Bacteroides pectinophilus sp. nov. and Bacteroides galacturonicus sp. nov.: two pectinolytic bacteria from the human intestinal tract

Studies on the physiological characteristics of two obligately anaerobic, rod-shaped bacteria from the human intestinal tract indicated that the organisms represented two previously undescribed species of Bacteroides, for which we propose the names Bacteroides pectinophilus (type strain, N3) and Bacteroides galacturonicus (type strain, N6). Both strains were pectinophilic; that is, they utilized as fermentable substrates for growth only pectin and a few related compounds. The two species differed significantly from each other in guanine plus cytosine content of the DNA, in substrate utilization patterns, and in other phenotypic characteristics. Both species deesterified pectin by means of an extracellular pectinesterase (EC 3.1.1.11) activity. Polygalacturonate (the main component of deesterified pectin) was depolymerized extracellularly with formation of unsaturated products by both species. The depolymerizing activity required Ca2+, functioned at a higher rate when polygalacturonate was the substrate as compared with pectin, and had an alkaline pH optimum. These data, as well as viscosity decrease studies and identification of products formed from polygalacturonate, indicated that the extracellular depolymerizing activity of either species was characteristic of an exopectate (exopolygalacturonate) lyase. The exopectate lyase activity had an unusual action pattern that resulted in terminal cleavage of unsaturated trigalacturonic acid units from polygalacturonate. An unsaturated trimer was the major product that accumulated in cell-free reaction mixtures, where it was not cleaved further. Growing cells of both Bacteroides species released the exopectate lyase into the external environment by processes that did not involve cell lysis to any significant extent.(ABSTRACT TRUNCATED AT 250 WORDS)     

Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rabbit caecal bacterium Bacteroides caccae

AIMS: To compare fermentation pattern in cultures of Bacteroides caccae supplied with pectin and glucose, and identify enzymes involved in metabolism of pectin. METHODS AND RESULTS: A strain KWN isolated from the rabbit caecum was used. Fermentation pattern, changes of viscosity and enzyme reactions products were determined. Cultures grown on pectin produced significantly more acetate and less formate, lactate, fumarate and succinate than cultures grown on glucose. Production of cell dry matter and protein per gram of substrate used was the same in pectin- and glucose-grown cultures. The principal enzymes that participated in the metabolism of pectin were extracellular exopectate hydrolase (EC 3.2.1.67), extracellular endopectate lyase (EC 4.2.2.2) and cell-associated 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (EC 4.1.2.14). The latter enzyme is unique to the Entner-Doudoroff pathway. Activities of pectinolytic enzymes in cultures grown on glucose were low. Activity of KDPG aldolase was similar in pectin- and glucose-grown cells. CONCLUSIONS: Metabolites and activities of pectin-degrading enzymes differed in cultures of B. caccae KWN grown on pectin and glucose. Yields of dry matter and protein were the same on both substrates. SIGNIFICANCE AND IMPACT OF THE STUDY: Information on metabolism of pectin in animal strains of Bacteroides is incomplete. This study extends the knowledge on metabolism in bacteria from the rabbit caecum.     

Purification and characterization of an extracellular pectate lyase from an Amycolata sp.

