Aerobic Bacterial Catabolism of Dimethylsulfoniopropionate

ABSTRACT. Dimethylsulfoniopropionate (DMSP) is an organosulfur zwitterion produced by various marine algae and Bacteria as an osmolyte, cryoprotectant, defence molecule and anti-oxidant. In the marine environment in particular, it can be degraded by the Bacteria in various ways. In this chapter we cover the biochemistry and physiology of the various pathways of DMSP catabolism, including the three core enzymes DMSP dethiomethylase (EC 4.4.1.3, the so-called “DMSP lyase”), DMSP demethylase (EC 2.1.1.269) and DMSP CoA transferase/lyase (EC 2.3.1.x). Six isoenzyme classes of DMSP dethiomethylase have been purified and confirmed in marine Bacteria thus far, with a further isoenzyme found in algae that may also occur in Bacteria – these are all discussed in detail. Methodologies for enzyme assays and the synthesis of DMSP hydrochloride are given, including those for radio- and stable-isotope labelling

Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the ‘Proteobacteria’, and four new families within the orders Nitrosomonadales and Rhodocyclales

The genus Thiobacillus comprises 4 species with validly published names, of which T. 17 aquaesulis DSM 4255T (= ATCC 43788T) is the only species that can grow heterotrophically 18 or mixotrophically – the rest being obligate autotrophs - and has a significant metabolic 19 difference in not producing tetrathionate during the oxidation of thiosulfate during 20 autotrophic growth. On the basis of this and differential chemotaxonomic properties and a 21 16S rRNA gene identity of 93.4% to the type species Thiobacillus thioparus DSM 505T, we 22 propose that it is moved to a novel genus Annwoodia gen. nov., for which the type species is 23 Annwoodia aquaesulis gen. nov., comb. nov. We confirm the position of the genus 24 Thiobacillus in the Betaproteobacteria falls within the Nitrosomonadales rather than the 25 Hydrogenophilales as previously proposed. Within the Nitrosomonadales we propose the 26 circumscription of genera to form the Thiobacilliaceae fam. nov. and the Sterolibacteriaceae 27 fam. nov. We propose the merging of the family Methylophilaceae into the 28 Nitrosomonadales, and that the Sulfuricellaceae be merged into the Gallionellaceae, leaving 29 the orders Methylophilales and Sulfuricellales defunct. In the Rhodocyclales we propose the 30 Azonexaceae fam. nov. and the Zoogloeaceae fam. nov. We also reject the 31 Hydrogenophilales from the Betaproteobacteria on the basis of a very low16S rRNA gene 32 identity with the class-proper as well as physiological properties, forming the 33 Hydrogenophilalia class. nov. in the ‘Proteobacteria’. We provide emended descriptions of 34 Thiobacillus, Hydrogenophilales, Hydrogenophilaceae, Nitrosomonadales, Gallionellaceae, 35 Rhodocyclaceae and the Betaproteobacteria

An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of 4 species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all 4 species of Thioalkalimicrobium to Thiomicrospira.

Thiomicrospira spp. are small sulfur-oxidising chemolithoautotrophic members of the Gammaproteobacteria. Whilst the type species Tms. pelophila and closely related Tms. thyasirae exhibit canonical spiral morphology under sub-optimal growth conditions, most species are vibrios or rods. The 16S rRNA gene diversity is vast, with identities as low as 91.6 % to Tms. pelophila versus Tms. frisia, for example. Thiomicrospira was examined with closely related genera Hydrogenovibrio and Thioalkalimicrobium and, to rationalise organisms on the basis of the 16S rRNA gene phylogeny, physiology and morphology, we reclassify Tms. kuenenii, Tms. crunogena, Tms. thermophila and Tms. halophila to Hydrogenovibrio kuenenii comb. nov., H. crunogenus corrig. comb. nov., H. thermophilus corrig. comb. nov., and H. halophilus corrig. comb. nov. We reclassify Tms. frisia, Tms. arctica, Tms. psychrophila and Tms. chilensis to Thiomicrorhabdus gen. nov., as Tmr. frisia comb. nov., Tmr. arctica comb. nov., Tmr. psychrophila comb. nov. and Tmr. chilensis comb. nov. – the type species of Thiomicrorhabdus is Tmr. frisia. We demonstrate Thioalkalimicrobium spp. fall in the genus Thiomicrospira sensu stricto, thus reclassifying them to Tms. aerophila corrig. comb. nov., Tms. microaerophila corrig. comb. nov., Tms. cyclica corrig. comb. nov.and Tms. sibirica corrig. comb. nov. We provide emended descriptions of the genera Thiomicrospira and Hydrogenovibrio and of Tms. thyasirae

