoites, which are injected into the bloodstream by mosquitos, are protected by an external coat protein that is unusual in containing many short repeated sequences. For example, that of P. falciparum, which causes the most deadly form of malaria, contains the sequence Asn-Ala-Asn-Pro repeated 37 times.q These coat proteins undergo unusually rapid evolution, which makes the preparation of vaccines difficult.1... 

Many of the other chapters in this volume deal with evolutionary analyses of specific genes and unique DNA sequences.24-28 There are, however, some evolutionary aspects unique to repeated DNA sequences. The most important of these factors is the amplification dynamics. Sequences become repetitive because there are amplification processes that make extra copies of them. These include retroposition and transposition mechanisms that would explain the majority of interspersed repeated DNA sequences, as well as recombination or replication slippage mechanisms that would probably explain most tandem replications. For any given repeated sequence, various factors may combine to increase or decrease the amplification rate of that sequence at various times in the evolutionary process. Thus, the dynamics of the amplification process could greatly affect the observed evolution of the family. This is particularly important in cross-species comparisons, because the amplification dynamics of a specific repeated DNA family may be altered in one species, relative to another. 

Once a sequence amplification event occurs, the nature of any selection on the copies is important. In many (or even most) cases, it appears that the majority of repeated DNA sequences represent pseudogenes, which mutate at a neutral rate of evolution.8 Along with amplification dynamics, the possible removal of repeated sequences must also be considered. Removal does not seem to play a major role with the interspersed repeated DNA elements,8,29 30 but it is likely to be important in tandemly repeated satellite elements. Other mechanisms might also alter evolution of parts of a repeated DNA sequence. For instance, human Alu family copies are initially rich in CpG dinucleotides. These sites appear to be approximately 10-fold more subject to mutation than other sites in the genome,19,31... 

All the above examples, from the Drosophila rDNA to human repeated sequences, indicate the extent to which a proper detailed analysis of variant repeat distributions that are either in states of transition or are permanently restricted yield important information on the rates, biases, and constraints of the underlying molecular mechanisms, the extent to which they are involved with the activities of one another, and the subtleties of the molecular drive process that underpin concerted evolution. They should discourage both the simplistic view of concerted evolution as an all-or-nothing phenomenon and the naive generalization that the dynamics of genomic turnover operate in the same way, in all species, for all time.13,14... 

The P propeller domain is a widespread protein organizational motif. Typically, p-propeller proteins are encoded by repeated sequences where each repeat unit corresponds to a twisted P-sheet structural motif these P-sheets are arranged in a circle around a central axis to generate the p-propeller structure. Two superfamilies of P-propeller proteins, the WD-repeat and Kelch-repeat families, exhibit similarities not only in struaure, but, remarkably, also in the types of molectdar functions they perform. Whde it is unlikely that WL) and Kelch repeats evolved from a common ancestor, their evolution into diverse families of similar function may reflect the evolutionary advantages of the stable core P-propeller fold. In this chapter, we examine the relationships between these two widespread protein families, emphasizing recently published work relating to the structure and funrtion of both Kelch and WD-repeat proteins. 

DNA of higher eukaryotes consists of unique and repeated sequences. Only -5% of human DNA encodes proteins and functional RNAs and the regulatory sequences that control their expression the remainder is merely spacer DNA between genes and introns within genes. Much of this DNA, -50% in humans, is derived from mobile DNA elements, genetic symbiots that have contributed to the evolution of contemporary genomes. 

Miesfeld R, Krystal M, Arnheim N (1981). A member of a new repeated sequence family which is conserved throughout eucaryotic evolution is found between the human delta and beta globin genes. Nucleic Acids Res. 9(22) 5931-5947. 

There are at least two reasons. One is the problem of concerted evolution of repeat sequences which may complicate phylogenetic interpretation. A second potentially confusing phenomenon is the fact that many, perhaps most, repetitive sequences are (or were) mobile pieces of DNA that have the ability to move within genomes and likely between genomes. If such sequences can move across species boundaries, i.e. be horizontally transfered, they would be misleading in analyses of phylogenies. 

The guinea pig has three satellite DNAs that contain repetitive sequences (Corneo et al., 1970b). One of these satellites, called the a-satellite , is composed of a basic repeating sequence of only 6 nucleotides and which is repeated out 10 times, although base substitutions (between 12 and 20 percent) during the course of evolution have introduc a considerable amount of sequence diversity (E. M. Southern, 1970). Several... 

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