The extracellular pectate lyase (EC 4.2.2.2) of a nonsporulating Amycolata sp. was purified to homogeneity by anion- and cation-exchange chromatographies followed by hydrophobic interaction chromatography. The enzyme cleaved polygalacturonate but not highly esterified pectin in a random endolytic transeliminative mechanism that led to the formation of a wide range of 4,5-unsaturated oligogalacturonates. As shown by high-performance anion-exchange chromatography and pulsed amperometric detection, these unsaturated oligogalacturonates were further depolymerized by the enzyme to the unsaturated dimer and trimer as final products. The pectate lyase had a molecular weight of 31,000 determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and a molecular mass of 30,000 Da determined by matrix-assisted laser desorption ionization mass spectrometry. The isoelectric point of the protein was 10. Maximum activity occurred at pH 10.25. Calcium was essential for activity, and EDTA inactivated the enzyme under standard assay conditions. Interestingly, EDTA did not inhibit the ability of the enzyme to cleave the native pectin (protopectin) of ramie (Boehmeria nivea) fibers. The Km value with sodium polygalacturonate as the substrate was 0.019 g liter-1. The purified enzyme lost its activity after a 1-h incubation at 50 degrees C but was stabilized by calcium or polygalacturonate. The N-terminal sequence showed high similarity within a stretch of 13 amino acids to the N-terminal sequences of pectate lyases PLa and PLe from Erwinia chrysanthemi. The Amycolata sp. did not produce additional isozymes of pectate lyase but produced further activities of pectinesterase, xylanase, and carboxymethyl cellulase when grown in a medium with decorticated bast fibers from ramie as the sole carbon source.     

Coordinated action of pectinesterase and polygalacturonate lyase complex of Clostridium multifermentans.

The polygalacturonate lyase and pectinesterase activities of Clostridium multifermentans, both produced extracellularly when the organism grows on pectin or polygalacturonate, have been suggested to be associated in a single complex. Both enzymic sites act on their respective substrates by single-chain action patterns, as shown by equivalent release of terminal tritium label and total product throughout the reaction. From these results, the Km and V of the lyase, and the amount of lyase activity present, we calculate the steady-state concentration of lyase substrate expected during action of the two sites on pectin if the sites are independent. No such steady-state concentration of lyase substrate was observed. Therefore, we conclude that the two types of active site act in a coordinated manner; the polysaccharide chain passes from the esterase site to the lyase site without intermediate dissociation and rebinding. This 'molecular disassembly line' constituted by the two sites may represent a system of general significance in synthesis and degradation of biological polymers.     

Microbiology of Wetwood: Importance of Pectin Degradation and Clostridium Species in Living Trees

Wetwood samples from standing trees of eastern cottonwood (Populus deltoides), black poplar (Populus nigra), and American elm (Ulmus americana) contained high numbers of aerobic and anaerobic pectin-degrading bacteria (10⁴ to 10⁶ cells per g of wood). High activity of polygalacturonate lyase (≤0.5 U/ml) was also detected in the fetid liquid that spurted from wetwood zones in the lower trunk when the trees were bored. A prevalent pectin-degrading obligately anaerobic bacterium isolated from these wetwoods was identified as Clostridium butyricum. Pectin decomposition by C. butyricum strain 4P1 was associated with an inducible polygalacturonate lyase and pectin methylesterase, the same types of pectinolytic activity expressed in the wetwood of these trees. The pH optimum of the extracellular polygalacturonate lyase was alkaline (near pH 8.5). In vitro tests with sapwood samples from a conifer (Douglas fir, Pseudotsuga menziesii) showed that tori in membranes of bordered pits are degraded by pure cultures of strain 4P1, polygalacturonate lyase enzyme preparations of strain 4P1, and mixed methanogenic cultures from the tree samples of wetwood. These results provide evidence that pectin in xylem tissue is actively degraded by C. butyricum strain 4P1 via polygalacturonate lyase activity. The importance of pectin degradation by bacteria, including Clostridium species, appears paramount in the formation and maintenance of the wetwood syndrome in certain living trees.     

Similarities in the Action Patterns of Exopolygalacturonate Lyase and Pectinesterase from Clostridium multifermentans

Exopolygalacturonate lyase and pectinesterase from Clostridium multifermentans were assayed simultaneously in the same reaction mixture which contained a highly esterified pectin, polymethyl polygalacturonic acid methyl glycoside. Lyase is specific for unesterified galacturonide residues and cannot degrade this substrate in the absence of the esterase. The rate for esterase was twice the rate for lyase throughout the entire course of the combined reaction. Thus, the molar ratio of the two enzyme activities was the same since the product of the lyase is an unsaturated digalacturonic acid containing two free carboxyl groups. Since clostridial exopolygalacturonate lyase is known to degrade polygalacturonate in a linear manner beginning from the reducing ends of polygalacturonate chains, it was apparent that clostridial pectinesterase must hydrolyze methyl groups in highly esterified pectins with an action pattern similar to that of the lyase. Otherwise it would be impossible for the two enzyme rates to have corresponded on the basis of a 2:1 ratio.     

