The bacterial parasite Pasteuria ramosa is not killed if it fails to infect: implications for coevolution

Strong selection on parasites, as well as on hosts, is crucial for fueling coevolutionary dynamics. Selection will be especially strong if parasites that encounter resistant hosts are destroyed and diluted from the local environment. We tested whether spores of the bacterial parasite Pasteuria ramosa were passed through the gut (the route of infection) of their host, Daphnia magna, and whether passaged spores remained viable for a “second chance” at infecting a new host. In particular, we tested if this viability (estimated via infectivity) depended on host genotype, whether or not the genotype was susceptible, and on initial parasite dose. Our results show that Pasteuria spores generally remain viable after passage through both susceptible and resistant Daphnia. Furthermore, these spores remained infectious even after being frozen for several weeks. If parasites can get a second chance at infecting hosts in the wild, selection for infection success in the first instance will be reduced. This could also weaken reciprocal selection on hosts and slow the coevolutionary process.     

Influence of day of postpartum breeding on pregnancy rate, pregnancy loss rate, and foaling rate in Thoroughbred mares

Records (years 2005-2007) were analyzed from a Thoroughbred stud farm in central Kentucky. Data from all breeding cycles of foaling mares were tabulated (3184 cycles of 2003 foaling mares bred between 7 and 163 days postpartum). A multiple logistic regression model employing Bayesian statistics was used to adjust for factors that significantly affected outcome; odds ratios (ORs) for pregnancy rate, pregnancy loss rate, and foaling rate were determined to examine the influence of day of postpartum breeding on these parameters. Mares bred before Day 22 (Day 0 = day of foaling) postpartum had a decreased OR for becoming pregnant (P < 0.05); the median OR for becoming pregnant (1.00) was not reached until Day 46 postpartum. Mares bred before Day 13 postpartum had an increased OR for pregnancy loss (P < 0.05). The median OR for pregnancy loss did not decline below 1.00 until Day 78 postpartum. Mares bred before Day 20 postpartum had a decreased OR for producing a foal (P < 0.05). The median OR for producing a foal (1.00) was not reached until Day 75 postpartum. We concluded that fertility (in terms of a higher OR for becoming pregnant and a lower OR for pregnancy loss, resulting in a higher OR for producing a foal) continued to improve in Thoroughbred mares for approximately 2.5 mo postpartum. These findings are of importance to management strategies directed at early postpartum breeding, and explain some of the reported drift in subsequent foaling dates of Thoroughbred mares, despite management practices that employ early postpartum breeding.     

Methane sources in arctic thermokarst lake sediments on the North Slope of Alaska

The permafrost on the North Slope of Alaska is densely populated by shallow lakes that result from thermokarst erosion. These lakes release methane (CH₄) derived from a combination of ancient thermogenic pools and contemporary biogenic production. Despite the potential importance of CH₄ as a greenhouse gas, the contribution of biogenic CH₄ production in arctic thermokarst lakes in Alaska is not currently well understood. To further advance our knowledge of CH₄ dynamics in these lakes, we focused our study on (i) the potential for microbial CH₄ production in lake sediments, (ii) the role of sediment geochemistry in controlling biogenic CH₄ production, and (iii) the temperature dependence of this process. Sediment cores were collected from one site in Siqlukaq Lake and two sites in Sukok Lake in late October to early November. Analyses of pore water geochemistry, sedimentary organic matter and lipid biomarkers, stable carbon isotopes, results from CH₄ production experiments, and copy number of a methanogenic pathway‐specific gene (mcrA) indicated the existence of different sources of CH₄ in each of the lakes chosen for the study. Analysis of this integrated data set revealed that there is biological CH₄ production in Siqlukaq at moderate levels, while the very low levels of CH₄ detected in Sukok had a mixed origin, with little to no biological CH₄ production. Furthermore, methanogenic archaea exhibited temperature‐dependent use of in situ substrates for methanogenesis, and the amount of CH₄ produced was directly related to the amount of labile organic matter in the sediments. This study constitutes an important first step in better understanding the actual contribution of biogenic CH₄ from thermokarst lakes on the coastal plain of Alaska to the current CH₄ budgets.     

