Glucosyl diglyceride lipid structures in Deinococcus radiodurans

Cell envelope diversity and evolution across the bacterial tree of life

The bacterial cell envelope is a complex multilayered structure conserved across all bacterial phyla. It is categorized into two main types based on the number of membranes surrounding the cell. Monoderm bacteria are enclosed by a single membrane, whereas diderm cells are distinguished by the presence of a second, outer membrane (OM). An ancient divide in the bacterial domain has resulted in two major clades: the Gracilicutes, consisting strictly of diderm phyla; and the Terrabacteria, encompassing monoderm and diderm species with diverse cell envelope architectures. Recent structural and phylogenetic advancements have improved our understanding of the diversity and evolution of the OM across the bacterial tree of life. Here we discuss cell envelope variability within major bacterial phyla and focus on conserved features found in diderm lineages. Characterizing the mechanisms of OM biogenesis and the evolutionary gains and losses of the OM provides insights into the primordial cell and the last universal common ancestor from which all living organisms subsequently evolved.

Spatial arrangement and density variations in the cell envelope of Deinococcus radiodurans

The cell envelope of the poly-extremophile bacterium Deinococcus radiodurans is renowned for its highly organized structure and unique functional characteristics. In this bacterium, a precise regularity characterizes not just the S-layer, but it also extends to the underlying cell envelope layers, resulting in a dense and tightly arranged configuration. This regularity is attributed to a minimum of three protein complexes located at the outer membrane level. Together, they constitute a recurring structural unit that extends across the cell envelope, effectively tiling the entirety of the cell body. Nevertheless, a comprehensive grasp of the vacant spaces within each layer and their functional roles remains limited. In this study, we delve into these aspects by integrating the state of the art with structural calculations. This approach provides crucial evidence supporting an evolutive pressure intricately linked to surface phenomena depending on the environmental conditions.

The cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions

The radiation-resistant bacterium Deinococcus radiodurans is known as the world’s toughest bacterium. The S-layer of D. radiodurans, consisting of several proteins on the surface of the cellular envelope and intimately associated with the outer membrane, has therefore been useful as a model for structural and functional studies. Its main proteinaceous unit, the S-layer deinoxanthin-binding complex (SDBC), is a hetero-oligomeric assembly known to contribute to the resistance against environmental stress and have porin functional features; however, its precise structure is unknown. Here, we resolved the structure of the SDBC at ∼2.5 Å resolution by cryo-EM and assigned the sequence of its main subunit, the protein DR_2577. This structure is characterized by a pore region, a massive β-barrel organization, a stalk region consisting of a trimeric coiled coil, and a collar region at the base of the stalk. We show that each monomer binds three Cu ions and one Fe ion and retains one deinoxanthin molecule and two phosphoglycolipids, all exclusive to D. radiodurans. Finally, electrophysiological characterization of the SDBC shows that it exhibits transport properties with several amino acids. Taken together, these results highlight the SDBC as a robust structure displaying both protection and sieving functions that facilitates exchanges with the environment.

Fatty Acids of Chthonomonas calidirosea, of a novel class Chthonomonadetes from a recently described phylum Armatimonadetes

