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1.  Molecular cloning and analysis of the gene encoding the thermostable penicillin G acylase from Alcaligenes faecalis. 
Alcaligenes faecalis penicillin G acylase is more stable than the Escherichia coli enzyme. The activity of the A. faecalis enzyme was not affected by incubation at 50 degrees C for 20 min, whereas more than 50% of the E. coli enzyme was irreversibly inactivated by the same treatment. To study the molecular basis of this higher stability, the A. faecalis enzyme was isolated and its gene was cloned and sequenced. The gene encodes a polypeptide that is characteristic of periplasmic penicillin G acylase (signal peptide-alpha subunit-spacer-beta subunit). Purification, N-terminal amino acid analysis, and molecular mass determination of the penicillin G acylase showed that the alpha and beta subunits have molecular masses of 23.0 and 62.7 kDa, respectively. The length of the spacer is 37 amino acids. Amino acid sequence alignment demonstrated significant homology with the penicillin G acylase from E. coli A unique feature of the A. faecalis enzyme is the presence of two cysteines that form a disulfide bridge. The stability of the A. faecalis penicillin G acylase, but not that of the E. coli enzyme, which has no cysteines, was decreased by a reductant. Thus, the improved thermostability is attributed to the presence of the disulfide bridge.
PMCID: PMC168649  PMID: 9292993
2.  COMPARISON OF SPHEROPLAST INDUCTION IN ALCALIGENES FAECALIS BY THREE DIFFERENT AGENTS 
Journal of Bacteriology  1962;84(6):1241-1244.
Lark, Cynthia (Saint Louis University, St. Louis, Mo.) and Robert Schichtel. Comparison of spheroplast induction in Alcaligenes faecalis by three different agents. J. Bacteriol. 84:1241–1244. 1962.—Alcaligenes faecalis strain LB was exposed to different concentrations of cycloserine, d-methionine, or penicillin. The time course of spheroplast induction by these agents was measured as a function of their concentration. The results were consistent with models in which cycloserine reversibly inhibited an intracellular enzyme, and d-methionine was built into a defective cell-wall unit. Penicillin simulated cycloserine. This was taken as further evidence that penicillin inhibits an enzyme associated with cell-wall synthesis.
PMCID: PMC278052  PMID: 16561981
3.  Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from Alcaligenes faecalis  
A thermostable penicillin G acylase from A. faecalis has been crystallized in two space groups: C2221 and P41212. X-ray diffraction data were collected to 3.3 and 3.5 Å resolution, respectively.
The enzyme penicillin G acylase (EC 3.5.1.11) catalyzes amide-bond cleavage in benzylpenicillin (penicillin G) to yield 6-aminopenicillanic acid, an intermediate chemical used in the production of semisynthetic penicillins. A thermostable penicillin G acylase from Alcaligenes faecalis (AfPGA) has been crystallized using the hanging-drop vapour-diffusion method in two different space groups: C2221, with unit-cell parameters a = 72.9, b = 86.0, c = 260.2 Å, and P41212, with unit-cell parameters a = b = 85.6, c = 298.8 Å. Data were collected at 293 K and the structure was determined using the molecular-replacement method. Like other penicillin acylases, AfPGA belongs to the N-terminal nucleophilic hydrolase superfamily, has undergone post-translational processing and has a serine as the N-­terminal residue of the β-chain. A disulfide bridge has been identified in the structure that was not found in the other two known penicillin G acylase structures. The presence of the disulfide bridge is perceived to be one factor that confers higher stability to this enzyme.
doi:10.1107/S1744309111053930
PMCID: PMC3310528  PMID: 22442220
thermostability; disulfide bridges; Ntn hydrolases; orthorhombic form; tetragonal form; calcium binding
4.  Purification and properties of inducible penicillin beta-lactamase isolated from Alcaligenes faecalis. 
An inducible penicillin beta-lactamase was purified from a strain of Alcaligenes faecalis resistant to beta-lactam antibiotics. The purified enzyme preparation gave a single protein band on polyacrylamide gel electrophoresis, and its molecular weight was 29,000 based on sodium dodecyl sulfate-acrylamide gel electrophoresis. Its isoelectric point was 5.9. The enzyme more rapidly hydrolyzed penicillins, such as penicillin G, ampicillin, carbenicillin, piperacillin, and cloxacillin, than it hydrolyzed cephalosporins. For the hydrolysis of penicillin G, the optimal pH was 5.5, and the optimal temperature was 35 degrees C. The enzyme activity was inhibited by iodine, Cu2+, Hg2+, and EDTA but was not inhibited by clavulanic acid and sulbactam.
