Y. Kashi

Evolutionary tuning knobs

Abstract Spontaneous mutations are the ultimate source of all natural genetic variation upon which evolution depends. Recent observations have revealed that many genes are associated with mutation-prone DNA tracts, each consisting of a simple motif repeated over and over in tandem. These simple sequence repeats (SSRs) may provide a previously unrecognized source of abundant quantitative genetic variation based on mutations that are frequent, site-specific and reversible, yet seldom substantially deleterious. Such sequences may be evolutionarily significant, equipping genomes and individual genes with adjustable ‘tuning knobs’ for efficient adaptation.

(TG)n uncovers a sex-specific hybridization pattern in cattle.

Screening of a bovine genomic library with the human minisatellite 33.6 probe uncovered a family of clones that, when used to probe Southern blots of bovine genomic DNA digested with the restriction enzyme HaeIII or MboI, revealed sexually dimorphic, but otherwise virtually monomorphic, patterns among the larger DNA fragments to which they hybridized. Characterization of one of these clones revealed that it contains different minisatellite sequences. The sexual dimorphism hybridization pattern observed with this clone was found to be due to multiple copies of two tandemly interspersed repeats: the simple sequence (TG)n and a previously undescribed 29-bp sequence. Both repeats appear to share many genomic loci including autosomal loci. In contrast, Southern analysis of AluI- or HinfI-digested bovine DNA with the (TG)n repeat used as a probe yielded substantial polymorphism. These results show that (i) different minisatellites can be found in a cluster, (ii) both simple and more complex repeated sequences other than the simple quaternary (GATA)n repeat can be sexually dimorphic, and (iii) simple repeats can reveal substantial polymorphism.

Mutability and evolvability: Indirect selection for mutability

How readily does mutability evolve? Petrie and Roberts (2007) have recently described a theoretical example of increased mutation rate based on female choice. Mutator alleles can also be favored by strong selection for phenotypic variation, such as that imposed by immunological attack against pathogens, together with stable linkage to beneficial mutations, provided by haploidy in microorganisms. But the special conditions required for these examples highlight two assumptions that have framed discussion of mutation-rate evolution for most of the past century (for example, Bataillon, 2000; Bell, 2005; Cotton and Pomiankowski, 2007). First, although close linkage may allow a mutator to hitchhike on selection for a beneficial allele, recombination, at least in sexually reproducing populations, will eventually separate the two. Second, because most non-neutral mutations are deleterious, the net effect of any mutator must be fitness reduction. Thus, natural selection of mutation rates has only one possible direction, that of reducing the frequency of mutation to zero (Williams, 1966). Regrettably, this classic but overstated conclusion remains influential. Even well-established exceptions like the contingency loci of some bacteria are routinely marginalized as special cases that depend on extreme and/or unusual circumstances (Sniegowski and Murphy, 2006).

How is it that microsatellites and random oligonucleotides uncover DNA fingerprint patterns

Minisatellites, microsatellites, and short random oligonucleotides all uncover highly polymorphic DNA fingerprint patterns in Southern analysis of genomic DNA that has been digested with a restriction enzyme having a 4-bp specificity. The polymorphic nature of the fragments is attributed to tandem repeat number variation of embedded minisatellite sequences. This explains why DNA fingerprint fragments are uncovered by minisatellite probes, but does not explain how it is that they are also uncovered by microsatellite and random oligonucleotide probes. To clarify this phenomenon, we sequenced a large bovine genomic BamHI restriction fragment hybridizing to the Jeffreys 33.6 minisatellite probe and consisting of small and large Sau3A-resistant subfragments. The large Sau3A subfragment was found to have a complex architecture, consisting of two different minisatellites, flanked and separated by stretches of unique DNA. The three unique sequences were characterized by sequence simplicity, that is, a higher than chance occurrence of tandem or dispersed repetition of simple sequence motifs. This complex repetitive structure explains the absence of Sau3A restriction sites in the large Sau3A subfragment, yet provides this subfragment with the ability to hybridize to a variety of probe sequences. It is proposed that a large class of interspered tracts sharing this complex yet simplified sequence structure is found in the genome. Each such tract would have a broad ability to hybridize to a variety of probes, yet would exhibit a dearth of restriction sites. For each restriction enzyme having 4-bp specificity, a subclass of such tracts, completely lacking the corresponding restriction sites, will be present. On digestion with the given restriction enzyme, each such tract would form a large fragment. The largest fragments would be those that contained one or more long minisatellite tracts. Some of these large fragments would be highly polymorphic by virtue of the included minisatellite sequences; by virtue of their complex structure, all would be capable of hybridizing to a wide variety of probes, uncovering a DNA fingerprint pattern.