Effects on NaeI-DNA recognition of the leucine to lysine substitution that transforms restriction endonuclease NaeI to a topoisomerase: a model for restriction endonuclease evolution.

Substituting lysine for leucine at position 43 (L43K) transforms NaeI from restriction endonuclease to topoisomerase and makes NaeI hypersensitive to intercalative anticancer drugs. Here we investigated DNA recognition by Nael-L43K. Using DNA competition and gel retardation assays, NaeI-L43K showed reduced affinity for DNA substrate and the ability to bind both single- and double-stranded DNA with a definite preference for the former. Sedimentation studies showed that under native conditions NaeI-L43K, like NaeI, is a dimer. Introduction of mismatched bases into double-stranded DNA significantly increased that DNA's ability to inhibit NaeI-L43K. Wild-type NaeI showed no detectable binding of either single-stranded DNA or mismatched DNA over the concentration range studied. These results demonstrate that the L43K substitution caused a significant change in recognition specificity by NaeI and imply that NaeI-L43K's topoisomerase activity is related to its ability to bind single-stranded and distorted regions in DNA. A mechanism is proposed for the evolution of the NaeI restriction-modification system from a topoisomerase/ligase by a mutation that abolished religation activity and provided a needed change in DNA recognition.     

Scale-dependent interactions between intrinsic and extrinsic processes reduce variability in protist populations

Interactions between intrinsic processes and extrinsic fluctuations can positively impact population persistence in ways often not predicted by classic ecological models. These interactions only arise when the intrinsic and extrinsic processes operate on the proper relative scales in time or space. Both metapopulation theory and resonance/attenuation theory suggest that interactions which lower population variability will occur when the intrinsic and extrinsic process occur on similar time scales. I performed an aquatic protist microcosm experiment to investigate how the relative frequencies of extrinsic density perturbations and intrinsic resource pulses impacted population variability. Population variability was lowest in the treatments of intermediate frequency, in which the extrinsic fluctuations and intrinsic processes were on the same time scale. This result is consistent with general theoretical predictions, and empirically documents the importance of considering scale in interactions between intrinsic and extrinsic processes that positively impact population persistence.     

Parameters of brown-headed cowbird Molothrus ater egg discrimination in warbling vireos Vireo gilvus

We examined which egg parameters warbling vireos Vireo gilvus use to discriminate brown-headed cowbird Molothrus ater eggs and, by comparing our results to other studies, tested the prediction that ejecter species with eggs more similar in appearance to cowbird eggs will be less tolerant of foreign eggs. In addition, we tested the hypothesis that egg characteristics influence the cost of ejection and probability of committing ejection errors. Warbling vireos ejected 100% of eggs with a cowbird spot pattern and only spot pattern significantly influenced the probability of ejecting a foreign egg, whereas size and nest stage did not. Foreign eggs that differed in two parameters were not ejected significantly more than those that differed in one parameter. Thus, warbling vireos appear to be less tolerant of foreign eggs than species with eggs more divergent from cowbird eggs. There was no significant difference in the number of vireo eggs that were damaged when foreign eggs of different sizes and spot patterns were ejected, which is counter to the assumptions of the evolutionary equilibrium hypothesis. Similarly, foreign egg characteristics did not significantly influence the probability of ejection errors. Finally, egg discrimination in warbling vireos appears to have evolved directly to counter cowbird parasitism because all conspecific eggs switched into their nests were accepted.