Purification and characterization of mucopolysaccharidase from an oral strain of Bacteroides sp.

A mucopolysaccharidase in the cell extract of an oral strain of Bacteroides sp. was purified to homogeneity by ammonium sulfate precipitation, DEAE-cellulose column chromatography, gel filtration on Sephadex G-200, and isoelectric focusing. Specific activity increased 110-fold and recovery was 2%. The molecular weight was determined to be 89,000 by gel filtration, and the isoelectric point was 7.0. The optimum pH for the activity was 6.5. The enzyme was inactivated by heating at 60 degrees C for 5 min. The purified mucopolysaccharidase degraded hyaluronic acid more rapidly than chondroitin and chondroitin sulfate A and C. However, it had no activity against chondroitin sulfate B, heparin, and heparan sulfate. Since unsaturated disaccharides were derived from the enzyme substrate, this enzyme was considered to be a mucopolysaccharide lyase.     

Purification and characterization of mucopolysaccharidase from an oral strain of Bacteroides sp

A mucopolysaccharidase in the cell extract of an oral strain of Bacteroides sp. was purified to homogeneity by ammonium sulfate precipitation, DEAE-cellulose column chromatography, gel filtration on Sephadex G-200, and isoelectric focusing. Specific activity increased 110-fold and recovery was 2%. The molecular weight was determined to be 89,000 by gel filtration, and the isoelectric point was 7.0. The optimum pH for the activity was 6.5. The enzyme was inactivated by heating at 60 degrees C for 5 min. The purified mucopolysaccharidase degraded hyaluronic acid more rapidly than chondroitin and chondroitin sulfate A and C. However, it had no activity against chondroitin sulfate B, heparin, and heparan sulfate. Since unsaturated disaccharides were derived from the enzyme substrate, this enzyme was considered to be a mucopolysaccharide lyase.     

Comparison of proteins involved in chondroitin sulfate utilization by three colonic Bacteroides species.

Three species of colonic bacteria can ferment the mucopolysaccharide chondroitin sulfate: Bacteroides ovatus, Bacteroides sp. strain 3452A (an unnamed DNA homology group), and B. thetaiotaomicron. Proteins associated with the utilization of chondroitin sulfate by B. thetaiotaomicron have been characterized previously. In this report we compare chondroitin lyases and chondroitin sulfate-associated outer membrane polypeptides of B. ovatus and Bacteroides sp. strain 3452A with those of B. thetaiotaomicron. All three species produce two soluble cell-associated chondroitin lyases, chondroitin lyase I and II. Purified enzymes from the three species have similar pH optima, Km values, and molecular weights. However, peptide mapping experiments show that the chondroitin lyases from B. ovatus and Bacteroides sp. strain 3452A are not identical to those of B. thetaiotaomicron. A cloned gene that codes for the chondroitin lyase II from B. thetaiotaomicron hybridized on a Southern blot with DNA from B. ovatus or Bacteroides sp. strain 3452A only when low-stringency conditions were used. Antibody to chondroitin lyase II from B. thetaiotaomicron did not cross-react with chondroitin lyase II from B. ovatus or Bacteroides sp. strain 3452A. Chondroitin lyase activity in all three species was inducible by chondroitin sulfate. B. ovatus and Bacteroides sp. strain 3452A, like B. thetaiotaomicron, have outer membrane polypeptides that appear to be regulated by chondroitin sulfate, but the chondroitin sulfate-associated outer membrane polypeptides differ in molecular weight. Despite these differences, the ability of intact bacteria to utilize chondroitin sulfate, as indicated by growth yields in carbohydrate-limited continuous culture and the rate at which the chondroitin lyases were induced, was the same for all three species.     