PMCID: PMC180105  PMID: 3873902
5.  Unusual Effects of Penicillin G and Chloramphenicol on the Growth of Moraxella osloensis 
Growth of exponential-phase liquid cultures of Moraxella osloensis was inhibited by 0.5 U of penicillin G per ml. For this organism, low concentrations of penicillin acted primarily in a bacteriostatic rather than in a bactericidal manner. At higher concentrations of penicillin some killing did take place, but the rate of killing was rather slow and appeared to be independent of penicillin concentration. Microscopic observation of cells from penicillin-treated cultures showed little or no cellular swelling or lysis. The total cell count did not decrease significantly during 6 h of incubation in 5,000 U of penicillin per ml. The rates of respiration, nucleic acid synthesis, and protein synthesis were not affected by the presence of penicillin. Attempts to counteract the bactericidal action of high concentrations of penicillin with growth inhibitory concentrations of chloramphenicol were unsuccessful, since chloramphenicol itself was more bactericidal than penicillin for M. osloensis.
PMCID: PMC429978  PMID: 335964
6.  Production of Cephalosporin C by Paecilomyces persicinus P-10 
After the growth of Paecilomyces persicinus P-10 in a glucose-peptone medium, filtrates were collected and analyzed for antibiotic antivity. Activities against Salmonella gallinarum ATCC 3030 and Alcaligenes faecalis ATCC 8750 (penicillin N-resistant strain) were obtained. Part of the former activity was readily inactivated by penicillinase. The fraction active against A. faecalis was isolated by passage through Amberlite XAD-2 and Amberlite IRA-68. The powder eventually obtained was subjected to paper chromatography followed by bioautography, and the activity obtained corresponded to that of a sample of cephalosporin C. Thin-layer chromatography was also employed to verify the presence of cephalosporin C in the P-10 powder. The active solids were further purified by means of paper chromatography in a solvent system consisting of n-butanol-acetic acid-water (60:15:25, vol/vol). The material obtained from this procedure yielded an infrared absorption spectrum identical to that of cephalosporin C. Similarly, the ultraviolet absorption of the purified preparation coincided with that of cephalosporin C. Exposure of the purified solids to cephalosporinase resulted in rapid inactivation of the antibiotic. In addition to penicillin N and cephalosporin C, filtrates of P. persicinus P-10 also contained deacetylcephalosporin C, deacetoxycephalosporin C, and cephalosporin P.
PMCID: PMC444669  PMID: 4157343
7.  Cloning, Overexpression, and Characterization of a Novel Thermostable Penicillin G Acylase from Achromobacter xylosoxidans: Probing the Molecular Basis for Its High Thermostability 
The gene encoding a novel penicillin G acylase (PGA), designated pgaW, was cloned from Achromobacter xylosoxidans and overexpressed in Escherichia coli. The pgaW gene contains an open reading frame of 2,586 nucleotides. The deduced protein sequence encoded by pgaW has about 50% amino acid identity to several well-characterized PGAs, including those of Providencia rettgeri, Kluyvera cryocrescens, and Escherichia coli. Biochemical studies showed that the optimal temperature for this novel PGA (PGA650) activity is greater than 60°C and its half-life of inactivation at 55°C is four times longer than that of another previously reported thermostable PGA from Alcaligenes faecalis (R. M. D. Verhaert, A. M. Riemens, J. V. R. Laan, J. V. Duin, and W. J. Quax, Appl. Environ. Microbiol. 63:3412-3418, 1997). To our knowledge, this is the most thermostable PGA ever characterized. To explore the molecular basis of the higher thermostability of PGA650, homology structural modeling and amino acid composition analyses were performed. The results suggested that the increased number of buried ion pair networks, lower N and Q contents, excessive arginine residues, and remarkably high content of proline residues in the structure of PGA650 could contribute to its high thermostability. The unique characteristic of higher thermostability of this novel PGA provides some advantages for its potential application in industry.
doi:10.1128/AEM.70.5.2764-2770.2004
PMCID: PMC404452  PMID: 15128530
8.  Isolation and characterization of a penicillinase from Pseudomonas cepacia 249. 
Pseudomonas cepacia has an inducible beta-lactamase which is responsible for its novel ability to catabolize beta-lactam compounds. The gene encoding this enzyme, penA, was cloned from a genomic library of P. cepacia 249 on the broad-host-range cosmid pLAFR. This separated the penA gene from the gene encoding a second beta-lactamase in P. cepacia 249. Expression of penA was inducible in an Escherichia coli host strain by low levels of penicillin. The 33,500-molecular-weight enzyme had penicillinase activity not inhibited by clavulanic acid or sulbactam and was highly active against piperacillin and azlocillin. In comparison with other inducible beta-lactamases produced by gram-negative organisms, the penA enzyme had many properties which were similar to those of the penicillinase produced by Alcaligenes faecalis. It was unlike the ampC-type cephalosporinase produced by Pseudomonas aeruginosa.
