EXCRETION AND DEGRADATION OF RIBONUCLEIC ACID BY BACILLUS SUBTILIS

Professor Arnold L. (Arny) Demain's historical position in the rise of industrial microbiology and biotechnology

This perspective text focuses on the pivotal role and historical position that the late Prof. Arnold L. (Arny) Demain has taken since the 1950s in the rise and impact of the field of industrial microbiology and biotechnology. His drive toward academic research with industrial potential-first at Merck & Co. and later at MIT-, his feeling for establishing cordial personal contacts with his students and postdocs (Arny's Army) and his ability for worldwide networking are outlined here, intertwined with the author's personal experiences and impressions. His scientific output is legendary as to research papers, comprehensive reviews, books, and lectures at conferences worldwide. Some of his research experiences in industry and academia are mentioned in a historical context as well as his relentless efforts to advocate the importance and impact of industrial microbiology and biotechnology as an essential green technology for our planet Earth.

Nucleobase-containing compounds evoke behavioural, olfactory, and transcriptional responses in model fishes

The sensory system of animals detects a massive and unknown array of chemical cues that evoke a diversity of physiological and behavioural responses. One group of nitrogen-containing carbon ring chemicals—nucleobases—are thought to be involved in numerous behaviours yet have received little attention. We took a top-down approach to examine responses evoked by nucleobases at behavioural, tissue, and gene expression levels. Fish generally avoided nucleobases, and this behaviour, when observed, was driven by purines but not pyrimidines. At the tissue level, olfactory neuron generator potential responses tended to be concentration specific and robust at concentrations lower than amino acid detection ranges. In terms of gene expression, more than 2000 genes were significantly upregulated following nucleobase exposure, some of which were expected (e.g., genes involved in purine binding) and some of which were not (e.g., tubulin-related genes). Humanized RNA pathway analysis showed that we had exposed the animal to a nucleobase. Our data indicate that responses to nucleobase-containing compounds may be highly structure based and are evident from changes in behaviour to mRNA expression. Many of these responses were surprising, and all provide numerous routes for further research endeavour.

Production of guanosine-5'-monophosphate and inosine-5'-monophosphate by fermentation

A biotin-requiring coryneform bacterium which produces glutamic acid was mutated to adenine dependency. The adenine-requiring strain, which excreted insoine-5'-monophosphate (IMP), was further mutated to xanthine dependency. As expected, IMP was also excreted by this mutant. The mutant strain was reverted to xanthine independence in an attempt to obtain a culture with an altered IMP dehydrogenase which would be less sensitive to feedback inhibition by guanosine-5'-monophosphate (GMP). A revertant was obtained which produced GMP and IMP, each at 0.5 g per liter. The reversion to xanthine independence had resulted in a concomitant requirement for isoleucine, leucine, and valine. Further mutation to increased nutritional requirements led to culture MB-1802, which accumulated 1 g per liter each of GMP and IMP. Both nucleotides were isolated in pure form. The concentrations of GMP and IMP produced by MB-1802 were four times that of cytidylate, uridylate, or adenylate, indicating that the mechanism of GMP and IMP production was direct and not via ribonucleic acid breakdown.

Bioavailability of dissolved organic nitrogen in treated effluents

The research objective was to assess dissolved organic nitrogen (DON) bioavailability in wastewater effluents from a pilot-scale nitrification plant and a laboratory-scale total nitrogen (TN) removal plant. The DON bioavailability was assessed using a 14-day bioassay protocol containing bacterial and algal inocula. Nitrogen species, dissolved organic carbon, chlorophyll a, and biomass (as total suspended solids and culturable cell counts) concentrations were measured to assess DON bioavailability. The results showed an increase in algal chlorophyll a concentration, with a concurrent increase in algal biomass over time; increased bacterial counts and a decrease in DON concentration over time; and increased carbon-to-nitrogen ratio at the end of the 14-day bioassay, indicating effluent DON bioavailability to algae and bacteria. Approximately 18 to 61% of the initial DON in low-total-nitrogen wastewater effluent (TN = 4 to 5 mg/L) sample was bioavailable. The results show that bacteria and algae uptake and release DON during their growth.

