86 research outputs found
Sulfur Respiration in a Marine Chemolithoautotrophic Beggiatoa Strain
The chemolithoautotrophic strain Beggiatoa sp. 35Flor shows an unusual migration behavior when cultivated in a gradient medium under high sulfide fluxes. As common for Beggiatoa spp., the filaments form a mat at the oxygenâsulfide interface. However, upon prolonged incubation, a subpopulation migrates actively downward into the anoxic and sulfidic section of the medium, where the filaments become gradually depleted in their sulfur and polyhydroxyalkanoates (PHA) inclusions. This depletion is correlated with the production of hydrogen sulfide. The sulfur- and PHA-depleted filaments return to the oxygenâsulfide interface, where they switch back to depositing sulfur and PHA by aerobic sulfide oxidation. Based on these observations we conclude that internally stored elemental sulfur is respired at the expense of stored PHA under anoxic conditions. Until now, nitrate has always been assumed to be the alternative electron acceptor in chemolithoautotrophic Beggiatoa spp. under anoxic conditions. As the medium and the filaments were free of oxidized nitrogen compounds we can exclude this metabolism. Furthermore, sulfur respiration with PHA under anoxic conditions has so far only been described for heterotrophic Beggiatoa spp., but our medium did not contain accessible organic carbon. Hence the PHA inclusions must originate from atmospheric CO2 fixed by the filaments while at the oxygenâsulfide interface. We propose that the directed migration of filaments into the anoxic section of an oxygenâsulfide gradient system is used as a last resort to preserve cell integrity, which would otherwise be compromised by excessive sulfur deposition occurring in the presence of oxygen and high sulfide fluxes. The regulating mechanism of this migration is still unknown
Effect of large magnetotactic bacteria with polyphosphate inclusions on the phosphate profile of the suboxic zone in the Black Sea
The Black Sea is the worldâs largest anoxic basin and a model system for studying processes across redox gradients. In
between the oxic surface and the deeper sulfidic waters there is an unusually broad layer of 10â40 m, where neither oxygen
nor sulfide are detectable. In this suboxic zone, dissolved phosphate profiles display a pronounced minimum at the upper and
a maximum at the lower boundary, with a peak of particulate phosphorus in between, which was suggested to be caused by
the sorption of phosphate on sinking particles of metal oxides. Here we show that bacterial polyphosphate inclusions within
large magnetotactic bacteria related to the genus Magnetococcus contribute substantially to the observed phosphorus peak,
as they contain 26â34% phosphorus compared to only 1â5% in metal-rich particles. Furthermore, we found increased gene
expression for polyphosphate kinases by several groups of bacteria including Magnetococcaceae at the phosphate
maximum, indicating active bacterial polyphosphate degradation. We propose that large magnetotactic bacteria shuttle up
and down within the suboxic zone, scavenging phosphate at the upper and releasing it at the lower boundary. In contrast to a
passive transport via metal oxides, this bacterial transport can quantitatively explain the observed phosphate profiles.We are grateful for the competent technical
assistance of Ronny Baaske, Christian Burmeister, Christin Laudan
and Christian Meeske. We are greatly indebted to Cindy Lee and Bo
Barker Jørgensen for providing extremely helpful comments on an
earlier version of the manuscript. Horst D. Schulz and RenĂŠ Friedland
are acknowledged for stimulating discussions on the modeling
approach. We thank the captain and the crew of the R/V âMaria S.
Merianâ for the excellent support on board and the DFG (MSM33) and
BMBF (01DK12043) for financing the cruise. The particle analysis
was funded by the BMBF (03F0663A). S.B. was funded by a BONUS
BLUEPRINT project (03F0679A awarded to KJ; http://blueprint-
project.org), supported by BONUS (Art 185), funded jointly by the EU
and the German Federal Ministry of Education and Research (BMBF).
T. S. was funded by the German research foundation (DFG) (awarded
to K.J., JU 367/16-1). Metagenome sequencing was done at the
Swedish National Genomics Infrastructure (NGI) at SciLifeLab
(Sweden).We are grateful for the competent technical
assistance of Ronny Baaske, Christian Burmeister, Christin Laudan
and Christian Meeske. We are greatly indebted to Cindy Lee and Bo
Barker Jørgensen for providing extremely helpful comments on an
earlier version of the manuscript. Horst D. Schulz and RenĂŠ Friedland
are acknowledged for stimulating discussions on the modeling
approach. We thank the captain and the crew of the R/V âMaria S.
Merianâ for the excellent support on board and the DFG (MSM33) and
BMBF (01DK12043) for financing the cruise. The particle analysis
was funded by the BMBF (03F0663A). S.B. was funded by a BONUS
BLUEPRINT project (03F0679A awarded to KJ; http://blueprint-
project.org), supported by BONUS (Art 185), funded jointly by the EU
and the German Federal Ministry of Education and Research (BMBF).
T. S. was funded by the German research foundation (DFG) (awarded
to K.J., JU 367/16-1). Metagenome sequencing was done at the
Swedish National Genomics Infrastructure (NGI) at SciLifeLab
(Sweden)
Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions
Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick
mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it
enters the water column. The genus Thiomargarita harbors the largest known freeliving
bacteria with cell sizes of up to 750 mm in diameter. In addition to their ability
to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store
large amounts of nitrate, phosphate and elemental sulfur internally. To date little is
known about their energy yielding metabolic pathways, and how these pathways
compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a
chain-forming âCandidatus Thiomargarita nelsonii Thio36â, and conduct a comparative
analysis to five draft and one full genome of other members of the Beggiatoaceae. âCa.
