The PhoBR two-component system regulates antibiotic biosynthesis in Serratia in response to phosphate

<p>Abstract</p> <p>Background</p> <p>Secondary metabolism in <it>Serratia </it>sp. ATCC 39006 (<it>Serratia </it>39006) is controlled via a complex network of regulators, including a LuxIR-type (SmaIR) quorum sensing (QS) system. Here we investigate the molecular mechanism by which phosphate limitation controls biosynthesis of two antibiotic secondary metabolites, prodigiosin and carbapenem, in <it>Serratia </it>39006.</p> <p>Results</p> <p>We demonstrate that a mutation in the high affinity phosphate transporter <it>pstSCAB-phoU</it>, believed to mimic low phosphate conditions, causes upregulation of secondary metabolism and QS in <it>Serratia </it>39006, via the PhoBR two-component system. Phosphate limitation also activated secondary metabolism and QS in <it>Serratia </it>39006. In addition, a <it>pstS </it>mutation resulted in upregulation of <it>rap</it>. Rap, a putative SlyA/MarR-family transcriptional regulator, shares similarity with the global regulator RovA (regulator of virulence) from <it>Yersina </it>spp. and is an activator of secondary metabolism in <it>Serratia </it>39006. We demonstrate that expression of <it>rap</it>, <it>pigA-O </it>(encoding the prodigiosin biosynthetic operon) and <it>smaI </it>are controlled via PhoBR in <it>Serratia </it>39006.</p> <p>Conclusion</p> <p>Phosphate limitation regulates secondary metabolism in <it>Serratia </it>39006 via multiple inter-linked pathways, incorporating transcriptional control mediated by three important global regulators, PhoB, SmaR and Rap.</p

RsmA, RsmC and FlhDC regulate sdhEygfX in Serratia

SdhE is required for the flavinylation and activation of succinate dehydrogenase and fumarate reductase (FRD). In addition, SdhE is conserved in proteobacteria (α, β and γ) and eukaryotes. Although the function of this recently characterized family of proteins has been determined, almost nothing is known about how their genes are regulated. Here, the RsmA (CsrA) and RsmC (HexY) post-transcriptional and post-translational regulators have been identified and shown to repress sdhEygfX expression in Serratia sp. ATCC 39006. Conversely, the flagella master regulator complex, FlhDC, activated sdhEygfX transcription. To investigate the hierarchy of control, we developed a novel approach that utilized endogenous CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated) genome-editing by a type I-F system to generate a chromosomal point mutation in flhC. Mutation of flhC alleviated the ability of RsmC to repress sdhEygfX expression, whereas RsmA acted in both an FlhDC-dependent and -independent manner to inhibit sdhEygfX. Mutation of rsmA or rsmC, or overexpression of FlhDC, led to increased prodigiosin, biosurfactant, swimming and swarming. Consistent with the modulation of sdhE by motility regulators, we have demonstrated that SdhE and FRD are required for maximal flagella-dependent swimming. Together, these results demonstrate that regulators of both metabolism and motility (RsmA, RsmC and FlhDC) control the transcription of the sdhEygfX operon.This work was supported by the Marsden Fund, Royal Society of New Zealand (RSNZ) to PCF and a Strategic Grant from the Otago School of Medical Sciences (OSMS) to MB. HGH was supported by a University of Otago Doctoral Scholarship, MBM by a Division of Health Sciences Career Development Post-doctoral Fellowship, BN by a Dean's Prestigious Summer Scholarship from the OSMS and PCF was supported by a Rutherford Discovery Fellowship (RSNZ). NRW and GPCS were supported by Biotechnology and Biological Sciences Research Council (BBSRC), UK awards to the GPCS laboratory. We thank members of the Fineran and Cook laboratories for helpful discussions, Tim Blower for plasmid pTRB32 and for critically reading the manuscript.This is the final version of the article. It first appeared from the Microbiology Society via http://dx.doi.org/10.1099/mic.0.00028

The Emergence and Evolution of the Multidimensional Organization

The article discusses multidimensional organizations and the evolution of complex organizations. The six characteristics of multidimensional organizations, disadvantages of the successful organizational structure that is categorized as a multidivisional, multi-unit or M-form, research by the Foundation for Management Studies which suggests that synergies across business divisions can be exploited by the M-form, a team approach to creating economic value, examples of multidimensional firms such as PricewaterhouseCoopers, and a comparison of various organization types including the matrix form are mentioned

The rsmS (ybaM) mutation causes bypass suppression of the RsmAB post-transcriptional virulence regulation system in enterobacterial phytopathogens.