Antibody Evasion by a Gammaherpesvirus O-Glycan Shield

All gammaherpesviruses encode a major glycoprotein homologous to the Epstein-Barr virus gp350. These glycoproteins are often involved in cell binding, and some provide neutralization targets. However, the capacity of gammaherpesviruses for long-term transmission from immune hosts implies that in vivo neutralization is incomplete. In this study, we used Bovine Herpesvirus 4 (BoHV-4) to determine how its gp350 homolog - gp180 - contributes to virus replication and neutralization. A lack of gp180 had no impact on the establishment and maintenance of BoHV-4 latency, but markedly sensitized virions to neutralization by immune sera. Antibody had greater access to gB, gH and gL on gp180-deficient virions, including neutralization epitopes. Gp180 appears to be highly O-glycosylated, and removing O-linked glycans from virions also sensitized them to neutralization. It therefore appeared that gp180 provides part of a glycan shield for otherwise vulnerable viral epitopes. Interestingly, this O-glycan shield could be exploited for neutralization by lectins and carbohydrate-specific antibody. The conservation of O-glycosylation sites in all gp350 homologs suggests that this is a general evasion mechanism that may also provide a therapeutic target

The Future of Precision Medicine : Potential Impacts for Health Technology Assessment

Objective Precision medicine allows health care interventions to be tailored to groups of patients based on their disease susceptibility, diagnostic or prognostic information or treatment response. We analyse what developments are expected in precision medicine over the next decade and consider the implications for health technology assessment (HTA) agencies. Methods We perform a pragmatic review of the literature on the health economic challenges of precision medicine, and conduct interviews with representatives from HTA agencies, research councils and researchers from a variety of fields, including digital health, health informatics, health economics and primary care research. Results Three types of precision medicine are highlighted as likely to emerge in clinical practice and impact upon HTA agencies: complex algorithms, digital health applications and ‘omics’-based tests. Defining the scope of an evaluation, identifying and synthesizing the evidence and developing decision analytic models will more difficult when assessing more complex and uncertain treatment pathways. Stratification of patients will result in smaller subgroups, higher standard errors and greater decision uncertainty. Equity concerns may present in instances where biomarkers correlate with characteristics such as ethnicity, whilst fast-paced innovation may reduce the shelf-life of guidance and necessitate more frequent reviewing. Discussion Innovation in precision medicine promises substantial benefits to patients, but will also change the way in which some health services are delivered and evaluated. As biomarker discovery accelerates and AI-based technologies emerge, the technical expertise and processes of HTA agencies will need to adapt if the objective of value for money is to be maintained

Chemolithoheterotrophy: Means to Higher Growth Yields from this Widespread Metabolic Trait

Chemolithoheterotrophy is a mixed metabolic mode in which heterotrophic growth is augmented by energy conserved from the oxidation of an inorganic electron donor such as thiosulfate or sulfide (or from sulfide moieties in methylated sulfur species). This results in an increased specific molar growth yield and a more efficient uptake of carbon from the carbon source, which can lead to more efficient biomass or product formation or more efficient degradation of pollutants etc. In this chapter we discuss the potential for harnessing this metabolic trait in biotechnology with critical evaluation of studies thus far

The microbiomes of wildlife and chemical pollution: Status, knowledge gaps and challenges

The effect of chemical pollution on the microbiomes of wildlife has been given little attention. A new concept is emerging where microbiomes are vital to host animal or plant health, and for ecosystems. Data are mainly on mammals, birds, and fish. Changing environmental conditions (e.g., salinity, pH, season) and exposure to chemicals alter the composition of gill, gut and skin microbiomes. Gut microbiomes are also modulated by diet, and exposure to chemicals including metals, nanomaterials, fungicides or microplastics. However, a change in the microbiome does not necessarily infer adverse effects on the host, with some evidence of co-adaptation. Environmental risk assessment for biocides and new nanomaterials should be revisited in context with microbiome-host interactions to better protect wildlife and ecosystems