A Gram-negative, aerobic, pink-pigmented, rod-shaped bacterium Chthonomonas calidirosea (strain T49(T)) with an optimal temperature for growth of 68 °C, isolated from soil samples from Hell's Gate in the Tikitere geothermal system (New Zealand), was the first cultivated bacterium of the novel phylum Armatimonadetes (formerly candidate division OP10). The lipid composition of C. calidirosea presents a number of unusual features both in the fatty acids and polar lipids. This contribution reports on the fatty acid profile of C. calidirosea. Transmethylation of bacterial biomass yielded fatty acid methyl esters and hydrocarbons, including squalene, partially hydrogenated squalenes, and diploptene. The only type of unsaturation found in C. calidirosea fatty acids was cis-Δ5, as revealed by GCMS of dimethyl disulfide (DMDS) adducts, and the lack of trans-unsaturation absorbance at 960-980 cm(-1) in the IR spectrum of fatty acids methyl esters. An unidentified component X with ECL 16.86 (BP1) and ECL 17.27 (BP20) was also observed, with molecular ion at m/z 282 ("17:1"). X did not form DMDS adducts, nor was affected by mild hydrogenation conditions, indicating the likely presence of a ring rather than unsaturation. The presence of a cyclopropane ring with cis-stereochemistry was confirmed by the (1)H-NMR spectrum. Hydrogenation of X in acetic acid resulted in formation of straight chain 17:0, 5-methyl- and 6-methyl-16:0 fatty acid methyl esters, thus confirming the structure of a novel 5,6-methylene hexadecanoic acid. The major fatty acids of a solid media-grown C. calidirosea were as follows (in weight % of total fatty acids): 16:0 (25.8), i17:0 (19.3), ai17:0 (13.5), 16:1∆5 (8.8), i17:1∆5 (6.8), 5,6-methylene 16:0 (5.2), i16:0 (4.4), 18:0 (3.6), 18:1∆5 (3.2).

Protein secretion and outer membrane assembly in Alphaproteobacteria

The assembly of beta-barrel proteins into membranes is a fundamental process that is essential in Gram-negative bacteria, mitochondria and plastids. Our understanding of the mechanism of beta-barrel assembly is progressing from studies carried out in Escherichia coli and Neisseria meningitidis. Comparative sequence analysis suggests that while many components mediating beta-barrel protein assembly are conserved in all groups of bacteria with outer membranes, some components are notably absent. The Alphaproteobacteria in particular seem prone to gene loss and show the presence or absence of specific components mediating the assembly of beta-barrels: some components of the pathway appear to be missing from whole groups of bacteria (e.g. Skp, YfgL and NlpB), other proteins are conserved but are missing characteristic domains (e.g. SurA). This comparative analysis is also revealing important structural signatures that are vague unless multiple members from a protein family are considered as a group (e.g. tetratricopeptide repeat (TPR) motifs in YfiO, beta-propeller signatures in YfgL). Given that the process of the beta-barrel assembly is conserved, analysis of outer membrane biogenesis in Alphaproteobacteria, the bacterial group that gave rise to mitochondria, also promises insight into the assembly of beta-barrel proteins in eukaryotes.

Structure and function of glycoglycerolipids in plants and bacteria

Phosphoglycerolipids are abundant membrane constituents in prokaryotic and eukaryotic cells. However, glycoglycerolipids are the predominant lipids in chloroplasts of plants and eukaryotic algae and in cyanobacteria. Membrane composition in chloroplasts and cyanobacteria is highly conserved, with monogalactosyldiacylglycerol (MGD) and digalactosyldiacylglycerol (DGD) representing the most abundant lipids. The genes encoding enzymes of galactolipid biosynthesis have been isolated from Arabidopsis. Galactolipids are crucial for growth under normal and phosphate limiting conditions. Furthermore, they are indispensable for maximal efficiency of photosynthesis. A wide variety of glycoglycerolipids is found in different bacteria. These lipids contain glucose or galactose, in some cases also mannose or other sugars with different glycosidic linkages in their head group. Some bacterial species produce unusual glycoglycerolipids, such as glycophospholipids or glycoglycerolipids carrying sugar head groups esterified with acyl residues. A number of genes coding for bacterial glycoglycerolipid synthases have been cloned and the enzymes characterized. In contrast to the breadth of information available on their structural diversity, much less is known about functional aspects of bacterial glycoglycerolipids. In some bacteria, glycoglycerolipids are required for membrane bilayer stability, they serve as precursors for the formation of complex membrane components, or they are crucial to support anoxygenic photosynthesis or growth during phosphate deficiency.