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PMCID: PMC172292  PMID: 3046483
9.  Identification of dimethyl disulfide-forming bacteria isolated from activated sludge. 
Twenty-four strains with high dimethyl disulfide (DMDS)-forming ability were isolated from activated sludge and identified to the genus level. These bacteria were classified into four groups (A, B, C, and D) by the API ZYM System (API System S.A., Montalieu, France). Group A (three strains) was identified as genus Lactobacillus by the API 20B System, by the method of Cowan and Steel, and by production of lactic acid as confirmed by gas-liquid chromatography. Group B (eight strains) was identified as genus Corynebacterium by API 20B and the Cowan and Steel method. Group C (one strain) was suggested to belong to genus Corynebacterium by the API 20B System. Group D (12 strains) was identified as genus Pseudomonas or Alcaligenes by the API 20B System, as genus Alcaligenes by the Cowan and Steel method, and as Achromobacter group Vd by the API 20NE System. However, on the basis of guanine-plus-cytosine contents in DNA and form of flagella, these strains were identified as genus Pseudomonas. Formation of DMDS from DL-methionine and S-methyl-L-cysteine was tested. DMDS-forming bacteria isolated from activated sludge formed DMDS from both precursors. In genus Pseudomonas, P. aeruginosa could not form DMDS from either precursor, but P. acidovorans, P. alcaligenes, P. pseudoalcaligenes, and P. testosteroni formed DMDS. In genus Alcaligenes, A. denitrificans subsp. xylosoxydans, A. denitrificans subsp. denitrificans, A. faecalis, and A. odorans formed DMDS from both precursors. Achromobacter group Vd formed DMDS from S-methyl-L-cysteine, but could not from DL-methionine.
PMCID: PMC203907  PMID: 3662505
10.  Contribution of permeability and sensitivity to inhibition of DNA synthesis in determining susceptibilities of Escherichia coli, Pseudomonas aeruginosa, and Alcaligenes faecalis to ciprofloxacin. 
To examine the correlation between bacterial cell susceptibility to ciprofloxacin and the magnitude of uptake and cell target sensitivity, the relative contribution of ciprofloxacin accumulation in intact cells and its ability to inhibit DNA synthesis were investigated among strains of Escherichia coli, Pseudomonas aeruginosa, and Alcaligenes faecalis. Uptake studies of [14C]ciprofloxacin demonstrated diffusion kinetics for P. aeruginosa and E. coli. Ciprofloxacin was more readily removed from E. coli J53 and A. faecalis ATCC 19018 by washing than from P. aeruginosa PAO503. These results indicate that the process of cell accumulation is different for P. aeruginosa in that the drug is firmly bound at an extracellular site. Whatever the washing conditions, A. faecalis accumulated less drug than either of the other two bacteria. Magnesium chloride (10 mM) caused a substantial decrease of ciprofloxacin accumulated and an increase in the MIC, depending upon the nature of the medium. The addition of carbonyl cyanide m-chlorophenylhydrazone caused a variable increase in drug accumulated, depending on the medium and the bacterial strain. The concentration of ciprofloxacin required to obtain 50% inhibition (ID50) of DNA synthesis for P. aeruginosa PAO503 and A. faecalis ATCC 19018 did not correlate with their corresponding MICs but did for E. coli J53. Treatment with EDTA decreased the ID50 of ciprofloxacin for P. aeruginosa PAO503 and its gyrA derivative by 5- and 2-fold, respectively, and decreased the ID50 for E. coli JB5R, a strain with a known decrease in OmpF, by 1.4-fold but did not decrease the ID50 for the normally susceptible E. coli J53. The ID(50) for P. aeruginosa obtained after EDTA treatment or in ether-permeabilized cells was higher than that obtained for the other two strains. The protonophore carbonyl cyanide m-chlorophenylhydrazone prevented killing by low ciprofloxacin concentrtaions, but sodium azide did not. The latter compound did not enhance killing in association with inhibition of a previously described energy-dependent efflux of ciprofloxacin susceptibility being the susceptibility to inhibition of DNA synthesis in E. coli, poor premeability associated with the small pore size of A. faecalis, and a combination of low permeability and reduced susceptibility of DNA synthesis to inhibition for P. aeruginosa.
PMCID: PMC172683  PMID: 2510591
11.  Paradoxical response of Enterococcus faecalis to the bactericidal activity of penicillin is associated with reduced activity of one autolysin. 
