Macromolecular crowding and the mandatory condensation of DNA in bacteria

Cellular DNA in bacteria is localized into nucleoids enclosed by cytoplasm. The forces which cause condensation of the DNA into nucleoids are poorly understood. We suggest that direct and indirect macromolecular crowding forces from the surrounding cytoplasm are critical factors for nucleoid condensation, and that within a bacterial cell these crowding forces are always present at such high levels that the DNA is maintained in a condensed state. The DNA affected includes not only the preexisting genomic DNA but also DNA that is newly introduced by viral infection, replication or other means.     

Macromolecular composition of the sarcolemma and endomysium in the rat

The macromolecular composition of sarcolemma and endomysium was studied by classical staining methods for glycosaminoglycans and using immunological techniques for proteins. Both proteoglycans and glycosaminoglycans (heparan sulphate, dermatan sulphate, chondroitin sulphate) could be detected in the sarcolemma. Type IV and type V collagen and laminin were found exclusively in the sarcolemma and endomysium. Type I and type III collagen as well as fibronectin were detected both in the endomysium and perimysium.     

Phospholipid composition of methane-utilizing bacteria.

The phospholipids of Methylococcus capsulatus, Methylosinus trichosporium, La Paz, and OBT were examined in relation to their qualitative and quantitative composition. M. capsulatus exhibited a phospholipid composition consisting of phosphatidylethanolamine, phosphatidylglycerol, cardiolipin, and phosphatidyl-choline. The esterified fatty acids were predominantly C16:0 and C16:1. M. trichosporium, La Paz, and OBT exhibited an essentially identical phospholipid composition consisting of phosphatidylmonomethylethanolamine, phosphatidyl-dimethylethanolamine, phosphatidylcholine, and phosphatidylglycerol. Only trace amounts (less than 1%) of cardiolipin were found in these organisms. The major esterified fatty acid in these organisms was C18:1 (87 to 90%). The monounsaturated fatty acids from all four organisms consisted of both cis and trans isomers, each of which contained delta8, delta9, delta10, and delta11 double-bond positional isomers.     

Macromolecular composition of Palaeozoic scolecodonts: insights into the molecular taphonomy of zoomorphs

Dutta, S., Hartkopf‐Fröder, C., Mann, U., Wilkes, H., Brocke, R. & Bertram, N. 2010: Macromolecular composition of Palaeozoic scolecodonts: insights into the molecular taphonomy of zoomorphs. Lethaia, Vol. 43, pp. 334–343. Biogeochemistry and molecular taphonomy of biopolymers of marine zoomorphs are poorly known. In order to obtain insights into this issue we report on the biogeomacromolecular composition of hand‐picked, well‐preserved scolecodonts of Ordovician, Silurian and Devonian age using micro‐Fourier transform infrared (micro‐FTIR) spectroscopy, Curie point pyrolysis‐gas chromatography‐mass spectrometry (Cupy‐GC‐MS) and tetramethylammonium hydroxide (TMAH)‐assisted thermochemolysis‐GC‐MS. The present study reveals that scolecodonts are composed of both aliphatic and aromatic moieties. The micro‐FTIR spectra of scolecodonts are characterized by aliphatic CH_x (3000–2800 and 1460–1450/cm) and CH₃ (1375/cm) absorptions and aromatic C=C (1560–1610/cm) and CH (3050/cm and 700–900/cm) absorptions. The major pyrolysis products from the scolecodonts include aromatic hydrocarbons such as alkylbenzenes, alkylnaphthalenes and alkylphenols. Aliphatic hydrocarbons are represented by a homologous series of n‐alkenes and n‐alkanes. The compounds released upon thermochemolysis with TMAH are saturated and unsaturated fatty acids (as their methyl esters), n‐alkenes/alkanes and aromatic acids (as their methyl esters). No protein/amino acid‐derived compounds have been recognized in the pyrolysates or in the thermochemolysates, and it is concluded that protein/amino acid‐related compounds, which are commonly found in the jaws of extant polychaetes, were destroyed due to diagenetic processes. Obviously, excellent morphological preservation and low thermal alteration are not paralleled by a similar degree of chemical preservation. □Biogeomacromolecules, micro‐FTIR, pyrolysis‐GC‐MS, scolecodonts, thermochemolysis‐GC‐MS.     

