Amino acid and glucose fermentation by Treponema denticola

Summary Treponema denticola was grown in serum-containing media to which ¹⁴C-labelled compounds were added. Determinations of radioactivity in the products formed indicated that the organism fermented alanine, cysteine, glycine, serine, and glucose. Fermentation products included acetate, lactate, succinate, formate, pyruvate, ethanol, CO₂, H₂S, and NH₃. The products formed from glucose constituted a small portion of the total products. Assays of enzymatic activities in cell extracts indicated that the organism degraded glucose via the Embden-Meyerhof pathway. T. denticola possessed a coenzyme A-dependent CO₂-pyruvate exchange activity associated with a clostridial-type clastic system for pyruvate metabolism. Phosphotransacetylase and acetate kinase activities were present in cell extracts. Acetyl phosphate formation and benzyl viologen reduction were detected when cell extracts were incubated with pyruvate, serine or cysteine. The data indicate that T. denticola is an amino acid fermenter and that it possesses the enzymes needed for the fermentation of glucose. However, glucose does not serve as the primary substrate when the organism grows in media including both this carbohydrate and amino acids.     

Amino acid fermentation and hydrogen transfer in mixed cultures

Abstract The degradation of the following amino acids was investigated in mixed cultures obtained from a waste water purification plant: aspartate, glutamate, serine, alanine, valine and leucine. Inhibition of sulfate-reducing bacteria in these mixed cultures by molybdate was found to inhibit amino acid degradation. The degradation of serine, alanine, valine and leucine was accelerated considerably by active sulfate reduction. The fermentation of aspartate and glutamate was not stimulated by the presence of sulfate-reducing bacteria. The existence of species which are able to ferment valine and leucine by coupling their oxidation to the reduction of exogenous acetate to butyrate was demonstrated.     

Amino acid fermentation in non-starter Lactobacillus spp. isolated from cheddar cheese

Amino acid fermentation profiles of nine strains of Lactobacillus spp., initially isolated from a 3-year-old Cheddar cheese, were determined using the Biolog MT microplatetrade mark method. Eight of the isolates were able to ferment amino acids, but only when incubated in the presence of exogenously supplied alpha-ketoglutaric acid that served as an acceptor in the initial transamination step in the fermentative degradation. The range of amino acids catabolized was strain dependent. Amino acid catabolites were detected by gas chromatography mass spectrometry (GCMS) in culture supernatant fluids of a representative non-starter lactic acid bacteria isolate Lactobacillus paracasei CI6.     

d-Pentose metabolism byBacteroides vulgatus strain 8482

Bacteroides vulgatus strain 8482 metabolizedd-arabinose by a mechanism involving a 32 (top to bottom) cleavage of the arabinose carbon skeleton. During growth in the presence of 1-¹⁴C-d-arabinose, acetate, propionate, and succinate were labeled, but during growth in the presence of 5-labeledd-arabinose, only labeled acetate and succinate were formed. The metabolism ofd-ribose by strain 8482 differed from that ford-arabinose. Strain 8482 converted glycolic acid and glycine to acetate and succinate, but not propionate, by a mechanism involving cleavage of the glycine and glycolic acid carbon skeletons and equilibration of carbons 1 and 2 of glycolic acid and glycine with nonequivalent metabolic pools. The metabolism ofd-arabinose,d-ribose,d-glycine, andd-glycolic acid by strain 8482 was similar, in some respects, to that ofBacteroides fragilis strain 2044, but differed substantially from the metabolism of the same substances byBacteroides ruminicola strain B₁4.     

Glutamine-stimulated amino acid and peptide incorporation in Bacteroides melaninogenicus.

The uptake of a number of amino acids and dipeptides by cells and spheroplasts of Bacteroides melaninogenicus was stimulated by the presence of glutamine; 50 mM glutamine induced maximum uptake of glycine or alanine, and glutamine stimulated the uptake of glycine over a wide concentration range (0.17 to 170 mM). Glutamine stimulated the uptake of the dipeptides glycylleucine and glycylproline at significantly faster rates compared with glycine and leucine. The amino acids whose uptake was stimulated by glutamine were incorporated into trichloroacetic acid-precipitable material, and the inclusion of chloramphenicol or puromycin did not affect this incorporation. The uptake of glutamine by cells was concentration dependent. In contrast, in the absence of chloramphenicol 79% of the glutamine taken up by cells supplied with a high external concentration (4.4 mM) was trichloroacetic acid soluble. Glutamate and alpha-ketoglutarate were identified in the intracellular pool of glutamine-incubated spheroplasts. The amino acids and peptides were incorporated into cell envelope material, and a portion (30 to 50%) of the incorporated amino acids could be removed by trypsinization or treatment with papain. The effect of glutamine was depressed by inhibitors of energy metabolism, suggesting that glutamine-stimulated incorporation is an energy-mediated effect.     