Ten clinical isolates of Enterococcus faecalis were examined for susceptibility to the bactericidal activity of penicillin. Four of these had MBCs of penicillin equal to 2 to 4 x the MIC, and six exhibited a paradoxical response to penicillin, i.e., the bactericidal activity of the antibiotic had a concentration optimum at 2 to 4 x the MIC and decreased significantly at concentrations above this. We found that the paradoxical response to penicillin was an intrinsic and stable property of a strain, but that its phenotypic expression was not homogeneous; only a fraction of the cell population that died at low concentrations was able to survive at high penicillin concentrations. The size of this fraction increased with increasing antibiotic concentration and reached a maximum in the late-log phase of growth. All 10 strains produced a lytic enzyme that was active on Micrococcus luteus heat-killed cells, whereas only some strains lysed E. faecalis heat-killed cells. Strains producing large amounts of the latter enzyme did not show the paradoxical response to penicillin, whereas mutants of these strains that lacked this enzymatic activity paradoxically responded to the antibiotic activity. In addition, from strains that showed paradoxical response to penicillin and produced only the enzyme that was active on M. luteus, it was possible to isolate mutants that were also capable of lysing E. faecalis cells and that were killed with similar efficiency by all concentrations above the MBC. On the basis of these findings, the paradoxical response to penicillin is explained as a property of certain strains of E. faecalis; this property is genetically characterized by alterations in synthesis or activity of one autolysin but phenotypically expressed only by a few cells that are in a particular physiological condition when exposed to high concentrations of antibiotics.
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PMCID: PMC171579  PMID: 2109578
12.  Microbial Purification of Postfermentation Medium after 1,3-PD Production from Raw Glycerol 
BioMed Research International  2013;2013:949107.
1,3-Propanediol (1,3-PD) is an important chemical product which can be used to produce polyesters, polyether, and polyurethanes. In the process of conversion of glycerol to 1,3-PD by Clostridium large number of byproducts (butyric, acetic and lactic acid) are generated in the fermentation medium. The aim of this work was to isolate bacteria strains capable of the utilization of these byproducts. Screening of 30 bacterial strains was performed using organic acids as carbon source. Selected isolates were taxonomically characterized and identified as Alcaligenes faecalis and Bacillus licheniformis. The most active strains, Alcaligenes faecalis JP1 and Bacillus licheniformis JP19, were able to utilize organic acids almost totally. Finally, it was find out that by the use of coculture (C. butyricum DSP1 and A. faecalis JP1) increased volumetric productivity of 1,3-PD production (1.07 g/L/h) and the yield equal to 0.53 g/g were obtained in bioreactor fermentation. Moreover, the only by-product present was butyric acid in a concentration below 1 g/L.
doi:10.1155/2013/949107
PMCID: PMC3807725  PMID: 24199204
13.  Identification of Amino Acid Residues Responsible for the Enantioselectivity and Amide Formation Capacity of the Arylacetonitrilase from Pseudomonas fluorescens EBC191 ▿ †  
Applied and Environmental Microbiology  2009;75(17):5592-5599.
The nitrilase from Pseudomonas fluorescens EBC191 converted (R,S)-mandelonitrile with a low enantioselectivity to (R)-mandelic acid and (S)-mandeloamide in a ratio of about 4:1. In contrast, the same substrate was hydrolyzed by the homologous nitrilase from Alcaligenes faecalis ATCC 8750 almost exclusively to (R)-mandelic acid. A chimeric enzyme between both nitrilases was constructed, which represented in total 16 amino acid exchanges in the central part of the nitrilase from P. fluorescens EBC191. The chimeric enzyme clearly resembled the nitrilase from A. faecalis ATCC 8750 in its turnover characteristics for (R,S)-mandelonitrile and (R,S)-2-phenylpropionitrile (2-PPN) and demonstrated an even higher enantioselectivity for the formation of (R)-mandelic acid than the nitrilase from A. faecalis. An alanine residue (Ala165) in direct proximity to the catalytically active cysteine residue was replaced in the nitrilase from P. fluorescens by a tryptophan residue (as found in the nitrilase from A. faecalis ATCC 8750 and most other bacterial nitrilases) and several other amino acid residues. Those enzyme variants that possessed a larger substituent in position 165 (tryptophan, phenylalanine, tyrosine, or histidine) converted racemic mandelonitrile and 2-PPN to increased amounts of the R enantiomers of the corresponding acids. The enzyme variant Ala165His showed a significantly increased relative activity for mandelonitrile (compared to 2-PPN), and the opposite was found for the enzyme variants carrying aromatic residues in the relevant position. The mutant forms carrying an aromatic substituent in position 165 generally formed significantly reduced amounts of mandeloamide from mandelonitrile. The important effect of the corresponding amino acid residue on the reaction specificity and enantiospecificity of arylacetonitrilases was confirmed by the construction of a Trp164Ala variant of the nitrilase from A. faecalis ATCC 8750. This point mutation converted the highly R-specific nitrilase into an enzyme that converted (R,S)-mandelonitrile preferentially to (S)-mandeloamide.
doi:10.1128/AEM.00301-09
PMCID: PMC2737917  PMID: 19581475
14.  Chemical Characterization, Crossfeeding and Uptake Studies on Hydroxamate Siderophore of Alcaligenes faecalis 
Indian Journal of Microbiology  2011;51(2):176-181.