Vitamin K composition of anaerobic gut bacteria

The menaquinone (vitamin K₂) composition of a wide range of obligately anaerobic bacteria was investigated using chromatographic and physicochemical techniques. Members of the genera Bifidobacterium, Butyrivibrio, Clostridium, Fusobacterium, Lachnospira, Megasphaera, Propionispira, Ruminococcus, Selenomonas, Succinovibrio and Succinomonas were found to lack menaquinones, In contrast, all species of the genera Actinomyces, Arachnia, Bacteroides, Propionibacterium, Veillonella and Wolinella examined possessed menaquinones. Considerable variation in length and degree of saturation of the C-3 isoprenyl side-chains of the menaquinones isolated from these taxa were evident. In addition to menaquinone, strains of Wolinella and Eubacterium lentum contained methylated menaquinones. The possible contribution of bacterial menaquinones to the total pool of vitamin K in the human gut is discussed.     

Fatty acid composition of selected prosthecate bacteria

The cellular fatty acid composition of 14 strains of Caulobacter species and types, two species of Prosthecomicrobium, and two species of Asticcacaulis was determined by gas-liquid chromatography. In most of these bacteria, the major fatty acids were octadecenoic acid (C18:1), hexadecenoic acid (C16:1) and hexadecanoic acid (C16:0). Some cyclopropane and branched chain fatty acids were detected in addition to the straight chained acids. Hydroxytetradecanoic acid was an important component of P. enhydrum but significant amounts of hydroxy acids were not detected in other prosthecate bacteria examined.Abbreviations DEGS diethylene glycol succinate - A measare of association Dedicated to Prof. R. Y. Stanier on the occasion of his 60th birthday     

Elemental composition of extremely alkaliphilic anaerobic bacteria

The contents of several chemical elements were assessed in the haloalkaliphilic acetogenic bacterium Natroniella acetigena and the alkaliphilic sulfate-reducing bacterium Desulfonatronum lacustre using X-ray microanalysis, stereoscanning microscopy, and mass spectrometry. The organisms were found to differ significantly in their relative contents of S, K, P, and Cl. The P/S ratio in cells of the alkaliphilic bacteria studied grown on mineral media at different pH was pH-dependent. With a pH increase from 9 to 10, potassium extrusion from cells was observed, suggesting that secondary K+/H+ antiport activity accounts for the homeostasis of cytosolic pH. Deenergization of bacterial cells in the presence of inhibitors and ionophores results in specific changes in the P/S ratio, which may be considered an indicator of the cell energetic state. In Natroniella acetigena, the content of intracellular Cl was directly proportional to the NaCl concentration in the medium. Some metals were shown to be necessary for the N. acetigena viability; the requirement for Ni and Co was absolute. Although little demand for Mg was characteristic of the bacteria studied, their growth was stimulated by an increase in Mg concentration, and the cell resistance to lysis was enhanced.     

DNA base composition of some sheathed bacteria

The DNA base composition of five recently isolated Haliscomenobacter hydrossis strains were compared with those of Sphaerotilus natans, Leptothrix cholodnii and Leptothrix discophora. The DNA base composition of H. hydrossis strains ranged from 48.3 to 49.7% GC, whereas the % GC values of S. natans, L. cholodnii and L. discophora were found to be 69.7, 69.6 and 71.2, respectively. These results indicate that Haliscomenobacter species and the microorganisms of the Sphaerotilus-Leptothrix group should not be classified into the same genus, as they are genetically at best remotely related.The reallocation of some Leptothrix species into the genus Sphaerotilus is not in contradiction with their DNA base composition.     

The evolution of genomic base composition in bacteria

Abstract. Guanine plus cytosine (GC) content ranges broadly among bacterial genomes. In this study, we explore the use of a Brownian-motion model for the evolution of GC content over time. This model assumes that GC content varies over time in a continuous and homogeneous manner. Using this model and a maximum-likelihood approach, we analyzed the evolution of GC content across several bacterial phylogenies. Using three independent tests, we found that the observed divergence in GC content was consistent with a homogeneous Brownian-motion model. For example, similar rates of GC content evolution were inferred in several different bacterial subclades, indicating that there is relatively little rate heterogeneity in GC content evolution over broad evolutionary time scales. We thus argue that the homogeneous Brownian-motion model provides a good working model for GC content evolution. We then use this model to determine the overall rate of GC content evolution among eubacteria. We also determine the time frame over which GC content remains similar in related taxa, using a flexible definition for "similarity" in GC content so that, depending on the context, more or less stringent criteria may be applied. Our results have implications for models of sequence evolution, including those used for phylogenetic reconstruction and for inferring unusual changes in GC content.