d-arabinose metabolism byBacteroides fragilis strain 2044

During growth in the presence of 1-14C-d-arabinose,Bacteroides fragilis strain 2044 formed labeled succinic, acetic, and propionic acis. Degradation of the acids by the Schmidt reaction revealed that at least 89% of the succinate radioactivity was found in the methylene carbons and that 75% and 84% of the label in propionate and acetate were found in the noncarboxyl carbons of these molecules. No label was found in acetate, propionate, or succinate during growth of strain 2044 in the presence of 5-3H-d-arabinose. Strain 2044 converted radioactivity from 1- or 2-labeled glycolic acid and glycine to succinate by a mechanism involving cleavage of the glycine and glycolic acid carbon skeletons. Label from 1- or 2-labeled glycine and 2 but not 1-labeled glycolic acid was found in acetate. Uniformly labeled 14C-glyoxalate gave rise to labeled acetate, but not succinate.Bacteroides fragilis strain 2044 metabolizesd-arabinose by a mechanism involving a 32 cleavage of the molecule.     

Deoxyribonucleic acid homologies among strains of Bacteroides melaninogenicus and related species

Saccharolytic, black-pigmented Bacteroides strains, which at present belong to the species Bacteroides melaninogenicus were classified on the basis of deoxyribonucleic acid (DNA) base ratios and DNA hybridization studies. These strains were divided into several DNA homology groups, which showed no or low mutual DNA homology. A DNA homology group with a percentage guanine plus cytosine (G + C) of 42–43% was formed by three strains of Bact. melaninogenicus subsp. melaninogenicus ; the type strain of this subspecies, strain ATCC 25845, had about 60% DNA homology with this group. Strain ATCC 15930, which has been assigned to this subspecies, had a percentage G + C of 47% and showed no DNA homology with the former group. All strains of Bact. melaninogenicus subsp. intermedius had a percentage G + C of 39–45%. A DNA homology group was formed by eight strains of this subspecies. The type strain of Bact. melaninogenicus subsp. intermedius , ATCC 25611, showed relatively low DNA homology with this main DNA homology group. A strain of Bact. melaninogenicus subsp. intermedius serotype C1 showed no DNA homology with the other strains tested. Furthermore two strains labelled 'Bact. melaninogenicus subsp. levii' were found to form a distinct DNA homology group. On the basis of the DNA homology results, the strains, which at present are classified in the species Bact. melaninogenicus , were clearly distinguished from strains of Bact. asaccharolyticus and Bact. gingivalis , and also from strains of related non-pigmented Bacteroides species.     

Metabolism of cellobiose and cellulose byBacteroides cellulosolvens

Summary The metabolism ofBacteroides cellulosolvens was studied on cellobiose and cellulose as energy and carbon sources. The growth rate was faster on cellobiose; however, growth on cellulose resulted in consumption of 55% more hexose equivalents, and in production of 49% more biomass, and 30% more metabolites (ethanol, acetate, and lactate). On each substrateB. cellulosolvens exhibited two distinct ranges of molar growth yields (Y _H g cells/mol hexose). At low substrate concentrations (less than 30 mmol) hexoseY _H values were 25.5 for cellulose and 28.5 for cellobiose, while at hexose levels greater than 30 mmolY _H values were 13.5 and 15, respectively. Shifts in metabolism towards greater lactic acid production resulted in decreased ATP production; however, this did not cause early growth cessation, as these shifts occurred after the drop inY _H.Issued as NRCC No. 27409.     