ATR-FTIR spectroscopy reveals bond formation during bacterial adhesion to iron oxide

The contribution of various bacterial surface functional groups to adhesion at hematite and ZnSe surfaces was examined using attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. When live Shewanella oneidensis, Pseudomonas aeruginosa, and Bacillus subtilis cells were introduced to a horizontal hematite (alpha-Fe(2)O(3))-coated internal reflection element (IRE), FTIR peaks emerged corresponding to bacterial phosphate group binding. These IR peaks were not observed when bacteria were introduced to the uncoated ZnSe IRE. When cells were added to colloidal suspensions of alpha-Fe(2)O(3) at pH 7, spectra included peaks corresponding to P-OFe and nu(COOH), the latter being attributed to bridging of carboxylate at mineral surface OH groups. Selected model organic compounds with P-containing functionalities (phenylphosphonic acid [PPA], adenosine 5'-monophosphate [AMP], 2'-deoxyadenyl(3'-->5')-2'-deoxyadenosine [DADA], and deoxyribonucleic acid [DNA]) produce spectra with similar peaks corresponding to P-OFe when adsorbed to alpha-Fe(2)O(3). The data indicate that both terminal phosphate/phosphonate and phosphodiester groups, either exuded from the cell or present as surface biomolecules, are involved in bacterial adhesion to Fe-oxides through formation of innersphere Fe-phosphate/phosphonate complexes.

Adhesion of bacterial exopolymers to alpha-FeOOH: inner-sphere complexation of phosphodiester groups

Extracellular polymeric substances (EPS) constitute a heterogeneous mixture of polyelectrolytes that mediate biomineralization and bacterial adhesion and stabilize biofilm matrixes in natural and artificial environments. Although nucleic acids are exuded extracellularly and are purported to be required for biofilm formation, direct evidence of the active mechanism is lacking. EPS were extracted from both Bacillus subtilis (a gram-positive bacterium) and Pseudomonas aeruginosa (a gram-negative bacterium) and their interaction with the goethite (alpha-FeOOH) surface was studied using attenuated total internal reflection infrared spectroscopy. Correspondence between spectral data and quantum chemical calculations demonstrate that phosphodiester groups of nucleic acids mediate the binding of EPS to mineral surfaces. Our data indicate that these groups emerge from the EPS mixture to form monodentate complexes with Fe centers on the goethite (alpha-FeOOH) surface, providing an energetically stable bond for further EPS or cell adhesion.

Pickles, Pectin, and Penicillin

My professional life has been devoted to the study of microbial products and their biosynthesis, regulation, and overproduction. These have included primary metabolites (glutamic acid, tryptophan, inosinic acid, guanylic acid, vitamin B(12), riboflavin, pantothenic acid, ethanol, and lactic acid) and secondary metabolites (penicillin, cephalosporins, streptomycin, fosfomycin, gramicidin S, rapamycin, indolmycin, microcin B17, fumagillin, mycotoxins, Monascus pigments, and tetramethylpyrazine). Other areas included microbial nutrition, strain improvement, bioconversions of statins and beta-lactams, sporulation and germination, plasmid stability, gel microdroplets, and the production of double-stranded RNA, the polymer xanthan, and enzymes (polygalacturonase, protease, cellulase). Most of the studies were carried out with me by devoted and hardworking industrial scientists for 15 years at Merck & Co. and by similarly characterized students, postdoctorals, and visiting scientists during my 32 years at the Massachusetts Institute of Technology. I owe much of my success to my mentors from academia and industry. My recent research activities with undergraduate students at the Charles A. Dana Research Institute for Scientists Emeriti (R.I.S.E.) at Drew University have been very rewarding and are allowing me to continue my career.

Association of Actinobacillus actinomycetemcomitans leukotoxin with nucleic acids on the bacterial cell surface

