What traits are carried on mobile genetic elements, and why?

Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes

Quantifying thermal adaptation of soil microbial respiration

Quantifying the rate of thermal adaptation of soil microbial respiration is essential in determining potential for carbon cycle feedbacks under a warming climate. Uncertainty surrounding this topic stems in part from persistent methodological issues and difficulties isolating the interacting effects of changes in microbial community responses from changes in soil carbon availability. Here, we constructed a series of temperature response curves of microbial respiration (given unlimited substrate) using soils sampled from around New Zealand, including from a natural geothermal gradient, as a proxy for global warming. We estimated the temperature optima (Topt) and inflection point (Tinf) of each curve and found that adaptation of microbial respiration occurred at a rate of 0.29 °C ± 0.04 1SE for Topt and 0.27 °C ± 0.05 1SE for Tinf per degree of warming. Our results bolster previous findings indicating thermal adaptation is demonstrably offset from warming, and may help quantifying the potential for both limitation and acceleration of soil C losses depending on specific soil temperatures

Crystal structure of the DNA-bound VapBC2 antitoxin/toxin pair from Rickettsia felis

Besides their commonly attributed role in the maintenance of low-copy number plasmids, toxin/antitoxin (TA) loci, also called ‘addiction modules’, have been found in chromosomes and associated to a number of biological functions such as: reduction of protein synthesis, gene regulation and retardation of cell growth under nutritional stress. The recent discovery of TA loci in obligatory intracellular species of the Rickettsia genus has prompted new research to establish whether they work as stress response elements or as addiction systems that might be toxic for the host cell. VapBC2 is a TA locus from R. felis, a pathogen responsible for flea-borne spotted fever in humans. The VapC2 toxin is a PIN-domain protein, whereas the antitoxin, VapB2, belongs to the family of swapped-hairpin β-barrel DNA-binding proteins. We have used a combination of biophysical and structural methods to characterize this new toxin/antitoxin pair. Our results show how VapB2 can block the VapC2 toxin. They provide a first structural description of the interaction between a swapped-hairpin β-barrel protein and DNA. Finally, these results suggest how the VapC2/VapB2 molar ratio can control the self-regulation of the TA locus transcription

Morphogenesis of the T4 tail and tail fibers

Remarkable progress has been made during the past ten years in elucidating the structure of the bacteriophage T4 tail by a combination of three-dimensional image reconstruction from electron micrographs and X-ray crystallography of the components. Partial and complete structures of nine out of twenty tail structural proteins have been determined by X-ray crystallography and have been fitted into the 3D-reconstituted structure of the "extended" tail. The 3D structure of the "contracted" tail was also determined and interpreted in terms of component proteins. Given the pseudo-atomic tail structures both before and after contraction, it is now possible to understand the gross conformational change of the baseplate in terms of the change in the relative positions of the subunit proteins. These studies have explained how the conformational change of the baseplate and contraction of the tail are related to the tail's host cell recognition and membrane penetration function. On the other hand, the baseplate assembly process has been recently reexamined in detail in a precise system involving recombinant proteins (unlike the earlier studies with phage mutants). These experiments showed that the sequential association of the subunits of the baseplate wedge is based on the induced-fit upon association of each subunit. It was also found that, upon association of gp53 (gene product 53), the penultimate subunit of the wedge, six of the wedge intermediates spontaneously associate to form a baseplate-like structure in the absence of the central hub. Structure determination of the rest of the subunits and intermediate complexes and the assembly of the hub still require further study

Rickettsia Phylogenomics: Unwinding the Intricacies of Obligate Intracellular Life

BACKGROUND: Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). METHODOLOGY/PRINCIPAL FINDINGS: We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (approximately 1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. CONCLUSION/SIGNIFICANCE: Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets

Assessing thermal acclimation of soil microbial respiration using macromolecular rate theory

Soil heterotrophic respiration is strongly controlled by temperature. Thus, understanding how soil microbial respiration will acclimate to global warming is important for accurate predictions of soil carbon loss. Thermal acclimation of soil respiration has typically been measured using the Q₁₀ temperature coefficient or comparing absolute rates of respiration with varying conclusions. Discrepancies in these findings may be a result of these approaches not accounting for the temperature optima associated with microbial respiration. To address this issue, we periodically measured the temperature response of respiration for soils incubated at 4, 10, 20, and 35 ºC for up to 310 days. We measured respiration rates from these soils placed in a temperature block for 5 h at ∼ 1 ºC increments with temperatures ranging from ∼ 4 to 50 ºC. To assess thermal acclimation, we used macromolecular rate theory to calculate the temperature optimum (Topt), the inflection point of the curve (Tinf), and the change in heat capacity of the transition state (ΔC‡p), as a measure of the temperature response. We compared changes in Topt, Tinf , and ΔC‡p over time between each of the long-term incubation temperatures. We found that Topt and Tinf increased and ΔC‡p decreased at higher long-term incubation temperatures after approximately six months. However, these results appear largely driven by changes in carbon availability, suggesting that the temperature response of soil microbial respiration changes only as soil carbon depletes. This novel approach offers a new perspective on how soil microbial communities may acclimate to climate change and may be relevant for modelling of soil carbon losses