Amino acid pairing

A set of amino acid pairings are presented which may allow protein-to-protein information transfers. Amino acid pairing is only possible on a parallel β ribbon and involves both the polypeptide backbones and the side chains. Model building revealed that of the 210 possible amino acid pairs of the standard 20 amino acids, no more than 26 could be built to meet standard criteria for bonding. Of these 26, 14 were found to be genetically encoded when the codons are read as if they paired in a parallel manner (i.e. in a manner reflecting the structural parallelism of the amino acid pairings); the other 12 pairings were derivatives of the coded pairings in which a single base of the codon triplet had been varied in accordance with Crick's (1966) “wobble hypothesis.” Evidence for the pairings is presented from colligative studies of polyamino acids. Ways of testing the hypothesis further are suggested. Its implications for the Central Dogma and theories of the origin of life are discussed.     

Synthesis and release of proteases byBacteroides fragilis

Protease production byBacteroides fragilis ATCC 25285 was determined in batch and continuous cultures. During exponential growth in batch culture, the majority of proteolysis was cell associated. However, as the bacteria reached stationary phase, most of the intracellular proteases were released into the culture medium. Measurements of alkaline phosphatase and -galactosidase, which are respectively periplasmic and cytoplasmic marker enzymes inB. fragilis, showed that secretion of proteases in the stationary phase was a discrete event and was not associated with a general release of cytoplasmic contents. When the bacterium was grown in continuous culture, cell-associated protease activity increased concomitantly with dilution rate (D=0.03–0.23/h). The ratio of intracellular to whole cell protease activity also increased with growth rate (11 at D=0.03/h; 11.7 at D=0.23/h). Extracellular protease activity was detected only in trace amounts in continuous cultures at the lowest dilution rate. Determinations of the distribution of extracellular protease activity in batch culture after 48 h incubation showed that the majority of proteolysis (ca. 90%) was soluble. Nevertheless, a proportion was associated with particulate fractions, which had high specific activities.     

Erythorbic acid fermentation

A brief review of the development of the research on erythorbic acid fermentation was presented. A previously proposed scheme of the acid biosynthesis has been proved to be correct. D-glucono-γ-lactone dehydrogenase was purified to 50 fold and compared with other lactone dehydrogenases. For the purpose of commercial development, screening and mutagenie treatments of strains and studies on fundamental cultural conditions were carried out. Penicillium, but no other genera, was obtained as a producer. The experiments of ultraviolet irradiation and various cultural conditions were successful in elevating the yield of the acid over 40% in jar-fermentor to glucose supplied. The continuous multibed extraction system of anion-exchange resin was developed and a yield of 19.2% of the acid from fermentation broth was obtained.     

Lipids of Bacteroides melaninogenicus

The lipids of Bacteroides melaninogenicus were readily extractable with chloroform-methanol. Three per cent of the fatty acids were not extractable. The neutral lipids contained 4% of the extractable fatty acids, the stench characteristic of these organisms, and 0.5 mumole of vitamin K(2) isoprenologues K(2)-35, K(2)-40, and K(2)-45 per g (dry weight). This is one-fifth to one-tenth of the vitamin K(2) level found in other bacteria. Ninety-six per cent of the extractable fatty acids were associated with the phospholipids (60 mumoles of lipid phosphate/g, dry weight), which consisted of the diacyl lipids phosphatidic acid, phosphatidyl serine, and phosphatidyl ethanolamine (with phosphatidyl glycerol and cardiolipin in one strain). The unusual phosphosphingolipids ceramide phosphorylethanolamine, ceramide phosphorylglycerol, and ceramide phosphorylglycerol phosphate accounted for 50 to 70% of the lipid phosphate. In protoheme-requiring strains, the protoheme concentration in the growth medium regulated the growth rate and the amount of enzymatically reducible cytochrome c. There were no gross changes in the lipid composition in cells containing different levels of enzymatically reducible cytochrome c.     

Amino acid propensities revisited

Statistical analysis of amino acid patterns in approximately 160,000 alpha-helices in experimentally determined structures revealed di-, tri-, and tetrapeptides, whose frequencies deviate most from the statistical model. Importantly, some sequences were never found in alpha- helices. This fact was detected initially with tripeptides, where nearly 1% of the possible sequences were never seen in the helical segments. For tetrapeptides, this effect is very strong and significant; almost 43% of the possible sequences never appear in alpha-helices. It is possible that there are some steric and energetic restrictions that do not allow these tetrameric amino acid sequences to form alpha-helical structure.