We report the production of two types of siderophores namely catecholate and hydroxamate in modified succinic acid medium (SM) from Alcaligenes faecalis. Two fractions of siderophores were purified on amberlite XAD, major fraction was hydroxamate type having a λmax at 224 nm and minor fraction appeared as catecholate with a λmax of 264 nm. The recovery yield obtained from major and minor fractions was 297 and 50 mg ml−1 respectively. The IEF pattern of XAD-4 purified siderophore suggested the pI value of 6.5. Cross feeding studies revealed that A. faecalis accepts heterologous as well as self (hydroxamate) siderophore in both free and iron complexed forms however; the rate of siderophore uptake was more in case of siderophores complexed to iron. Siderophore iron uptake studies indicated the differences between hydroxamate siderophore of A. faecalis and Alc E, a siderophore of Alcaligenes eutrophus.
doi:10.1007/s12088-011-0129-y
PMCID: PMC3209891  PMID: 22654161
Siderophores; IEF; Crossfeeding; Iron uptake
15.  Cellular fatty acids of Alcaligenes and Pseudomonas species isolated from clinical specimens. 
Journal of Clinical Microbiology  1975;1(5):414-419.
The cellular fatty acid composition of 25 clinical isolates of Alcaligenes and Pseudomonas was determined by gas-liquid chromatography (GLC). The GLC fatty acid profiles of three species of Pseudomonas were markedly different from those of Alcaligenes. The most significant differences were the presence and relative amounts of hydroxy, branched-chain, and cyclopropane fatty acids. One of the major fatty acids in A. faecalis was a 17-carbon cyclopropane (17 delta) acid, whereas a 15-carbon branched-chain acid (13-methyl tetradecanoate) characterized isolates of P. putrefaciens. The determination of these fatty acids by GLC provides a rapid and specific means of distinguishing clinical isolates of Pseudomonas and Alcaligenes.
PMCID: PMC275133  PMID: 1176611
16.  Metabolism of fensulfothion by a soil bacterium, Pseudomonas alcaligenes C1. 
Fensulfothion (O,O-diethyl O-[4-(methylsulfinyl)phenyl]phosphorothioate), an organophosphorus pesticide used to control the golden nematode Heterodera rostochiensis, is used as a source of carbon by microorganisms isolated from soils treated with the pesticide. Two of the microbial isolates, Pseudomonas alcaligenes C1 and Alcaligenes sp. strain NC3, used more than 80% of the pesticide in 120 h in culture when supplemented as a source of carbon. P. alcaligenes C1, which showed maximal growth on fensulfothion, degraded the compound to p-methylsulfinyl phenol and diethyl phosphorothioic acid. The phenolic metabolite could be identified by conventional spectral analysis, whereas the spectral patterns of the phosphorus-containing metabolite suggested that the compound was complexed with some cellular molecules. However, utilization of the phosphoric acid ester and ethanol by P. alcaligenes C1 suggested that the microbe attacks fensulfothion by an initial hydrolysis of the compound and subsequent utilization of the phosphoric acid ester. The pathway of degradation of fensulfothion by P. alcaligenes is of great value in the detoxification of the pesticide residues and also in the environmentally stable phosphoric acid esters.
PMCID: PMC239414  PMID: 6226243
17.  Size of diffusion pore of Alcaligenes faecalis. 
The diffusion pore of the outer membrane of Alcaligenes faecalis was shown to be substantially smaller than the Escherichia coli porin pore. In experiments with intact cells, pentoses and hexoses penetrated into the NaCl-expanded periplasm, whereas saccharides of Mr greater than 342 did not. Cells treated with 0.5 M saccharides of Mr greater than 342 weighed 33 to 38% less than cells treated with isotonic solution, suggesting that these saccharides do not permeate through the outer membrane. The diffusion rates of various solutes through the liposome membranes reconstituted from the Mr-43,000 outer membrane protein showed the following characteristics. (i) The relative diffusion rates of pentoses, hexoses, and methylhexoses appeared to be about 1.0, 0.6, and negligibly small, respectively. (ii) The diffusion rate of glucose appeared to be about 1/10th that with the E. coli B porin. (iii) The diffusion rate of gluconic acid was five to seven times higher than that of glucose. (iv) The diffusion rates of beta-lactam antibiotics appeared to be 40 to less than 10% of those with the E. coli B porin.