Conservation of Structure and Protein-Protein Interactions Mediated by the Secreted Mycobacterial Proteins EsxA,EsxB, and EspA

Mycobacterium tuberculosis EsxA and EsxB proteins are founding members of the WXG100 (WXG) protein family, characterized by their small size (∼100 amino acids) and conserved WXG amino acid motif. M. tuberculosis contains 11 tandem pairs of WXG genes; each gene pair is thought to be coexpressed to form a heterodimer. The precise role of these proteins in the biology of M. tuberculosis is unknown, but several of the heterodimers are secreted, which is important for virulence. However, WXG proteins are not simply virulence factors, since nonpathogenic mycobacteria also express and secrete these proteins. Here we show that three WXG heterodimers have structures and properties similar to those of the M. tuberculosis EsxBA (MtbEsxBA) heterodimer, regardless of their host species and apparent biological function. Biophysical studies indicate that the WXG proteins from M. tuberculosis (EsxG and EsxH), Mycobacterium smegmatis (EsxA and EsxB), and Corynebacterium diphtheriae (EsxA and EsxB) are heterodimers and fold into a predominately α-helical structure. An in vivo protein-protein interaction assay was modified to identify proteins that interact specifically with the native WXG100 heterodimer. MtbEsxA and MtbEsxB were fused into a single polypeptide, MtbEsxBA, to create a biomimetic bait for the native heterodimer. The MtbEsxBA bait showed specific association with several esx-1-encoded proteins and EspA, a virulence protein secreted by ESX-1. The MtbEsxBA fusion peptide was also utilized to identify residues in both EsxA and EsxB that are important for establishing protein interactions with Rv3871 and EspA. Together, the results are consistent with a model in which WXG proteins perform similar biological roles in virulent and nonvirulent species.The WXG100 (WXG; pfam06013) proteins are a class of effector molecules found in gram-positive bacteria (26). WXG proteins are characterized by their small size (∼ 100 amino acids [aa]) and the presence of a WXG motif, or its structural equivalent, near the midpoint of their primary sequence (26). Bioinformatic analyses have shown that one WXG gene is frequently positioned near, or directly adjacent to, a second, related, WXG gene (14). The gene pairs characterized thus far encode proteins that associate to form 1:1 complexes (20, 31). The WXG proteins were once thought to be restricted to the mycobacteria, but homologues have now been detected in species of Bacillus, Listeria, Streptomyces, and Corynebacterium, among others, and the Pfam server lists >89 distinct WXG-encoding species and strains (10).The identification of WXG proteins encoded by the pathogens Mycobacterium tuberculosis (15, 17, 19, 36), Mycobacterium marinum (13), and Staphylococcus aureus (5) has created significant interest in the proteins'' biological activity. Nevertheless, these proteins are not a priori virulence factors (39), since organisms expressing WXG proteins are not necessarily capable of causing disease. In addition to pathogenesis, the WXG proteins are associated with processes as disparate as zinc homeostasis (24) and conjugal gene transfer (9, 11). A model for the mechanism(s) of action of these proteins that includes an explanation for their apparent functional versatility is at present lacking. One reason for this ambiguity may be the near-absence of studies comparing virulence-associated and non-virulence-associated WXG proteins, which is a goal of this study.The M. tuberculosis secreted virulence factors EsxA (also called ESAT-6, or Rv3875) and EsxB (CFP-10; Rv3874) are the founding members of the WXG family, and M. tuberculosis derivatives defective in EsxA and EsxB are attenuated (17, 19, 36). The results of biochemical and structural studies indicate that EsxA and EsxB form a tightly associated heterodimer, EsxAB (25, 30, 31). The M. tuberculosis genome contains 23 WXG genes, named esxA to esxW, and the majority of these are expressed as tandem pairs (26). Of the pairs, five, including esxA and esxB, are contained within larger, highly conserved genetic loci, called esx-1 to esx-5 (Fig. ​(Fig.1).1). These loci have been the focus of much research, since mutants of esx-1 are attenuated, and esx-3 and esx-5 are necessary for in vitro growth of M. tuberculosis and M. marinum (1, 2, 32-34). The esx loci are proposed to encode secretory apparatuses dedicated to the secretion of their cognate WXG proteins (1).Open in a separate windowFIG. 