Estimating the temperature optima of soil priming

Understanding the temperature response of soil microbial respiration is essential for predicting carbon (C) losses as the planet warms. As fresh, labile C inputs can further accelerate soil C loss (priming effect), determining if priming is temperature sensitive has important implications for global C cycling and remains relatively unexplored. We conducted a series of 5-h incubations for five different soil orders at 40 discrete temperatures with added ¹³C-labelled glucose and measured soil microbial respiration. We then estimated the temperature response of microbial respiration attributable to (1) the added glucose, (2) the soil organic matter (SOM), and (3) soil priming. The relative proportion of the priming response varied with temperature and the magnitude of these changes differed by soil type. We found that the temperature response of microbial respiration attributable to priming and to the added glucose were unimodal and could be modelled using Macromolecular Rate Theory (MMRT). This suggests that biological mechanisms play a strong role in shaping the temperature response of priming. In contrast, respiration derived from SOM typically increased continuously with increasing temperature. Using MMRT we estimated a temperature optimum (Topt) and inflection point (Tinf) from each of the temperature response curves for microbial respiration derived from the added glucose and from soil priming. The temperature response of respiration from soil priming (Topt = 30.6 ºC and Tinf = 12.8 ºC) was significantly lower than from the added glucose (Topt = 42.4 ºC and Tinf = 14.5 ºC), which indicates that priming is more temperature sensitive. This study demonstrates that soil priming itself is temperature sensitive and responds differently to warming than the bulk soil, which may alter soil C stocks in ways not previously predicted. Further exploration of the temperature sensitivity of priming therefore warrants inclusion in future discussions of soil microbial responses to climate change

Contrasting temperature responses of soil respiration derived from soil organic matter and added plant litter

Accurate description of temperature response and sensitivity of different carbon pools within soil is critical for accurately modelling soil carbon stocks and changes. Inconsistent sampling, incubation and fractionation methods highlights the need for new approaches to this area of study. We developed and tested a new protocol which allowed measurement of the temperature response of two carbon pools within soil. A Horotiu silt loam soil, wet up to 60% maximum water holding capacity, was mixed with 13C-enriched plant litter and incubated for 5 or 20 h, at 30 discrete temperatures (~ 2-50 Celsius degree). A mixing model was used to separate respired CO2 into litter and soil organic matter sourced carbon pools, which were then fitted using macromolecular rate theory. Overall, litter sourced respiration had a low Topt (the temperature where respiration rate is maximal) and was less temperature sensitive (Q10) than soil organic matter sourced respiration, which was more Arrhenius-like. We attribute these differences in temperature parameters to the factors that control the availability of carbon to microbes from the labile litter (enzyme kinetics with a clear temperature optimum) compared to the relatively stable soil organic matter (desorption and diffusion that exhibit Arrhenius behaviour). The developed method is rapid and reliable and may be suited to exploring temperature response of a variety of 13C-labelled pools in soil and more clearly demonstrates that labile carbon has very different temperature response than more stable carbon pools in soil

Quantifying thermal adaptation of soil microbial respiration

Quantifying the rate of thermal adaptation of soil microbial respiration is essential in determining potential for carbon cycle feedbacks under a warming climate. Uncertainty surrounding this topic stems in part from persistent methodological issues and difficulties isolating the interacting effects of changes in microbial community responses from changes in soil carbon availability. Here, we constructed a series of temperature response curves of microbial respiration (given unlimited substrate) using soils sampled from around New Zealand, including from a natural geothermal gradient, as a proxy for global warming. We estimated the temperature optima (Topt) and inflection point (Tinf) of each curve and found that adaptation of microbial respiration occurred at a rate of 0.29 °C ± 0.04 1SE for Topt and 0.27 °C ± 0.05 1SE for Tinf per degree of warming. Our results bolster previous findings indicating thermal adaptation is demonstrably offset from warming, and may help quantifying the potential for both limitation and acceleration of soil C losses depending on specific soil temperatures