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PMCID: PMC172180  PMID: 2835003
18.  DEGRADATION OF ERGOTHIONEINE BY CELL-FREE EXTRACTS OF ALCALIGENES FAECALIS II.  
Journal of Bacteriology  1963;85(3):654-657.
Booth, James S. (University of Southern California, Los Angeles) and Milo D. Appleman. Degradation of ergothioneine by cell-free extracts of Alcaligenes faecalis. II. Production of glutamic acid. J. Bacteriol. 85:654–657. 1963.—On the basis of oxidation and paper chromatographic procedures, glutamic acid was identified as the end product of ergothioneine degradation by cell-free extracts of Alcaligenes faecalis. Hydrogen sulfide and ammonia yields were determined. Several differences between the metabolism of whole cells and cell-free extracts were noted. Cleavage of the imidazole ring by cell-free extracts appeared to be hydrolytic rather than oxidative.
PMCID: PMC278197  PMID: 14042946
19.  Unbalanced growth and macromolecular synthesis in Streptococcus mutans FA-1. 
Infection and Immunity  1976;13(3):941-948.
The continued synthesis of deoxyribonucleic acid, protein, cell wall peptidoglycan and intracellular iodophilic polysaccharide (IPS) by Streptococcus mutans strain FA-1 after several treatments intended to inhibit protein synthesis was studied. Exponential-phase cultures were: (i) simultaneously deprived of two required amino acids (cystine and leucine) that are not present in the cell wall peptidoglycan of this species; (ii) depreived of required amino acids (lysine or glutamate plus glutamine ) that are present in both peptidoglycan and protein; or (iii) treated with tetracycline. Each of these three types of treatment was accompanied by a different pattern of unbalanced growth. The patterns of unbalanced growth that accompanied treatments (i) or (ii) differed substantially from the patterns observed previously for Streptococcus faecalis ATCC 9790, a noncariogenic organism that does not contain IPS. In contrast to S. faecalis 9790, S. mutans FA-1 failed to accumulate peptidoglycan and thicken its wall when deprived of non-wall amino acids. Instead, S. mutans FA-1 continued to accumulate IPS to levels substantially higher than those found in exponential-phase cells. Again, in contrast to S. faecalis, S. mutans FA-1 failed to autolyze upon deprivation of essential precursors of wall peptidoglycan. Under conditions of lysine of glutamate/glutamine deprivation, S. mutans FA-1 continued to accumulate IPS to very high levels. Treatment with tetracycline did result in peptidoglycan accumulation and wall thickening in a manner very similar to that observed previously for inhibition of protein synthesis in S. faecalis. Realtively little IPS synthesis continued after tetracycline treatment. Accumulation of IPS appeared to occur when both ribonucleic acid and peptidoglycan synthesis were severely inhibited. The observations are discussed in terms of the survival of cariogenic organisms in the oral environment.
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PMCID: PMC420698  PMID: 1270138
20.  Microbial Fermentation of Rice Straw: Nutritive Composition and In Vitro Digestibility of the Fermentation Products 
Applied Microbiology  1975;29(4):510-514.
Rice straw was fermented with Cellulomonas sp. and Alcaligenes faecalis. Microbial cells and undigested residue, as well as chemically treated (NaOH or NH4OH) and untreated straws, were analyzed for nutrient composition and in vitro digestibility. In a typical fermentation, 75% of the rice straw substrate was digested, and 18.6% of the total substrate weight that disappeared was recovered as microbial protein. The microbial cell fraction was 37% protein and 5% crude fiber; the residue was 12% protein and 45% crude fiber. The microbial protein amino acid profile was similar to alfalfa, except for less cysteine. The microbial cells had more thiamine and less niacin than Torula yeast. In vitro digestibility of the microbial protein was 41.2 to 55%; that of cellulose was 52%.
PMCID: PMC187016  PMID: 804853
21.  Cloning, nucleotide sequence, and expression in Escherichia coli of the gene for poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis. 
Journal of Bacteriology  1989;171(1):184-189.
The extracellular poly(3-hydroxybutyrate) depolymerase gene from Alcaligenes faecalis T1 was cloned into Escherichia coli DH1 by using the plasmid pUC8. An A. faecalis T1 genomic library was prepared in E. coli from a partial Sau3AI digest and screened with antibody against the depolymerase. Of the 29 antibody-positive clones, 1 (pDP14), containing about 4 kilobase pairs of A. faecalis T1 DNA, caused expression of a high level of depolymerase activity in E. coli. The enzyme purified from E. coli was not significantly different from the depolymerase of A. faecalis in molecular weight, immunological properties, peptide map, specific activity, or substrate specificity. Most of the expressed enzyme was found to be localized in the periplasmic space of E. coli, although about 10% of the total activity was found in the culture medium. Results of a deletion experiment with pDP14 showed that a large SalI fragment of about 2 kilobase pairs was responsible for expression of the enzyme in E. coli. The nucleotide sequence of the large SalI fragment has been determined. Comparison of the deduced amino terminus with that obtained from sequence analysis of the purified protein indicated that poly(3-hydroxybutyrate) depolymerase exists as a 488-amino-acid precursor with a signal peptide of 27 amino acids.