Actinobacillus actinomycetemcomitans, a periodontopathic gram-negative bacterium, produces a leukotoxin that is a member of the RTX cytotoxin family. Although genes may function in toxin secretion, the leukotoxin is not secreted extracellularly but remains associated with the bacterial cell surface. We report here that this toxin-cell surface association is mediated by nucleic acids and directly demonstrate that the extracellular secretion of toxin occurs in growing cultures with increased ionic strength of medium. All examinations were performed with freshly harvested A. actinomycetemcomitans 301-b from anaerobic fructose-limited chemostat cultures. The occurrence of cell surface-localized DNA was shown by directly digesting whole cells with the restriction endonuclease EcoRI or HindIII, which yielded many DNA fragments. The cell surface DNA constituted about 20% of the total cellular DNA. The leukotoxin was released from the whole cells by digestion with DNase I as well as restriction endonucleases. Because the leukotoxin binds ionically to DNA, it is dependent on the ionic strength of buffers or media. Accordingly, the toxin was released from cells suspended in saline at pH 7.5 in the presence of increasing amounts of MgCl2 (0 to 10 mM) or NaCl (0 to 50 mM). Moreover, a considerable quantity of leukotoxin was detected in the culture supernatant of fructose-limited chemostat cultures when sodium succinate solution was pumped into the steady state as an additional salt (30 and then 50 mM). This toxin-DNA association was also found in well-characterized strains including not only the leukotoxin-producing ATCC 29522 but also the toxin production-variable ATCC 29523 and the non-leukotoxin-producing ATCC 33384 when these strains were grown in the chemostat culture.

Inhibition of the plaquing efficiency of T4r+ bacteriophage by subtilisin

The mechanism by which the replicative cycle of T4r(+) phage is inhibited by certain nonhost bacterial systems was investigated. Some Bacillaceae, especially Bacillus subtilis, decreased the plaquing efficiency of this virus more than 95% within 24 hr of exposure. Sarcina lutea and Micrococcus sp. both failed to cause any significant change in the infectivity of T4r(+) phage. Preliminary investigations into the nature of the inhibitory substance(s) suggested that an extracellularly elicited protein was at least partially responsible for this effect. Further analysis has implicated subtilisin, an exoprotease from B. subtilis, as the cause of some, if not all, of the observed decrease in plaquing efficiency. Gel-filtration chromatography of control and treated (14)C-labeled T4r(+) phage showed a wide dispersal of phage-specific material of these particles after 24 hr of exposure to pure subtilisin or to expended medium exoprotease from B. subtilis. It was concluded that B. subtilis exoprotease is capable of chemically altering the structure of the phage capsid, thus causing a decrease in its plaquing efficiency.

Spontaneous transformation in Bacillus subtilis

Cultures ofBacillus subtilisrelease transforming DNA during the early exponential and stationary phases of growth. The pattern of release of transforming DNA was followed by measuring transformation in a system consisting of a non-transformable DNA donor and a differently marked transformable recipient. Transformation in this system seems to be at least as efficient as that induced by purified DNA. Fluorescence microscopy revealed that released DNA remained bound extracellular to intact cells. The release of DNA during early exponential growth seemed to be correlated with the cells' proneness to lysis; both DNA release and cell lysis were inhibited by chloramphenicol. In stationary cells, the release of DNA was neither correlated with a similar proneness to lysis nor inhibited by chloramphenicol.

Phosphohydrolases of a Bacillus subtilis mutant accumulating inosine and hypoxanthine

Although adenine-requiring auxotrophs of Bacillus subtilis accumulate large quantities of inosine or hypoxanthine, or of both, they do not accumulate inosine-5'-monophosphate (IMP). Experiments directed at understanding this phenomenon were conducted with an adenineless auxotroph and with a mutant derived from it which lacked alkaline phosphohydrolase. It was found that B. subtilis contains four different phosphohydrolases. Only one is an extracellular enzyme; it is a 5'-nucleotide phosphohydrolase which can be inhibited by addition of CuSO(4) to the medium. Of the three cellular enzymes, only one, an acid phosphohydrolase, cannot attack 5'-nucleotides; this enzyme is not repressed by inorganic phosphate. One of the two remaining surface-bound enzymes is a nonspecific alkaline phosphohydrolase which attacks both 5'-nucleotides and p-nitrophenyl phosphate; this is the only phosphohydrolase that is markedly repressed by inorganic phosphate. The other surface-bound enzyme is a nonrepressible 5'-nucleotide phosphohydrolase with double pH optima: one at neutrality and the other near pH 9.0. The experiments indicate that the absence of IMP in the extracellular broth is due to degradation of internally accumulated IMP to inosine by the cellular 5'-nucleotide phosphohydrolase.

