David S. Thaler

The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants

The requirement for DNA sequence homology in generalized genetic recombination is greatly relaxed in bacterial mutL,mutS and mutH mutants deficient in mismatch repair. In such mutants, inter-generic recombination occurs efficiently between Escherichia coli and Salmonella typhimurium, which are ∼20% divergent in DNA sequence. This finding has implications for speciation, for regulating recombination between diverged repeated sequences, and for hitherto difficult interspecies hybridizations.

Microbial genetics. The tinkerer's evolving tool-box.

By knowing the mechanisms through which genetic variants are generated, we should gain a better understanding of evolution. Two new papers — one theoretical and one experimental — show that mutator alleles (which can lead to a huge increase in mutation rate) can speed up the rate at which bacteria adapt to a changing environment, even if these alleles remain at a low frequency.

Quorum Sensing Influences Vibrio harveyi Growth Rates in a Manner Not Fully Accounted For by the Marker Effect of Bioluminescence

Background The light-emitting Vibrios provide excellent material for studying the interaction of cellular communication with growth rate because bioluminescence is a convenient marker for quorum sensing. However, the use of bioluminescence as a marker is complicated because bioluminescence itself may affect growth rate, e.g. by diverting energy. Methodology/Principal Findings The marker effect was explored via growth rate studies in isogenic Vibrio harveyi (Vh) strains altered in quorum sensing on the one hand, and bioluminescence on the other. By hypothesis, growth rate is energy limited: mutants deficient in quorum sensing grow faster because wild type quorum sensing unleashes bioluminescence and bioluminescence diverts energy. Findings reported here confirm a role for bioluminescence in limiting Vh growth rate, at least under the conditions tested. However, the results argue that the bioluminescence is insufficient to explain the relationship of growth rate and quorum sensing in Vh. A Vh mutant null for all genes encoding the bioluminescence pathway grew faster than wild type but not as fast as null mutants in quorum sensing. Vh quorum sensing mutants showed altered growth rates that do not always rank with their relative increase or decrease in bioluminescence. In addition, the cell-free culture fluids of a rapidly growing Vibrio parahaemolyticus (Vp) strain increased the growth rate of wild type Vh without significantly altering Vhs bioluminescence. The same cell-free culture fluid increased the bioluminescence of Vh quorum mutants. Conclusions/Significance The effect of quorum sensing on Vh growth rate can be either positive or negative and includes both bioluminescence-dependent and independent components. Bioluminescence tends to slow growth rate but not enough to account for the effects of quorum sensing on growth rate.

Design for an aging brain

Vaillancourt and Newell (Neurobiol. of Aging 2001) show that although many aging systems decrease in complexity as anticipated by Lipsitz and Goldberger (JAMA 1992), other aging systems increase in complexity. Vaillancourt and Newell explain the discrepancy by proposing that systems with a point attractor decrease in complexity with age, whereas those with an oscillating attractor increase in complexity with age. Vaillancourt and Newell are certainly correct that no one direction fits all results. Aging and death sometimes follow from a system being too simple, or, too complex. A perspective, based on the work of W. Ross Ashby (1956 and http://pespmc1.vub.ac.be/ASHBBOOK.html) is used in this commentary to consider why some systems become apparently more simple and others more complex as they age. In this Ashby-inspired view the measured complexity of a systems Responses to Disturbances is proportional to the ratio D/R, where D and R are sets containing the variety of possible disturbances and responses. The model expands on Ashbys by proposing that D consists of two components, Dp and Du. Dp consists of disturbances that are a function of the systems perception. Responses to Dp are often anticipatory and the response itself dominates the outcome. Du are disturbances that are unavoidable. Outcomes decrease or increase in measured entropy as a function of changes in (Dp + Du)/R. The variety of elements in both Dp and R decrease with age. When D/R decreases with age, the system shows less complexity. Conversely when D/R increases with Age, the results become more entropic.