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PMCID: PMC209571  PMID: 2644188
22.  Replacement of Lysine by Hydroxylysine and Its Effects on Cell Lysis in Streptococcus faecalis 
Journal of Bacteriology  1965;90(3):575-588.
Shockman, Gerald D. (Temple University, Philadelphia, Pa.), J. Stuart Thompson, and Margaret J. Conover. Replacement of lysine by hydroxylysine and its effects on cell lysis in Streptococcus faecalis. J. Bacteriol. 90:575–588. 1965.—Hydroxylysine was not significantly incorporated by Streptococcus faecalis ATCC 9790 or 8043 until exponential growth ceased as a result of lysine exhaustion. Uptake was then rapid and virtually complete within 1 hr. Lysine absence, rather than physiological age, seemed to be the governing factor. Hydroxylysine uptake rapidly reached a peak in the acid-soluble fraction, suggesting a precursor role for substances in this fraction. Substitution of hydroxylysine for lysine was much more efficient in mucopeptide synthesis than in protein synthesis. In wall medium, less than 1% of the incorporated hydroxylysine was found in the protein fraction. Addition of lysine to both growth and wall media inhibited both further hydroxylysine uptake and transfer of hydroxylysine from acid-soluble to mucopeptide or protein fractions. Hydroxylysine resulted in decreased penicillin susceptibility only after it was postexponentially incorporated. This effect was physiologically similar to that seen after threonine deprivation or chloramphenicol treatment. Hydroxylysine incorporation increased resistance to autolysis, but failed to decrease lysozyme susceptibility when measured after heat inactivation of autolysis. Electron microscopy of negatively stained cells showed increased thickness of cell walls containing hydroxylysine. Thus, most of the effects of replacement of lysine by hydroxylysine resemble those seen after deprivation of a nonwall amino acid (e.g., threonine or valine) or after chloramphenicol treatment. Each of these conditions results in inhibition of protein synthesis while permitting cell-wall synthesis to continue, resulting in autolysis-resistant, thick-walled cells.
PMCID: PMC315694  PMID: 16562051
23.  Biochemical and molecular characterization of the Pseudomonas lemoignei polyhydroxyalkanoate depolymerase system. 
Journal of Bacteriology  1995;177(3):596-607.
Pseudomonas lemoignei has five different polyhydroxyalkanoate (PHA) depolymerase genes (phaZ1 to phaZ5), which encode the extracellularly localized poly(3-hydroxybutyrate) (PHB) depolymerases C, B, and D, poly(3-hydroxyvalerate) (PHV) depolymerase, and PHB depolymerase A, respectively. Four of the five genes (phaZ1 to phaZ4) have been cloned, and one of them (phaZ1) was studied in detail earlier (D. Jendrossek, B. Müller, and H. G. Schlegel, Eur. J. Biochem. 218:701-710, 1993). The fifth PHA depolymerase gene (phaZ5) was identified by colony hybridization of recombinant Escherichia coli clones with a phaZ5-specific oligonucleotide. The nucleotide sequence of a 3,704-bp EcoRI fragment was determined and found to contain two large open reading frames (ORFs) which coded for a polypeptide with significant similarities to glycerol-3-phosphate dehydrogenases of various sources (313 amino acids; M(r), 32,193) and for the precursor of PHB depolymerase A (PhaZ5; 433 amino acids; M(r), 44,906). The PHV depolymerase gene (phaZ4) was subcloned, and the nucleotide sequence of a 3,109-bp BamHI fragment was determined. Two large ORFs (ORF3 and ORF4) that represent putative coding regions were identified. The deduced amino acid sequence of ORF3 (134 amino acids; M(r), 14,686) revealed significant similarities to the branched-chain amino acid aminotransferase (IlfE) of enterobacteria. ORF4 (1,712 bp) was identified as the precursor of a PHV depolymerase (567 amino acids; M(r), 59,947). Analysis of primary structures of the five PHA depolymerases of P. lemoignei and of the PHB depolymerases of Alcaligenes faecalis and Pseudomonas pickettii revealed homologies of 25 to 83% to each other and a domain structure: at their N termini, they have typical signal peptides of exoenzymes. The adjacent catalytic domains are characterized by several conserved amino acids that constitute putative catalytic triads which consist of the consensus sequence of serine-dependent hydrolases including the pentapeptide G-X-S-X-G, a conserved histidine and aspartate, and a conserved region resembling the oxyanion hole of lipases. C terminal of the catalytic domain an approximately 40-amino-acid-long threonine-rich region (22 to 27 threonine residues) is present in PhaZ1, PhaZ2, PhaZ3, and PhaZ5. Instead of the threonine-rich region