1.Genetic map of the esx-1 loci of M. tuberculosis and M. smegmatis. The M. tuberculosis esx-1 genes discussed in the text are indicated by white arrows, as are their M. smegmatis homologues. The M. tuberculosis map also shows the Rv3884 and Rv3885 genes, which are part of the adjacent esx-2 locus. pRD1-2F9 is the cosmid that was used to create an esx-1-specific prey library. pRD1-2F9 includes the Rv3860 to Rv3885 genes, thus encompassing the entire esx-1 locus and part of esx-2. The four genes below the M. smegmatis map include defective insertion sequences (ISs) inserted into MSMEG_0075.Although the majority of genes required for the secretion of the EsxAB heterodimer are encoded from within esx-1, additional non-esx-1 genes are necessary for secretion. In particular, one M. tuberculosis locus, esp, encodes three proteins essential for EsxAB secretion (12, 23). The first gene of the operon encodes a protein, EspA, that is cosecreted with EsxAB via the ESX-1 apparatus (12). Although no direct physical evidence has been presented, the inference from the interdependent cosecretion of the three proteins is that they likely form a complex, which is secreted by the ESX-1 apparatus. In this paper we provide the first genetic evidence that these three proteins interact.The lack of a genetic assay for the study of ESX-1 activity in M. tuberculosis has hindered the identification of all of the protein components of the apparatus and all of the substrates that it secretes. However, the fast-growing, nonpathogenic organism Mycobacterium smegmatis has a conserved esx-1 locus that is essential for DNA transfer, and we have exploited this requirement for genetic studies (9). These analyses have shown that the M. smegmatis ESX-1 apparatus is functionally related to that of M. tuberculosis (11) and that M. smegmatis encodes non-esx-1 genes necessary for the secretion of the EsxAB heterodimer, including orthologues of EspA (9).Here we have examined whether the secondary and quaternary structures of M. tuberculosis EsxA and EsxB are prototypical for other, functionally distinct and evolutionarily distant members of the WXG family (Fig. ​(Fig.2A).2A). Comparisons were made to homologues encoded by M. smegmatis (esxA and esxB), Corynebacterium diphtheriae (esxA and esxB), and an additional non-virulence-related pair from M. tuberculosis (esxG and esxH, encoded from the esx-3 locus). Structural characterization of these proteins establishes that their secondary and quaternary structures are conserved, with each pair folding into a predominately α-helical structure and associating to form a heterodimer. We next devised and tested the utility of a novel strategy to identify proteins that interact specifically with these WXG heterodimers. This involved fusing EsxB and EsxA to create a biomimetic heterodimer for use in mycobacterial two-hybrid experiments. We reasoned that the use of this unique bait would allow the detection of proteins that interact with both components of the native heterodimer and that these proteins would normally go undetected in the conventional, single-protein two-hybrid screens. Indeed, using this approach, we identified novel protein partners of M. tuberculosis EsxBA (MtbEsxBA). We show for the first time that EspA proteins from M. tuberculosis and M. smegmatis interact with the EsxBA heterodimer (from both species) but not with EsxA or EsxB alone. We also provide evidence for promiscuity between the different M. tuberculosis ESX apparatuses by showing that EsxBA, encoded by esx-1, can interact with Esx proteins encoded by esx-2. Taken together, our studies suggest that the WXG proteins possess similar structures and properties, regardless of the host species and the apparent biological function.Open in a separate windowFIG. 2.Sequence alignment of WXG proteins characterized in this study and the strategy used to facilitate their expression. (A) Amino acid sequence alignment of four pairs of WXG proteins. Conserved sequences are in boldface, and the signature WXG motif is indicated with asterisks. Three residues in Rv3874 (EsxB) and a single residue in Rv3875 (EsxA) are underlined; they are the sites of amino acid substitutions discussed in the text that abrogate Rv3871 interactions. (B) (Bottom) Scheme for coexpression of tandemly arranged WXG genes. (Top) The ribbon cartoon (30) shows how the two monomers are freed from the expressed fusion protein by thrombin cleavage (scissors) at the peptide tether (balls and sticks).     