Changing the pace of evolution

Abstract In biological evolution, the rate of mutations is “encoded” by enzymes which can be mutated like any other gene. Inspired by this feature, we present a simple Brownian motion model, in which the temperature itself is a dynamical variable. Intrawell and interwell relaxations occur at different “temperatures” and have different dynamics, and the Kramers time becomes asymptotically linear in the barrier height for large heights.

Hereditary stability and variation in evolution and development

Evolution and development are both lineage processes but are often conceptualized as occurring by different and mutually exclusive mechanisms. It is conventionally asserted that evolution occurs via the random generation of diversity and the subsequent survival of those that pass selection. On the other hand, development is too often presented as proceeding via the unfolding of a deterministic program encoded in the DNA sequence. In biology, universal generalizations are rare and dogmas are often wrong for particular cases. Deterministic mechanisms contribute some of the new DNA sequences that subsequently become substrates for natural selection. Conversely, stochastic and selective mechanisms are intrinsic to development, and also to maintenance of the immune, and possibly, nervous systems. Cancer appears to be another process that straddles distinctions between evolutionary and developmental modes of hereditary change and stabilization. DNA sequence changes are an essential feature of many cancers, but there are also aspects of the disease similar to developmental lineage gone awry. The literature suggests that the cellular changes that give rise to cancer occur by mechanisms commonly associated with both evolutionary and developmental lineage pathways.

Sex is for sisters: intragenomic recombination and homology-dependent mutation as sources of evolutionary variation

Sex and recombination generate variation via processes that depend on an underlying complementarity between participants. Sex between DNA segments depends on their sequences having enough in common. Viewed in this way, sex does not depend on genes that originate in separate cells. Sex in the single genome uses many of the same mechanisms as intergenomic sex but has not been properly appreciated as a source of variation or as a selectable process. Mutation is the generation of new sequences rather than the novel grouping of pre-existing alleles. Mechanisms of mutation that depend on pre-existing sequence similarities in the haploid genome are a source of variation with significant and special characteristics.

Synthetic peptide analogs compared with phage display

Phage display techniques have been used extensively to identify peptide ligands of antibodies. One such library having a random 12 amino acid sequence at the Nterminus of the gene III protein (pIII) of phage Ml3 was used to identify peptide ligands for a murine anti-phosphocholine IgA class antibody, McPC603. A high-resolution X-ray structure of the target antibody is available, but peptide ligands have not been previously described [1].

C1q-binding peptides share sequence similarity with C4 and induce complement activation

Two peptide motifs that bind to C1q have been identified from phage displayed libraries. A first panning cycle recovered phage that displayed a [N/S]PFxL motif. A synthetic peptide with that motif blocked those phage from binding to C1q. A second panning cycle was conducted with the [N/S]PFxL motif peptide present, leading to recovery of phage displaying a different motif, SHY. The two motifs are specific for C1q and are competed by DNA and the cognate synthetic peptide but not by immunoglobulins. Phage displayed peptide sequences containing the [N/S]PFxL have significant sequence similarity to a region of complement component C4, suggesting a possible site of interaction between C4, or one of its processed forms, and C1q. The SHY motif peptide induces C4 consumption in a hemolytic assay, suggesting that it activates C1 independent of immune complexes. This peptide may activate C1 by a mechanism similar to the beta-amyloid peptides found in Alzheimers disease.

MEPS parameters and graph analysis for the use of recombination to construct ordered sets of overlapping clones

Homologous recombination can provide a basis for the construction of an ordered set of overlapping clones. The principle is to make two libraries, each in a vector that has a different selectable marker flanking the insert site. Recombination between the flanking markers, leading to a selectable phenotype, can only occur as the consequence of crossing over between inserts. The two libraries are crossed in a matrix, allowing the construction of an ordered set. The logic, akin to S. Benzers (1961, Genetics 47:403-415) for the arrangement of deletion and point mutations, has a graph theoretic formulation, which helps to cope with the complex and noisy data inherent in the physical mapping of genomes rich in repeated sequences. The minimum length of identity required for homologous recombination is called the MEPS (minimum efficient processing segment) and is a property of each recombination pathway. The amount and the type of sequence similarity required for two sequences to recombine is different from that implied by either the conservation of restriction sites or by most procedures of hybridization.