SUMMARY Cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. In several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. Understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing virulence while allowing the immune system of the host to clear bacterial infection, an approach likely to reduce the selective pressures for development of resistance. We provide here an up-to-date overview of the molecular basis and physiological implications of cell-to-cell signaling systems in Gram-negative bacteria, focusing on the well-studied bacterium Pseudomonas aeruginosa . All of the known cell-to-cell signaling systems in this bacterium are described, from the most-studied systems, i.e., N -acyl homoserine lactones (AHLs), the 4-quinolones, the global activator of antibiotic and cyanide synthesis (GAC), the cyclic di-GMP (c-di-GMP) and cyclic AMP (cAMP) systems, and the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), to less-well-studied signaling molecules, including diketopiperazines, fatty acids (diffusible signal factor [DSF]-like factors), pyoverdine, and pyocyanin. This overview clearly illustrates that bacterial communication is far more complex than initially thought and delivers a clear distinction between signals that are quorum sensing dependent and those relying on alternative factors for their production.

Success in nature depends upon an ability to perceive and adapt to the surrounding environment. Bacteria are not an exception; they recognize and constantly adjust to changing situations by sensing environmental and self‐produced signals, altering gene expression accordingly. Autoinducer‐2 (AI‐2) is a signal molecule produced by LuxS, an enzyme found in many bacterial species and thus proposed to enable interspecies communication. Two classes of AI‐2 receptors and many layers and interactions involved in downstream signalling have been identified so far. Although AI‐2 has been implicated in the regulation of numerous niche‐specific behaviours across the bacterial kingdom, interpretation of these results is complicated by the dual role of LuxS in signalling and the activated methyl cycle, a crucial central metabolic pathway. In this article, we present a comprehensive review of the discovery and early characterization of AI‐2, current developments in signal detection, transduction and regulation, and the major studies investigating the phenotypes regulated by this molecule. The development of novel tools should help to resolve many of the remaining questions in the field; we highlight how these advances might be exploited in AI‐2 quorum quenching, treatment of diseases, and the manipulation of beneficial behaviours caused by polyspecies communities.

Several important pathogens cause disease by surviving and replicating within host cells. Bacterial proliferation is the product of both replication and killing undergone by the population. However, these processes are difficult to distinguish, and are usually assessed together by determination of net bacterial load. In addition, measurement of net load does not reveal heterogeneity within pathogen populations. This is particularly important in persistent infections in which slow or nongrowing bacteria are thought to have a major impact. Here we report the development of a reporter system based on fluorescence dilution that enables direct quantification of the replication dynamics of Salmonella enterica serovar Typhimurium (S. Typhimurium) in murine macrophages at both the population and single-cell level. We used this technique to demonstrate that a major S. Typhimurium virulence determinant, the Salmonella pathogenicity island 2 type III secretion system, is required for bacterial replication but does not have a major influence on resistance to killing. Furthermore, we found that, upon entry into macrophages, many bacteria do not replicate, but appear to enter a dormant-like state. These could represent an important reservoir of persistent bacteria. The approach could be extended to other pathogens to study the contribution of virulence and host resistance factors to replication and killing, and to identify and characterize nonreplicating bacteria associated with chronic or latent infections.

The mammalian gut microbiota harbors a diverse ecosystem where hundreds of bacterial species interact with each other and their host. Given that bacteria use signals to communicate and regulate group behaviors (quorum sensing), we asked whether such communication between different commensal species can influence the interactions occurring in this environment. We engineered the enteric bacterium, Escherichia coli, to manipulate the levels of the interspecies quorum sensing signal, autoinducer-2 (AI-2), in the mouse intestine and investigated the effect upon antibiotic-induced gut microbiota dysbiosis. E. coli that increased intestinal AI-2 levels altered the composition of the antibiotic-treated gut microbiota, favoring the expansion of the Firmicutes phylum. This significantly increased the Firmicutes/Bacteroidetes ratio, to oppose the strong effect of the antibiotic, which had almost cleared the Firmicutes. This demonstrates that AI-2 levels influence the abundance of the major phyla of the gut microbiota, the balance of which is known to influence human health.