Endo-polygalacturonate lyase of Cytophaga johnsonii

Summary An extracellular endopolygalacturonate lyase of Cytophaga johnsonii was purified from the culture filtrate. It appeared to be homogeneous as judged by polyacrylamide gel electrophoresis at pH 8.6 as well as pH 4.3. The purified enzyme had a pH optimum around 9.0 and required Ca⁺⁺ ions for its maximum activity. The apparent K _mfor polygalacturonic acid was found to be 0.22%. Both paper and column chromatography indicated formation and accumulation of an unsaturated monomer along with unsaturated di-, tri-, tetra- and pentamers from polygalacturonic acid by the enzyme action, indicating that the enzyme cleaved the substrate randomly in a non-hydrolytic manner. The glycosidic linkage next to the non-reducing end of polygalacturonic acid was not resistant to attack by this enzyme unlike in other known polygalacturonate lyases.Abbreviations PG lyase Polygalacturonate lyase - Tris Tris (hydroxymethyl) aminomethane     

Evidence that polygalacturonic acid may not be a major source of carbon and energy for some colonic Bacteroides species.

Five Bacteroides species that are found in the human colon can utilize polygalacturonic acid (PGA) when they are grown in laboratory media: Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides ovatus, Bacteroides fragilis subsp. a, and Bacteroides sp. strain 3452A (an unnamed DNA-DNA homology group). PGA-degrading enzymes from B. thetaiotaomicron have been isolated and characterized previously. To determine whether a PGA lyase activity in human feces could be attributed to any of these species, we first determined the properties of PGA lyases from the other four Bacteroides species. PGA lyases from all the Bacteroides species were soluble, cell associated, and inducible by PGA. All had similar pH optima (8.4 to 8.8) and similar molecular weights (50,000). All activities were enhanced by calcium. The PGA lyases from the five species differed with respect to isoelectric point: B. thetaiotaomicron (pI 7.5), B. vulgatus (pI 7.7), B. ovatus (pI 5.8, 7.2), B. fragilis subsp. a (pI 6.1), and Bacteroides sp. strain 3452A (pI 7.7). The PGA lyase activity in human feces resembled those of the Bacteroides PGA lyases in that it had a pH optimum of 8.4 to 8.8 and was enhanced by calcium. However, it differed from the Bacteroides PGA lyases both with respect to isoelectric point (pI 4.2 to 4.4) and molecular weight (100,000). On the basis of these findings, it appears that the PGA lyase activity in human feces is not produced by any of the Bacteroides species surveyed in this survey. Moreover, there was no detectable PGA lyase activity in feces that had the same properties as the Bacteroides enzymes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Evidence that polygalacturonic acid may not be a major source of carbon and energy for some colonic Bacteroides species

Five Bacteroides species that are found in the human colon can utilize polygalacturonic acid (PGA) when they are grown in laboratory media: Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides ovatus, Bacteroides fragilis subsp. a, and Bacteroides sp. strain 3452A (an unnamed DNA-DNA homology group). PGA-degrading enzymes from B. thetaiotaomicron have been isolated and characterized previously. To determine whether a PGA lyase activity in human feces could be attributed to any of these species, we first determined the properties of PGA lyases from the other four Bacteroides species. PGA lyases from all the Bacteroides species were soluble, cell associated, and inducible by PGA. All had similar pH optima (8.4 to 8.8) and similar molecular weights (50,000). All activities were enhanced by calcium. The PGA lyases from the five species differed with respect to isoelectric point: B. thetaiotaomicron (pI 7.5), B. vulgatus (pI 7.7), B. ovatus (pI 5.8, 7.2), B. fragilis subsp. a (pI 6.1), and Bacteroides sp. strain 3452A (pI 7.7). The PGA lyase activity in human feces resembled those of the Bacteroides PGA lyases in that it had a pH optimum of 8.4 to 8.8 and was enhanced by calcium. However, it differed from the Bacteroides PGA lyases both with respect to isoelectric point (pI 4.2 to 4.4) and molecular weight (100,000). On the basis of these findings, it appears that the PGA lyase activity in human feces is not produced by any of the Bacteroides species surveyed in this survey. Moreover, there was no detectable PGA lyase activity in feces that had the same properties as the Bacteroides enzymes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Comparison of proteins involved in chondroitin sulfate utilization by three colonic Bacteroides species