A high-throughput strategy to screen 2D crystallization trials of membrane proteins

Electron microscopy of two-dimensional (2D) crystals has demonstrated potential for structure determination of membrane proteins. Technical limitations in large-scale crystallization screens have, however, prevented a major breakthrough in the routine application of this technology. Dialysis is generally used for detergent removal and reconstitution of the protein into a lipid bilayer, and devices for testing numerous conditions in parallel are not readily available. Furthermore, the small size of resulting 2D crystals requires electron microscopy to evaluate the results and automation of the necessary steps is essential to achieve a reasonable throughput. We have designed a crystallization block, using standard microplate dimensions, by which 96 unique samples can be dialyzed simultaneously against 96 different buffers and have demonstrated that the rate of detergent dialysis is comparable to those obtained with conventional dialysis devices. A liquid-handling robot was employed to set up 2D crystallization trials with the membrane proteins CopA from Archaeoglobus fulgidus and light-harvesting complex II (LH2) from Rhodobacter sphaeroides. For CopA, 1 week of dialysis yielded tubular crystals and, for LH2, large and well-ordered vesicular 2D crystals were obtained after 24 h, illustrating the feasibility of this approach. Combined with a high-throughput procedure for preparation of EM-grids and automation of the subsequent negative staining step, the crystallization block offers a novel pipeline that promises to speed up large-scale screening of 2D crystallization and to increase the likelihood of producing well-ordered crystals for analysis by electron crystallography.     

Molecular diversity in engineered protein libraries

Engineered protein libraries, defined here as a collection of different mutant variants of a single specific protein, are intentionally designed to be rich in molecular diversity and can span ranges from as little as 400 different variants to greater than 10(12) members per library. The goal of engineering libraries is to generate new protein variants, identified upon screening, that possess desired novel properties. Exploitation of the natural organization of the genetic code has led to 'focused' libraries that are lower in overall complexity yet biased towards variants with preferred biophysical properties. An emerging trend, in which computational algorithms are blended with in vivo screens, is also leading towards greater and more rapid success in the field of protein design.     

Signal integration and crosstalk during thymocyte migration and emigration

The thymus produces self-tolerant functionally competent T cells. This process involves the import of multipotent haematopoietic progenitors that are then signalled to adopt the T cell fate. Expression of T cell-specific genes, including those encoding the T cell receptor (TCR), is followed by positive and negative selection and the eventual export of mature T cells. Significant progress has been made in elucidating the signals that direct progenitor cell trafficking to, within and out of the thymus. These advances are the subject of this Review, with a particular focus on the role of reciprocal cooperative and regulatory interactions between TCR- and chemokine receptor-mediated signalling.     

Phosphate position is key in mediating transmembrane ion channel TMEM16A–phosphatidylinositol 4,5-bisphosphate interaction

TransMEMbrane 16A (TMEM16A) is a Ca²⁺-activated Cl⁻ channel that plays critical roles in regulating diverse physiologic processes, including vascular tone, sensory signal transduction, and mucosal secretion. In addition to Ca²⁺, TMEM16A activation requires the membrane lipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂). However, the structural determinants mediating this interaction are not clear. Here, we interrogated the parts of the PI(4,5)P₂ head group that mediate its interaction with TMEM16A by using patch- and two-electrode voltage-clamp recordings on oocytes from the African clawed frog Xenopus laevis, which endogenously express TMEM16A channels. During continuous application of Ca²⁺ to excised inside–out patches, we found that TMEM16A-conducted currents decayed shortly after patch excision. Following this rundown, we show that the application of a synthetic PI(4,5)P₂ analog produced current recovery. Furthermore, inducible dephosphorylation of PI(4,5)P₂ reduces TMEM16A-conducted currents. Application of PIP₂ analogs with different phosphate orientations yielded distinct amounts of current recovery, and only lipids that include a phosphate at the 4′ position effectively recovered TMEM16A currents. Taken together, these findings improve our understanding of how PI(4,5)P₂ binds to and potentiates TMEM16A channels.