Biology subjects

Sinninghe Damste, J. S.

Publications and source records attributed to Sinninghe Damste, J. S..

5 recordsLinked to original sources

bioRxiv2026

Towards understanding the bacterial biosynthesis of branched GDGTs: Identification of iso-diabolic acid-based tetraester and mixed ether/ester, membrane-spanning lipid intermediates in members of the Bacillota

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane-spanning lipids (MSLs) resembling archaeal membrane lipids, as they form monolayers and are linked to glycerol backbones via ether bonds. Ubiquitous in soils, sediments, and aquatic environments, their distributions are widely applied as paleoclimate proxies for reconstructing past temperature and pH. Despite this, understanding of their biological origins and functional role in cells remain incomplete. While some Acidobacteria are known producers of brGDGTs, genomic evidence and environmental surveys indicate additional bacterial contributors. In this study, we report the first detection of potential brGDGT biosynthetic intermediates in Bacillota. Ultra-high pressure liquid chromatography high resolution multi-stage mass spectrometry (UHPLC-HRMSn) revealed membrane-spanning diglycerol lipids which contained iso-diabolic acid (13,16-dimethyl octacosanedioic acid)-derived alkyl chains. These diglycerol lipids displayed diverse structures, including tetraesters, mixed ester/ether combinations, and vinyl ether bonds. Additionally, open membrane spanning lipids analogous to brGTGTs were also identified. Notably, all brGDGT and brGTGT analogues were detected with a phosphatidylglycerol head group. Experiments showed that the two Bacillota strains, which produce these brGDGT biosynthetic intermediates, responded differently to changes in temperature and oxygen availability, suggesting that environmental regulation of brGDGT-related lipids is taxonomically dependent. Based on these findings, we propose a biosynthetic pathway for brGDGT formation and highlight the physiological implications for interpreting brGDGT-based paleoclimate proxies. This work expands the known diversity of bacterial sources of brGDGTs and provides new insights into the ecological and evolutionary significance of these lipids. IMPORTANCEBranched GDGTs (brGDGTs) are bacterial membrane spanning lipids which form a monolayer, linked through ether bonds to the glycerol backbone, characteristics more commonly found in archaeal membrane lipids. They are commonly used in paleoclimate proxies to assess past temperature and pH but their predictive power is hampered by the lack of information regarding their biological producers. Branched GDGTs have been detected in just a few species of the Acidobacteria but there are strong indications that other bacterial phyla also contribute to the pool of brGDGTs in the environment. Here, we report for the first time the production of potential brGDGT intermediates in Bacillota species. This study demonstrates that brGDGTs likely occur much more widespread in the bacterial domain than previously thought and opens a new chapter both in the understanding of the function of these membrane lipids and their use in paleoclimatology.

microbiology↗

bioRxiv2023

Selective lipid recruitment by an archaeal DPANN symbiont from its host

The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus - Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e. nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.

microbiology↗

bioRxiv2022

Disentangling the lipid divide: Identification of key enzymes for the biosynthesis of unusual Membrane-spanning and Ether lipids in Bacteria

Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea possess membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer of membrane-spanning lipids (MSLs). Exceptions to this lipid divide are the production by some bacterial species of (ether-bound) MSLs, formed by tail-tail condensation of fatty acids resulting in the formation of (iso) diabolic acids (DAs), which are the likely precursors of paleoclimatological relevant branched glycerol dialkyl glycerol tetraether molecules. However, the enzymes responsible for their production are unknown. Here, we report the discovery of bacterial enzymes responsible for the condensation reaction of fatty acids and for ether bond formation, and confirm that the building blocks of iso-DA are branched iso-FAs. Phylogenomic analyses of the key biosynthetic genes reveal a much wider diversity of potential MSL (ether)-producing bacteria than previously thought, with significant implications for our understanding of the evolution of lipid membranes.

microbiology↗

bioRxiv2020

Reconstructing the diet, trophic level, and migration pattern of Mysticete whales based on baleen isotopic composition.

Baleen from mysticete whales is a well-preserved proteinaceous material that can be used to identify migrations and feeding habits for species whose migration pathways are unknown. Analysis of {delta}13C and {delta}15N from bulk baleen has been used to infer migration patterns for individuals. However, this approach has fallen short of identifying migrations between regions as it is difficult to determine variations in isotopic shifts without temporal sampling of prey items. Here we apply analysis of {delta}15N values of amino acids to five baleen plates belonging to three species, revealing novel insights on trophic position, metabolic state, and migration between regions. Humpback and minke whales had higher reconstructed trophic levels than fin whales (3.4-3.5 versus 2.7-2.9, respectively) as expected due to different feeding specialization. Isotopic niche areas between baleen minima and maxima were well separated, indicating regional resource use for individuals during migration that aligned with isotopic gradients in Atlantic Ocean particulate organic matter. {delta}15N values from phenylalanine confirmed regional separation between the niche areas for two fin whales as migrations occurred and elevated glycine and threonine {delta}15N values revealed physiological changes due to fasting. Simultaneous resolution of trophic level and physiological changes allow for identification of regional migrations in mysticetes.

ecology↗

bioRxiv2018

Bridging the divide: bacteria synthesizing archaeal membrane lipids

Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol, while Bacteria/Eukarya produce membranes consisting of ester-bound fatty acids. This dichotomy in membrane lipid composition or lipid divide is believed to have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis is that LUCA possessed a mixed heterochiral archaeal/bacterial membrane, however no natural microbial representatives supporting this scenario have been shown to exist today. Here, we demonstrate that bacteria of the Fibrobacteres-Chlorobi-Bacteroidetes (FCB) group superphylum and related candidate phyla encode a complete pathway for archaeal membrane lipid biosynthesis in addition to the bacterial fatty acid membrane pathway. Key genes were expressed in the environment and their recombinant expression in E. coli resulted in the formation of a mixed archaeal/bacterial membrane. Our results support the existence of mixed membranes in natural environments and their stability over large evolutionary timescales, thereby bridging a once-thought fundamental divide in biology.

evolutionary biology↗