T. nelsonii Thio36â is able to respire nitrate to both ammonium and dinitrogen, which
allows them to flexibly respond to environmental changes. Genes for sulfur oxidation
and inorganic carbon fixation confirmed that âCa. T. nelsonii Thio36â can function as
a chemolithoautotroph. Carbon can be fixed via the CalvinâBensonâBassham cycle,
which is common among the Beggiatoaceae. In addition we found key genes of
the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation
pathway. Surprisingly, âCa. T. nelsonii Thio36â also encodes key genes of the C2-
cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration
in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based
energy bifurcation pathway coupled to a NaC-translocating membrane complex (Rnf).
The coupling of these pathways may be key to surviving long periods of anoxia. As
other Beggiatoaceae âCa. T. nelsonii Thio36â encodes many genes similar to those
of (filamentous) cyanobacteria. In summary, the genome of âCa. T. nelsonii Thio36â
provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals
unique genomic features for the Thiomargarita lineage within the Beggiatoaceae
Emergent Phenomena Induced by Spin-Orbit Coupling at Surfaces and Interfaces
Spin-orbit coupling (SOC) describes the relativistic interaction between the
spin and momentum degrees of freedom of electrons, and is central to the rich
phenomena observed in condensed matter systems. In recent years, new phases of
matter have emerged from the interplay between SOC and low dimensionality, such
as chiral spin textures and spin-polarized surface and interface states. These
low-dimensional SOC-based realizations are typically robust and can be
exploited at room temperature. Here we discuss SOC as a means of producing such
fundamentally new physical phenomena in thin films and heterostructures. We put
into context the technological promise of these material classes for developing
spin-based device applications at room temperature
Video-supported Analysis of Beggiatoa Filament Growth, Breakage, and Movement
A marine Beggiatoa sp. was cultured in semi-solid agar with opposing oxygen-sulfide gradients. Growth pattern, breakage of filaments for multiplication, and movement directions of Beggiatoa filaments in the transparent agar were investigated by time-lapse video recording. The initial doubling time of cells was 15.7âÂąâ1.3 h (meanâÂąâSD) at room temperature. Filaments grew up to an average length of 1.7âÂąâ0.2 mm, but filaments of up to approximately 6 mm were also present. First breakages of filaments occurred approximately 19 h after inoculation, and time-lapse movies illustrated that a parent filament could break into several daughter filaments within a few hours. In >20% of the cases, filament breakage occurred at the tip of a former loop. As filament breakage is accomplished by the presence of sacrificial cells, loop formation and the presence of sacrificial cells must coincide. We hypothesize that sacrificial cells enhance the chance of loop formation by interrupting the communication between two parts of one filament. With communication interrupted, these two parts of one filament can randomly move toward each other forming the tip of a loop at the sacrificial cell
NASH limits anti-tumour surveillance in immunotherapy-treated HCC
Hepatocellular carcinoma (HCC) can have viral or non-viral causes(1-5). Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification of patients for optimal response to therapy is an unmet need(6,7). Here we report the progressive accumulation of exhausted, unconventionally activated CD8(+)PD1(+) T cells in NASH-affected livers. In preclinical models of NASH-induced HCC, therapeutic immunotherapy targeted at programmed death-1 (PD1) expanded activated CD8(+)PD1(+) T cells within tumours but did not lead to tumour regression, which indicates that tumour immune surveillance was impaired. When given prophylactically, anti-PD1 treatment led to an increase in the incidence of NASH-HCC and in the number and size of tumour nodules, which correlated with increased hepatic CD8(+)PD1(+)CXCR6(+), TOX+, and TNF+ T cells. The increase in HCC triggered by anti-PD1 treatment was prevented by depletion of CD8(+) T cells or TNF neutralization, suggesting that CD8(+) T cells help to induce NASH-HCC, rather than invigorating or executing immune surveillance. We found similar phenotypic and functional profiles in hepatic CD8(+)PD1(+) T cells from humans with NAFLD or NASH. A meta-analysis of three randomized phase III clinical trials that tested inhibitors of PDL1 (programmed death-ligand 1) or PD1 in more than 1,600 patients with advanced HCC revealed that immune therapy did not improve survival in patients with non-viral HCC. In two additional cohorts, patients with NASH-driven HCC who received anti-PD1 or anti-PDL1 treatment showed reduced overall survival compared to patients with other aetiologies. Collectively, these data show that non-viral HCC, and particularly NASH-HCC, might be less responsive to immunotherapy, probably owing to NASH-related aberrant T cell activation causing tissue damage that leads to impaired immune surveillance. Our data provide a rationale for stratification of patients with HCC according to underlying aetiology in studies of immunotherapy as a primary or adjuvant treatment
Structure Analysis of Entamoeba histolytica DNMT2 (EhMeth)
In eukaryotes, DNA methylation is an important epigenetic modification that is generally involved in gene regulation. Methyltransferases (MTases) of the DNMT2 family have been shown to have a dual substrate specificity acting on DNA as well as on three specific tRNAs (tRNAAsp, tRNAVal, tRNAGly). Entamoeba histolytica is a major human pathogen, and expresses a single DNA MTase (EhMeth) that belongs to the DNMT2 family and shows high homology to the human enzyme as well as to the bacterial DNA MTase M.HhaI. The molecular basis for the recognition of the substrate tRNAs and discrimination of non-cognate tRNAs is unknown. Here we present the crystal structure of the cytosine-5-methyltransferase EhMeth at a resolution of 2.15 Ă
, in complex with its reaction product S-adenosyl-L-homocysteine, revealing all parts of a DNMT2 MTase, including the active site loop. Mobility shift assays show that in vitro the full length tRNA is required for stable complex formation with EhMeth
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