Antibiotic-resistant pathogens are profoundly important to human health, but the environmental reservoirs of resistance determinants are poorly understood. The origins of antibiotic resistance in the environment is relevant to human health because of the increasing importance of zoonotic diseases as well as the need for predicting emerging resistant pathogens. This Review explores the presence and spread of antibiotic resistance in non-agricultural, non-clinical environments and demonstrates the need for more intensive investigation on this subject.

To gain insight into the diversity and origins of antibiotic resistance genes, we identified resistance genes in the soil in an apple orchard using functional metagenomics, which involves inserting large fragments of foreign DNA into Escherichia coli and assaying the resulting clones for expressed functions. Among 13 antibioticresistant clones, we found two genes that encode bifunctional proteins. One predicted bifunctional protein confers resistance to ceftazidime and contains a natural fusion between a predicted transcriptional regulator and a ␤-lactamase. Sequence analysis of the entire metagenomic clone encoding the predicted bifunctional ␤-lactamase revealed a gene potentially involved in chloramphenicol resistance as well as a predicted transposase. A second clone that encodes a predicted bifunctional protein confers resistance to kanamycin and contains an aminoglycoside acetyltransferase domain fused to a second acetyltransferase domain that, based on nucleotide sequence, was predicted not to be involved in antibiotic resistance. This is the first report of a transcriptional regulator fused to a ␤-lactamase and of an aminoglycoside acetyltransferase fused to an acetyltransferase not involved in antibiotic resistance.

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Replication origins in a genome are inherently different in their base sequence and in their response to temporal and cell cycle regulation signals for DNA replication. To investigate the chromosomal determinants that influence the efficiency of initiation of DNA replication genome-wide, we made use of a reverse strategy originally used for the isolation of replication initiation mutants in Saccharomyces cerevisiae. In yeast, replication origins isolated from chromosomes support the autonomous replication of plasmids. These replication origins, whether in the context of a chromosome or a plasmid, will initiate efficiently in wild-type cells but show a dramatically contrasted efficiency of activation in mutants defective in the early steps of replication initiation. Serial passages of a genomic library of autonomously replicating sequences (ARSs) in such a mutant allowed us to select for constitutively active ARSs. We found a hierarchy of preferential initiation of ARSs that correlates with local transcription patterns. This preferential usage is enhanced in mutants defective in the assembly of the prereplication complex (pre-RC) but not in mutants defective in the activation of the pre-RC. Our findings are consistent with an interference of local transcription with the assembly of the pre-RC at a majority of replication origins.

Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 g/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou's evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria.

Mcm1 is an essential protein required for the efficient replication of minichromosomes and the transcriptional regulation of early cell cycle genes in Saccharomyces cerevisiae. In this study, we report that Mcm1 is an abundant protein that associates globally with chromatin in a punctate pattern. We show that Mcm1 is localized at replication origins and plays an important role in the initiation of DNA synthesis at a chromosomal replication origin in vivo. Using purified Mcm1 protein, we show that Mcm1 binds cooperatively to multiple sites at autonomously replicating sequences. These results suggest that, in addition to its role as a transcription factor for the expression of replication genes, Mcm1 may influence the local structure of replication origins by direct binding.

Replication of DNA must be inherently accurate and precisely regulated. It is therefore not surprising that the mechanism for the initiation of DNA replication is both complex and conserved. Initiation of DNA synthesis involves the assembly of a multicomponent complex at designated sites known as replication origins. While the protein components of the prereplication complex (pre-RC) used in this initiation process are conserved in all eukaryotes (5), there is little in common between the nucleotide sequences of replication origins within each eukaryote and between different eukaryotes (29).In Saccharomyces cerevisiae, replication origins (ORI) consist of defined sequences of about 200 bp that can replicate autonomously independently of their native chromosomal environment. These autonomously replicating sequences (ARSs) are modular in structure. They contain a ubiquitous 11-bp (5Ј-WTTTAYRTTTW) ARS consensus sequence (ACS) (11,22,63) where the origin recognition complex (ORC) binds (4). In certain ARSs, a 10-of-11 match of the ACS is sufficient for ORC recognition (64). The ACS is essential but not sufficient for autonomous replication. cis elements on the 5Ј (C domain) or the 3Ј (B domain) flanking sequences of the ACS are also required (12). Elements in the B domain of one particular ARS, ARS1, have been characterized in great detail. Three elements, known as B1, B2, and B3, have been identified (44). B1 is protected by the ORC (55), whereas B3 is protected by Abf1 (41) or Mcm1 (17) in in vitro footprinting analyses. Initiation of DNA synthesis at ARS1 has been mapped to a region between the B1 and B2 elements (6). Two of the three B elements in combination with the ACS are sufficient to promote autonomous replication. Although B elements of different ARSs are not conserved in nucleotide sequence, they are interchangeable between certain ARSs (31, 54, 61). The differences in size and modular composition of replication origins suggest that there are many ways to assemble a functional replication origin from a finite set of modules (60)(61)(62)65). The plasticity in the organization of replication origins is further illustrated by the dispensability of the B elements altogether in the presence of the C domain in several telomeric ARSs (13). However, because the C domain is generally larger, elements in the C domain have not been characterized.The redundant functions of the B and C domains in promoting replication initiation suggest that although the process of pre-RC assembly may be conserved, there are many ways to create an environment conducive to this assembly process. The concept of alternative pathways for creating an environment for pre-RC assembly is especially appealing in higher eukaryotes, where there appears not to be a unifying mechanism for site selection for pre-RC assembly. In Xenopus oocytes, replication initiation occurs at random sequences (38). In mammalian cells, initiation occurs at multiple sites within replication zones that are defined by their chromosomal contexts rather than nucleotide...

Recent studies linking DNA replication proteins to transcriptional silencing suggest that some of the same mechanisms that facilitate the initiation of replication at origins might be involved in establishing repressed chromatin at silencer elements. Our ongoing studies of several mutants of the replication initiation factor Mcm10 of budding yeast revealed an associated defect in the production of mating type pheromones. This observation prompted us to look more directly at the effect of MCM10 mutations on the expression of a reporter gene in the mating type locus and to assay for physical interactions between Mcm10 and known silencing factors. Our findings, that Mcm10 mutants disrupt mating loci silencing and that Mcm10 interacts with Sir2 and Sir3, suggest that Mcm10 also plays an essential, and separable role in transcriptional silencing.