PhaZ4 and the PHB depolymerases of A. faecalis and P. pickettii contain an approximately 90-amino-acid-long sequence resembling the fibronectin type III module of eucaryotic extracellular matrix proteins. The function of the fibronectin type III module in PHA depolymerases remains obscure. Two types of C-terminal sequences apparently represent substrate-binding sites; the PHB type is present in the PHB depolymerases of A. faecalis and P. pickettii and in PhaZ2, PhaZ3, and PhaZ5 and the PHV type is present in the PHV-hydrolyzing depolymerases (PhaZ4 and PhaZ1). phaZ1 was transferred to A. eutrophus H16 and JMP222. All transconjugants of both strains were able to grow with extracellular PHB as a carbon source and produced translucent halos on PHB-containing solid media. PhaZ1, PhaZ2, PhaZ4, and PhaZ5 were purified from P. lemoignei and from recombinant E. coli; the processing sites of the precursors in E. coli were the same as in P. lemoignei, and similar substrate specificities were determined for the wild-type and the recombinant proteins. All PHA depolymerases hydrolyzed PHB at high specific activities. PhaZ1 and PhaZ4 additionally cleaved PHV, and PhaZ4 hydrolyzed poly(4-hydroxybutyrate). None of the depolymerases was able to hydrolyze polyactide or PHA consisting of monomers with more than five carbon atoms. While the wild-type depolymerase proteins were glycosylated and found to contain glucose and N-acetylglucosamine, none of the recombinant proteins was glycosylated. PHB hydrolysis was dependent on divalent cations such as Ca2+ and was inhibited by the presence of EDTA.
PMCID: PMC176633  PMID: 7836292
24.  Excretion of Lipoteichoic Acid by Group A Streptococci 
Journal of Clinical Investigation  1978;61(3):671-677.
Group A streptococci were grown in the presence of [2-3H]glycerol. Concentrated suspensions of the labeled organisms were incubated with and without penicillin. [3H]Glycerol-labeled material accumulated in the supernates in increasing amounts with increasing concentrations of penicillin, ranging from 0 to 50 U/ml. The excretion of labeled material occurred in the absence of nucleic acid synthesis or bacteriolysis indicating that the phenomenon is independent of cell multiplication or decay. The accumulation of label was paralleled by an accumulation of erythrocyte-sensitizing material measured by passive hemagglutination tests for lipoteichoic acid antigen, indicating that a portion of the labeled material possessed the properties of lipoteichoic acid. Culture supernates were fractionated by column chromatography, and the materials obtained were analyzed by electrophoresis on sodium dodecyl sulfate polyacrylamide, thin-layer chromatography, and paper chromatography. The ability of the same materials to bind to human erythrocytes and epithelial cells was tested. The culture supernate contained lipoteichoic acid, deacylated lipoteichoic acid, glycerol phosphate, and free glycerol. Penicillin caused an increase in the amounts of each of the excreted materials. Streptococci that were stimulated with penicillin to lose their lipoteichoic acid (previously shown to mediate adherence of group A streptococci) lost their ability to adhere to buccal mucosal cells, suggesting that penicillin may influence bacterial ecology by mechanisms other than killing sensitive organisms.
PMCID: PMC372580  PMID: 346604
25.  Penicillin-netilmicin synergism against Streptococcus faecalis. 
The combination of penicillin plus netilmicin was synergistic in vitro against 28 strains of Streptococcus faecalis and compared favorably with penicillin in combination with gentamicin. Similarly, penicillin plus netilmicin was as effective as penicillin plus gentamicin in the therapy of 67 rabbits with enterococcal endocarditis produced with a streptomycin-susceptible (S) or a streptomycin-resistant (R) strain of S. faecalis. After 5 days of infection, control rabbits had bacterial titers of 10(10) colony-forming units (CFU)/g of vegetation. Those treated with penicillin plus netilmicin had mean titers of 10(5.2) and 10(5.1) CFU/g for S and R strains, respectively, and those treated with penicillin plus gentamicin had mean valve titers of 10(5.8) CFU/g for both strains. After 10 days of therapy, mean valve titers with penicillin plus netilmicin were 10(3.8) and 10(4.7) CFU/g, and with penicillin plus gentamicin they were 10(4.5) and 10(5.4) CFU/g for S and R strains, respectively. Thus, if netilmicin proves to be less toxic than other aminoglycoside antibiotics, it may have potential usefulness in the therapy of enterococcal endocarditis.
PMCID: PMC352259  PMID: 122522

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