Glycoengineering of cyanobacterial thylakoid membranes for future studies on the role of glycolipids in photosynthesis

The lipid composition of thylakoid membranes is conserved from cyanobacteria to angiosperms. The predominating components are monogalactosyl- and digalactosyldiacylglycerol. In cyanobacteria, thylakoid membrane biosynthesis starts with the formation of monoglucosyldiacylglycerol which is C4-epimerized to the corresponding galactolipid, whereas in plastids monogalactosyldiacylglycerol is formed at the beginning. This suggests that galactolipids have specific functions in thylakoids. We wanted to investigate whether galactolipids can be replaced by glycosyldiacylglycerols with headgroups differing in their epimeric and anomeric details as well as the attachment point of the terminal hexose in diglycosyldiacylglycerols. For this purpose putative glycosyltransferase sequences were identified in databases to be used for functional expression in various host organisms. From 18 newly identified sequences, four turned out to encode glycosyltransferases catalyzing final steps in glycolipid biosynthesis: two alpha-glucosyltransferases, one beta-galactosyltransferase and one beta-glucosyltransferase. Their functional annotation was based on detailed structural characterization of the new glycolipids formed in the transformant hosts as well as on in vitro enzymatic assays. The expression of alpha-glucosyltransferases in the cyanobacterium Synechococcus resulted in the accumulation of the new alpha-galactosyldiacylglycerol which is ascribed to epimerization of the corresponding glucolipid. The expression of the beta-glucosyltransferase led to a high proportion of new beta-glucosyl-(1-->6)-beta-galactosyldiacylglycerol almost entirely replacing the native digalactosyldiacylglycerol. These results demonstrate that modifications of the glycolipid pattern in thylakoids are possible.

Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample

The ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the Sonoran Desert and a nonarid soil from a Louisiana forest to various doses of ionizing radiation using a (60)Co source. The numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. Bacterial isolates surviving doses of 30 kGy were recovered from the Sonoran Desert soil, while no isolates were recovered from the nonarid forest soil after exposure to doses greater than 13 kGy. The phylogenetic diversities of the surviving culturable bacteria were compared for the two soils using 16S rRNA gene sequence analysis. In addition to a bacterial population that was more resistant to higher doses of ionizing radiation, the diversity of the isolates was greater in the arid soil. The taxonomic diversity of the isolates recovered was found to decrease as the level of ionizing-radiation exposure increased. Bacterial isolates of the genera Deinococcus, Geodermatophilus, and Hymenobacter were still recovered from the arid soil after exposure to doses of 17 to 30 kGy. The recovery of large numbers of extremely ionizing-radiation-resistant bacteria from an arid soil and not from a nonarid soil provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of other DNA repair systems that protect cells against commonly encountered environmental stressors, such as desiccation. The diverse group of bacterial strains isolated from the arid soil sample included 60 Deinococcus strains, the characterization of which revealed nine novel species of this genus.

Binding of glycoglycerolipid derived from membranes of Acholeplasma laidlawii PG8 and synthetic analogues to lymphoid cells

A component that binds to human lymphoid cells was isolated from the membranes of Acholeplasma laidlawii PG8. The component was extracted using the Bligh-Dyer method and purified using a silica-gel column and TLC. The active component was identified as 3-O:-[2'-O-(alpha-D-glucopyranosyl)- 6'-O-acyl-alpha-D-glucopyranosyl]-1,2-di-O- acyl-sn-glycerol (GAGDG) using (1)H- and (13)C-NMR and GC-MS. The compositions of the major saturated fatty acids were nC (14) (17.8%), isoC(14) (10.7%) and nC (16) (34.9%) as determined by GC-MS. The amounts of unsaturated species were less than 10% of those of the corresponding saturated acids. GAGDGs which have three tetradecanoyl groups were synthesized. These synthetic GAGDGs, as well as GAGDGs derived from A. laidlawii membranes, had a high binding affinity for MOLT-4 and HUT-78 (human T cell lines), Raji (a B cell line), HL-60 (a monoblastoid cell line) and primary cultured human T cells. The binding affinities of GAGDGs with an isoC(14) acyl group was higher than those with nC(14) and nC(16) acyl groups. The binding to lymphoid cells reveals a novel biological activity of GAGDGs.