Molecular sieving by Neurospora cell walls during secretion of invertase isozymes

Trevithick, John R. (University of Wisconsin Medical School, Madison), and Robert L. Metzenberg. Molecular sieving by Neurospora cell walls during secretion of invertase isozymes. J. Bacteriol. 92: 1010-1015. 1966.-The secretion of invertase by young mycelia of Neurospora was studied. The process of secretion was found to be dependent upon growth. The results indicate that fractionation of light invertase, the monomer, from heavy invertase, the aggregated form, occurs at the cell wall. Neurospora strains wild type, crisp, osmotic, and the double mutant crisp osmotic were tested. An inverse relation exists between the fraction of the total invertase activity of the culture which the mold secretes into the medium and the degree of fractionation, defined as the ratio of the fraction of the invertase secreted into the medium that is light invertase to the fraction of the invertase remaining associated with the cells that is light invertase. The hypothesis is offered that the increased secretion of invertase and decreased degree of fractionation seen in osmotic mutants, and to a lesser extent in the other mutants, can be explained by an increased porosity of the cell wall.

Death of Bacillus subtilis Auxotrophs Due to Deprivation of Thymine, Tryptophan, or Uracil

Pritikin, William B. (University of California, Los Angeles), and W. R. Romig . Death of Bacillus subtilis auxotrophs due to deprivation of thymine, tryptophan, or uracil, J. Bacteriol. 92: 291–296. 1966.—Auxotrophic mutants of Bacillus subtilis 168 that require either tryptophan, uracil, or thymine died rapidly when deprived of any of these compounds. Phage PBS1 was produced by infected B. subtilis 168 ( thy try-2 ) deprived of thymine. Phage PBS1 was not produced by infected B. subtilis 168 ( try-2 ) deprived of tryptophan or infected B. subtilis 168-15 ( try-2 ura ) deprived of uracil. B. subtilis 168 thy try-2 and 168-15 could be transduced by phage PBS1 after prolonged deprivation of tryptophan or uracil, respectively. When B. subtilis 168-15 was transduced to uracil independence by phage PBS1, the uracil-independent transductants became immune to uracil-less death within 10 min of exposure to phage, and began to multiply within 2 hr after exposure to phage at an incubation temperature of 46 C.

Biochemical and physical changes in shaken suspensions of Pasteurella pestis

Pasteurella pestis, harvested after 24 to 30 hr of growth in a casein hydrolysate medium at 26 C, was resuspended and shaken in 3% lactose-0.1 m phosphate buffer for 4 hr at the same temperature. Certain characteristics of these starved cells were compared with those of control cells. No differences in the amounts of cellular carbohydrate or lipid were detected. The concentrations of the principal free amino acids were greater in the shaken cells, except that they contained no measureable arginine, and the normally large pools of intracellular tricarboxylic acid cycle intermediates were reduced. Greater viable-cell counts resulted with the cells that were shaken in lactose buffer than with the control cells when each was incubated at 5 C for several weeks. However, the reduced viabilities were apparent losses caused by the formation of aggregates of cells. The clumping of cells was caused by the polymerization of extracellular nucleic acids, principally deoxyribonucleic acid, that were excreted by the cells. Cell clumping could be partially prevented by prior shaking of the suspended cells, which removed some of the deleterious material, or by the action of crystalline deoxyribonuclease.

Influence of glutamic acid on the endogenous respiration of Bacillus subtilis

Clifton, C. E. (Stanford University, Stanford, Calif.), and John Cherry. Influence of glutamic acid on the endogenous respiration of Bacillus subtilis. J. Bacteriol. 91:546-550. 1966.-Amino acids serve as the major initial endogenous substrate for Bacillus subtilis. The endogenous activity of freshly harvested washed cells is high and falls off rapidly with time of shaking at 30 C to lower but still significant levels. The rate of O(2) consumption after the addition of glutamic acid also decreases as the cells age, but more slowly than noted for endogenous respiration. When cells were fed glutamate as soon as possible after harvesting, an apparent stimulation of endogenous respiration was noted. However, endogenous activity was inhibited if the cell suspensions were shaken for at least 1 hr before addition of the glutamate. Similar results were obtained with glycerol or glucose as exogenous substrates. Variation in rates of respiration with age of the cells, inherent instability of B. subtilis, and possible utilization of substances initially excreted by the cells appear to account for the variations noted regarding the influence of an exogenous substrate on endogenous respiration.