Plant cell wall degrading enzymes (PCWDEs) are the primary virulence determinants of soft rotting bacteria such as the potato pathogen, Pectobacterium atrosepticum. The regulation of secondary metabolite (Rsm) system controls production of PCWDEs in response to changing nutrient conditions. This work identified a new suppressor of an rsmB mutation - ECA1172 or rsmS (rsmB suppressor). Mutants defective in rsmB (encoding a small regulatory RNA), show reduced elaboration of the quorum sensing molecule (N-3-oxohexanoyl-homoserine lactone; OHHL) and PCWDEs. However, OHHL and PCWDE production were partially restored in an rsmB, rsmS double mutant. Single rsmS mutants, overproduced PCWDEs and OHHL relative to wild type P. atrosepticum and exhibited hypervirulence in potato. RsmS overproduction also resulted in increased PCWDEs and OHHL. Homology searches revealed rsmS conservation across pathogens such as Escherichia coli (ybaM), Dickeya solani, Klebsiella pneumoniae and Shigella flexneri. An rsmS mutant of Pectobacterium carotovorum ATCC39048 showed bypass of rsmB-dependent repression of PCWDEs and OHHL production. P. carotovorum ATCC39048 produces the β-lactam antibiotic, 1-carbapen-2-em-3-carboxylic acid (a carbapenem). Production of the antibiotic was repressed in an rsmB mutant but partially restored in an rsmB, rsmS double mutant. This work highlights the importance of RsmS, as a conserved pleiotropic regulator of virulence and antibiotic biosynthesis.James Hutton Institut

Advances and challenges of life cycle assessment (LCA) of greenhouse gas removal technologies to fight climate changes

Several greenhouse gas removal technologies (GGRTs), also called negative emissions technologies (NET) have been proposed to help meet the Paris Climate Agreement targets. However, there are many uncertainties in the estimation of their effective greenhouse gas (GHG) removal potentials, caused by their different levels of technological development. Life Cycle Assessment (LCA) has been proposed as one effective methodology to holistically assess the potential of different GGRT removal approaches but no common framework is currently available for benchmarking and policy development. In this article, challenges for LCA are reviewed and discussed together with some alternative approaches for assessment of GGRTs. In particular, GGRTs pose challenges with regards to the functional unit, the system boundary of the LCA assessment, and the timing of emissions. The need to account within LCA of GGRTs for broader implications which involve environmental impacts, economic, social and political drivers is highlighted. A set of recommendations for LCA of GGRTs are proposed for a better assessment of the GGRTs and better accounting of their carbon removal potentials to meet the targets established within the Paris Agreement

What is epistemic blame?

PostprintPeer reviewe

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration of the mechanisms of survival, drug-resistance and virulence of pathogens. Next-generation sequencing (NGS) technologies are contributing to a massive expansion of transcriptomics in all fields and are reducing the cost, time and performance barriers presented by conventional approaches. However, bioinformatic tools for the analysis of the sequence data sets produced by these technologies can be daunting to researchers with limited or no expertise in bioinformatics. Here, we constructed a semi-automated, bioinformatic workflow system, and critically evaluated it for the analysis and annotation of large-scale sequence data sets generated by NGS. We demonstrated its utility for the exploration of differences in the transcriptomes among various stages and both sexes of an economically important parasitic worm (Oesophagostomum dentatum) as well as the prediction and prioritization of essential molecules (including GTPases, protein kinases and phosphatases) as novel drug target candidates. This workflow system provides a practical tool for the assembly, annotation and analysis of NGS data sets, also to researchers with a limited bioinformatic expertise. The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. This system is now utilized routinely for the analysis of data sets from pathogens of major socio-economic importance and can, in principle, be applied to transcriptomics data sets from any organism

Worldwide impacts of climate change on energy for heating and cooling

The energy sector is not only a major contributor to greenhouse gases, it is also vulnerable to climate change and will have to adapt to future climate conditions. The objective of this study is to analyze the impacts of changes in future temperatures on the heating and cooling services of buildings and the resulting energy and macro-economic effects at global and regional levels. For this purpose, the techno-economic TIAM-WORLD (TIMES Integrated Assessment Model) and the general equilibrium GEMINI-E3 (General Equilibrium Model of International-National Interactions between Economy, Energy and Environment) models are coupled with a climate model, PLASIM-ENTS (Planet-Simulator - Efficient Numerical Terrestrial Scheme). The key results are as follows. At the global level, the climate feedback induced by adaptation of the energy system to heating and cooling is found to be insignificant, partly because heating and cooling-induced changes compensate and partly because they represent a limited share of total final energy consumption. However, significant changes are observed at regional levels, more particularly in terms of addi- tional power capacity required to satisfy additional cooling services, resulting in increases in electricity prices. In terms of macro-economic impacts, welfare gains and losses are associated more with changes in energy exports and imports than with changes in energy consumption for heating and cooling. The rebound effect appears to be non-negligible. To conclude, the coupling of models of different nature was successful and showed that the energy and economic impacts of climate change on heating and cooling remain small at the global level, but changes in energy needs will be visible at more local scale