Integrated conjugative plasmid drives high frequency chromosomal gene transfer in Sulfolobus islandicus

Gene transfer in crenarchaea has been observed within natural and experimental populations of Sulfolobus. However, the molecular factors that govern how gene transfer and recombination manifest themselves in these populations is still unknown. In this study, we examine a plasmid-mediated mechanism of gene transfer in S. islandicus that results in localized high frequency recombination within the chromosome. Through chromosomal marker exchange assays with defined donors and recipients, we find that while bidirectional exchange occurs among all cells, those possessing the integrated conjugative plasmid, pM164, mobilize a nearby locus at a significantly higher frequency when compared to a more distal marker. We establish that traG is essential for this phenotype and that high frequency recombination can be replicated in transconjugants after plasmid transfer. Mapping recombinants through genomic analysis, we establish the distribution of recombinant tracts with decreasing frequency at increasing distance from pM164. We suggest the bias in transfer is a result of an Hfr (high frequency recombination)-like conjugation mechanism in this strain. In addition, we find recombinants containing distal non-selected recombination events, potentially mediated by a different host-encoded marker exchange (ME) mechanism

Evolutionary causes and consequences of diversified CRISPR immune profiles in natural populations

Abstract Host-pathogen co-evolution is a significant force which shapes the ecology and evolution of all types of organisms, and such interactions are driven by resistance and immunity mechanisms of the host. Diversity of resistance and immunity can affect the co-evolutionary trajectory of both host and pathogen. The microbial CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system is one host immunity mechanism which offers a tractable model for examining the dynamics of diversity in an immune system. In the present article, we review CRISPR variation observed in a variety of natural populations, examine the forces which can push CRISPRs towards high or low diversity, and investigate the consequences of various levels of diversity on microbial populations

CRISPR Associated Diversity within a Population of Sulfolobus islandicus

Predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. A new form of microbial resistance, CRISPRs (clustered regularly interspaced short palindromic repeats) are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral DNA is inserted into the host's chromosome, thereby rendering the host resistant to further infection. Few studies have linked this form of resistance to population dynamics in natural microbial populations.We examined sequence diversity in 39 strains of the archeaon Sulfolobus islandicus from a single, isolated hot spring from Kamchatka, Russia to determine the effects of CRISPR immunity on microbial population dynamics. First, multiple housekeeping genetic markers identify a large clonal group of identical genotypes coexisting with a diverse set of rare genotypes. Second, the sequence-specific CRISPR spacer arrays split the large group of isolates into two very different groups and reveal extensive diversity and no evidence for dominance of a single clone within the population.The evenness of resistance genotypes found within this population of S. islandicus is indicative of a lack of strain dominance, in contrast to the prediction for a resistant strain in a simple predator-prey interaction. Based on evidence for the independent acquisition of resistant sequences, we hypothesize that CRISPR mediated clonal interference between resistant strains promotes and maintains diversity in this natural population

The population structure of Pseudomonas aeruginosa is characterized by genetic isolation of exoU+ and exoS+ lineages

The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intra-group but limited inter-group recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly over-represented in Group A compared to Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly over-represented in Group B compared to Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts

Bacterial Death Results from Mutations Made in Translocation Peptide of Leucyl-tRNA Synthetase

The family of aminoacyl-tRNA synthetases (aaRSs) ensures the fidelity of translation through providing a pool of correctly aminoacylated tRNA products that become incorporated by the ribosome. Leucyl-tRNA synthetase (LeuRS) has two functionally separate domains, one is the aminoacylation domain and the other is the CP1 editing domain. LeuRS can aminoacylate noncognate amino acids, therefore it relies on the CP1 editing domain to hydrolyze misaminoacylated tRNA products before they are released from the enzyme. The LeuRS enzyme must undergo a structural transition state in its reaction cycle in order to translocate the 3\u27 acceptor stem of tRNA 30 Å from the aminoacylation active site to the CP1 domain hydrolytic active site. The translocation event is difficult to study, but we believe that we have generated mutations within LeuRS that alter the translocation event of tRNA. The mutations that we have generated lead to bacterial death in Escherichia coli (E. coli). Circular dichorism experiments indicate that our mutations do not significantly alter the secondary structure of LeuRS. In vitro biochemical studies demonstrate that these mutations reduce the rates of aminoacylation and hydrolysis, while also displaying misaminoacylation activity. We attribute these biochemical findings to the resulting bacterial death that is caused by these mutation

Jellyfish

The South Carolina Department of Natural Resources published a series of educational webpages and brochures on marine science. This issue focuses on jellyfish

Bacterial Death Results from Mutations Made in Translocation Peptide of Leucyl-tRNA Synthetase

The family of aminoacyl-tRNA synthetases (aaRSs) ensures the fidelity of translation through providing a pool of correctly aminoacylated tRNA products that become incorporated by the ribosome. Leucyl-tRNA synthetase (LeuRS) has two functionally separate domains, one is the aminoacylation domain and the other is the CP1 editing domain. LeuRS can aminoacylate noncognate amino acids, therefore it relies on the CP1 editing domain to hydrolyze misaminoacylated tRNA products before they are released from the enzyme. The LeuRS enzyme must undergo a structural transition state in its reaction cycle in order to translocate the 3\u27 acceptor stem of tRNA 30 Å from the aminoacylation active site to the CP1 domain hydrolytic active site. The translocation event is difficult to study, but we believe that we have generated mutations within LeuRS that alter the translocation event of tRNA. The mutations that we have generated lead to bacterial death in Escherichia coli (E. coli). Circular dichorism experiments indicate that our mutations do not significantly alter the secondary structure of LeuRS. In vitro biochemical studies demonstrate that these mutations reduce the rates of aminoacylation and hydrolysis, while also displaying misaminoacylation activity. We attribute these biochemical findings to the resulting bacterial death that is caused by these mutation

Predicting Quiescence: The Dependence of Specific Star Formation Rate on Galaxy Size and Central Density at 0.5<z<2.5

In this paper, we investigate the relationship between star formation and structure, using a mass-complete sample of 27,893 galaxies at $0.5<z<2.5$ selected from 3D-HST. We confirm that star-forming galaxies are larger than quiescent galaxies at fixed stellar mass (M$_{\star}$). However, in contrast with some simulations, there is only a weak relation between star formation rate (SFR) and size within the star-forming population: when dividing into quartiles based on residual offsets in SFR, we find that the sizes of star-forming galaxies in the lowest quartile are 0.27$\pm$0.06 dex smaller than the highest quartile. We show that 50% of star formation in galaxies at fixed M$_{\star}$ takes place within a narrow range of sizes (0.26 dex). Taken together, these results suggest that there is an abrupt cessation of star formation after galaxies attain particular structural properties. Confirming earlier results, we find that central stellar density within a 1 kpc fixed physical radius is the key parameter connecting galaxy morphology and star formation histories: galaxies with high central densities are red and have increasingly lower SFR/M$_{\star}$, whereas galaxies with low central densities are blue and have a roughly constant (higher) SFR/M$_{\star}$ at a given redshift. We find remarkably little scatter in the average trends and a strong evolution of $>$0.5 dex in the central density threshold correlated with quiescence from $z\sim0.7-2.0$. Neither a compact size nor high-$n$ are sufficient to assess the likelihood of quiescence for the average galaxy; rather, the combination of these two parameters together with M$_{\star}$ results in a unique quenching threshold in central density/velocity.Comment: 20 pages, 15 figures, and 2 tables; Accepted for publication in the Astrophysical Journa