Three species of colonic bacteria can ferment the mucopolysaccharide chondroitin sulfate: Bacteroides ovatus, Bacteroides sp. strain 3452A (an unnamed DNA homology group), and B. thetaiotaomicron. Proteins associated with the utilization of chondroitin sulfate by B. thetaiotaomicron have been characterized previously. In this report we compare chondroitin lyases and chondroitin sulfate-associated outer membrane polypeptides of B. ovatus and Bacteroides sp. strain 3452A with those of B. thetaiotaomicron. All three species produce two soluble cell-associated chondroitin lyases, chondroitin lyase I and II. Purified enzymes from the three species have similar pH optima, Km values, and molecular weights. However, peptide mapping experiments show that the chondroitin lyases from B. ovatus and Bacteroides sp. strain 3452A are not identical to those of B. thetaiotaomicron. A cloned gene that codes for the chondroitin lyase II from B. thetaiotaomicron hybridized on a Southern blot with DNA from B. ovatus or Bacteroides sp. strain 3452A only when low-stringency conditions were used. Antibody to chondroitin lyase II from B. thetaiotaomicron did not cross-react with chondroitin lyase II from B. ovatus or Bacteroides sp. strain 3452A. Chondroitin lyase activity in all three species was inducible by chondroitin sulfate. B. ovatus and Bacteroides sp. strain 3452A, like B. thetaiotaomicron, have outer membrane polypeptides that appear to be regulated by chondroitin sulfate, but the chondroitin sulfate-associated outer membrane polypeptides differ in molecular weight. Despite these differences, the ability of intact bacteria to utilize chondroitin sulfate, as indicated by growth yields in carbohydrate-limited continuous culture and the rate at which the chondroitin lyases were induced, was the same for all three species.     

Cellular and environmental factors affecting the synthesis of polygalacturonate lyase byBacillus subtilis

Summary Cellular and environmental factors affecting the synthesis of polygalacturonate lyase in batch and chemostat cultures ofBacillus subtilis were investigated. The lyase was produced constitutively during growth on a wide range of carbon sources in a defined minimal medium and in medium containing complex organic carbon and nitrogen sources. The highest activity was obtained during batch growth in minimal medium containing glucose and ammonium sulphate. Over 99% of the activity was present extracellularly in the supernatant medium at all stages of the batch growth cycle. Two distinct differential rates of synthesis were observed during exponential growth. The lyase was unable to attack pectin rapidly unless pectin methyl-esterase was also present. Pectin was a poor substrate for growth and polygalacturonate lyase induction because the organism did not produce pectin methyl-esterase. In continuous-flow chemostat cultures with glucose medium, polygalacturonate lyase activity declined to a very low level owing to the selection of non-productive mutant strains. Loss of activity did not occur when polypectate was the carbon source. Steady-state specific polygalacturonate lyase activity in polypectate medium was relatively independent of dilution rate in the range 0.04 to 0.36/h. When polypectate was supplied in excess of the growth requirement lyase activity was 5 times higher than during polypectate-limited growth.     