SummarySpvC is encoded by the Salmonella virulence plasmid. We have investigated the biochemical function of SpvC and the mechanism by which it is secreted by bacteria and translocated into infected macrophages. We constructed a strain carrying a deletion in spvC and showed that the strain is attenuated for systemic virulence in mice. SpvC can be secreted in vitro by either the SPI-1 or SPI-2 type III secretion systems. Cell biological and genetic experiments showed that translocation of the protein into the cytosol of macrophages by intracellular bacteria is dependent on the SPI-2 T3SS. Using antibodies specific to phospho-amino acids and mass spectrometry we demonstrate that SpvC has phosphothreonine lyase activity on full-length phospho-Erk (pErk) and a synthetic 13-amino-acid phospho-peptide containing the TXY motif. A Salmonella strain expressing spvC from a plasmid downregulated cytokine release from infected cells.

Pathogenic organisms exert a negative impact on host health, revealed by the clinical signs of infectious diseases. Immunity limits the severity of infectious diseases through resistance mechanisms that sense and target pathogens for containment, killing, or expulsion. These resistance mechanisms are viewed as the prevailing function of immunity. Under pathophysiologic conditions, however, immunity arises in response to infections that carry health and fitness costs to the host. Therefore, additional defense mechanisms are required to limit these costs, before immunity becomes operational as well as thereafter to avoid immunopathology. These are tissue damage control mechanisms that adjust the metabolic output of host tissues to different forms of stress and damage associated with infection. Disease tolerance is the term used to define this defense strategy, which does not exert a direct impact on pathogens but is essential to limit the health and fitness costs of infection. Under this argument, we propose that disease tolerance is an inherent component of immunity.

[1] Across contractional orogens, the equivalency between decadal convergence rates from geodetic GPS data and geologic shortening rates at time scales of thousands or millions of years has rarely been documented. Here, we present an example from the northern margin of Chinese Pamir, where the Main Pamir Thrust is tectonically quiescent, and recent deformation is concentrated on the Pamir Frontal Thrust (PFT). Based on dated and faulted fluvial terraces, magnetostratigraphy, and mapping, the horizontal shortening rate of the PFT is $6-7 mm/a at time scales of both $18.4 ka and $0.35 Ma, comparable to the geodetic rate of $6-9 mm/a across the same zone, implying that modern geodetic rates are a reasonable proxy for geologic rates since $0.35 Ma. Comparing this example with studies in other contractional orogens, we conjecture that a match or mismatch of geologicgeodetic rates typically depends on the time scale of observation, fault geometry, and fault mechanics. Citation: Li, T.,

Piggyback basins on the margins of growing orogens commonly serve as sensitive recorders of the onset of thrust deformation and changes in source areas. The Bieertuokuoyi piggyback basin, located in the hanging wall of the Pamir Frontal Thrust, provides an unambiguous record of the outward growth of the northeast Pamir margin in northwest China from the Miocene through the Quaternary. To reconstruct the deformation along the margin, we synthesized structural mapping, stratigraphy, magnetostratigraphy, and cosmogenic burial dating of basin fill and growth strata. The Bieertuokuoyi basin records the initiation of the Pamir Frontal Thrust and the Takegai Thrust~5-6 Ma, as well as clast provenance and paleocurrent changes resulting from the Pliocene-to-Recent uplift and exhumation of the Pamir to the south. Our results show that coeval deformation was accommodated on the major structures on the northeast Pamir margin throughout the Miocene to Recent. Furthermore, our data support a change in the regional kinematics around the Miocene-Pliocene boundary (~5-6 Ma). Rapid exhumation of NE Pamir extensional domes, coupled with cessation of the Kashgar-Yecheng Transfer System on the eastern margin of the Pamir, accelerated the outward propagation of the northeastern Pamir margin and the southward propagation of the Kashi-Atushi fold-and-thrust belt in the southern Tian Shan. This coeval deformation signifies the coupling of the Pamir and Tarim blocks and the transfer of shortening north to the Pamir frontal faults and across the quasi-rigid Tarim Basin to the southern Tian Shan Kashi-Atushi fold-and-thrust system.