类芽胞杆菌碱性果胶裂解酶的纯化与酶学性质表征

从类芽胞杆菌Paenibacillus sp.WZ008的发酵上清液中纯化得到一个高活力碱性果胶裂解酶,经SDS-PAGE电泳估算其亚基相对分子质量为4.5×104。通过对该酶进行酶学性质研究发现：该酶能催化裂解果胶酸、低酯果胶和高酯果胶;酶催化反应最适温度范围为55～60℃,最适pH为9.6,在最适条件下以低酯果胶为底物酶的比酶活达3 021.6 U/mg;Ca2＋能增强该酶的活力,而Mn2＋,Ba2＋和EDTA强烈抑制该酶活力;当没有Ca2＋存在时,高度酯化的果胶是该酶的最适底物,在4 mmol/L Ca2＋存在时,该酶以果胶酸为底物比酶活最高（25 467 U/mg）。该酶N端序列比对分析发现与类芽胞杆菌Paenibacillus amylolyticus strain 27c64果胶裂解酶高度同源。     

Pectate lyase from Fusarium solani f. sp. pisi: purification, characterization, in vitro translation of the mRNA, and involvement in pathogenicity

Since indirect experimental evidence suggested that penetration of Fusarium solani f. sp. pisi into its host (Pisum sativum) involved pectin-degrading enzymes (W. K?ller, C. R. Allan, and P. E. Kolattukudy (1982) Physiol, Plant Pathol. 20, 47-60), direct tests were made for the production of such degradative enzymes by this pathogen. When the organism was grown on pectin, a pectate lyase (EC 4.2.2.2) was released into the media. This lyase was purified to apparent homogeneity from the culture filtrate by a two-step process involving passage through DEAE-Sephacel followed by hydrophobic interaction chromatography on octyl-Sepharose. The enzyme cleaved polygalacturonate chains in an endo fashion. The molecular mass of the mature extracellular form of this enzyme was estimated to be 26 kDa. The isoelectric point of the enzyme was 8.3 and the optimum pH for activity was 9.4. Calcium was required for activity and evidence is presented that calcium probably interacts with the substrate rather than the enzyme. When antibodies prepared against this enzyme were used for Western blot analysis of the extracellular culture fluid, a single band was observed at 26 kDa. Following in vitro translation of poly(A)+ RNA, a 29-kDa precursor polypeptide was precipitated by the antibodies. Antibodies inhibited both the catalytic activity of the enzyme and the ability of the fungus to infect pea stems, strongly suggesting that this lyase is involved in pathogenesis.     

Pectinolytic enzymes of oral spirochetes from humans

Five strains of obligately anaerobic, pectin-fermenting spirochetes were isolated from the subgingival plaque of humans. The strains produced two extracellular enzymatic activities that functioned in pectin degradation. One of these enzymatic activities was pectin methylesterase (EC 3.1.1.11), and the other was pectate lyase (EC 4.2.2.2) of the endo type. The data indicate that the cumulative action of these two enzymatic activities brought about depolymerization of pectin in spirochete cultures. Pectin- or polygalacturonate-degrading hydrolases were not detected. A cell-associated lyase activity that catalyzed polygalacturonate breakdown was present in one of the spirochete strains. In addition to pectin, the isolates utilized polygalacturonic, glucuronic, or galacturonic acid as fermentable substrate but did not neutral sugars, amino acids, or other substrates tested. Although the oral spirochetes did not ferment hyaluronic acid, one of the strains grew in coculture with a hyaluronidase-producing Peptostreptococcus strain in a medium containing hyaluronic acid as fermentable substrate. Two of the isolates were identified as Treponema pectinovorum strains on the basis of their substrate utilization pattern, end products of fermentation, other phenotypic characteristics, and the guanine-plus-cytosine content of their DNA. Even though the pectinolytic isolates were specialized with respect to the fermentable substrates they utilized, they appeared to compete successfully with other microorganisms in their habitat.     

Fermentation of pectin by a newly isolated Clostridium thermosaccharolyticum strain

Abstract By enrichment on pectin a thermophilic anaerobic bacterium was isolated. This strain, identified as Clostridium thermosaccharolyticum , was capable of fast growth on pectin (μ_max 0.58 h⁻¹) forming acetate, butyrate, hydrogen, carbon dioxide, methanol and traces of ethanol. The optimum temperature for growth was 58°C and the optimal pH was 6. The initial breakdown of pectin was catalysed by methylesterase and polygalacturonate hydrolase activity; no polygalacturonate lyase activity was found.