Control of diaminopimelate decarboxylase by L-lysine during growth and sporulation of Bacilluscereus

Effect of Water Activity on Conidia Germination in Aspergillus flavus

In this study, we explored the mechanism underlying Aspergillus flavus conidia germination inhibited by decreased water activity. The impact of low water activity was analyzed at 4 h, 8 h and 12 h. Additionally, we demonstrated that low water activity affected cell shape and decreased cell sizes. Transcriptomics found numerous differentially expressed genes (DEGs) during the first 12 h of germination, with 654 DEGs observed among 4 h, 8 h and 12 h. In particular, more DEGs were detected at 8 h of germinating. Therefore, proteomics was performed at 8 h, and 209 differentially expressed proteins (DEPs) were speculated, with 94 up-regulated and 115 down-regulated. Combined analysis of KEGG of transcriptomics and proteomics demonstrated that the dominant pathways were nutrient metabolism and translation. We also found several DEGs and DEPs in the Mitogen Activated Protein Kinase (MAPK) pathway. Therefore, we concluded that low water activity inhibited conidia germination, causing unregular morphology. In addition, low water activity influenced expression of creA, TreB in carbohydrate metabolism, Clr4, RmtA in amino acid metabolism and RPL37, RPL3 in translation in Aspergillus flavus.

Drought-induced soil microbial amino acid and polysaccharide change and their implications for C-N cycles in a climate change world

High microbial carbon (MBC) demand, a proxy for energy demand (cost), during soil microbial response to stressors such as drought are a major gap in understanding global biogeochemical cycling of carbon (C) and nitrogen (N). The dynamics of two dominant microbial pools (amino acids; AA and exopolymeric substances; EPS) in soils exposed to drying and C and N amendment to mimic both low and high nutrient soil habitats were examined. It was hypothesized that dynamics of EPS and AA (osmolytes) would be greater when soil drying was preceded by a pulse of bioavailable C and N. Drying reduced AA content, even as overall soil MBC increased (~35%). The increase in absolute amounts and mol% of certain AA (eg: Taurine, glutamine, tyrosine, phenylalanine) in the driest treatment (−10 MPa) were similar in both soils regardless of amendment suggesting a common mechanism underlying the energy intensive acclimation across soils. MBC and EPS, both increased ~1.5X and ~3X due to drying and especially drying associated with amendment. Overall major pools of C and N based microbial metabolites are dynamic to drying (drought), and thus have implications for earth’s biogeochemical fluxes of C and N, perhaps costing 4–7% of forest fixed photosynthetic C input during a single drying (drought) period.

Establishing a Multivariate Model for Predictable Antisense RNA-Mediated Repression

Recent advances in our understanding of RNA folding and functions have facilitated the use of regulatory RNAs such as synthetic antisense RNAs (asRNAs) to modulate gene expression. However, despite the simple and universal complementarity rule, predictable asRNA-mediated repression is still challenging due to the intrinsic complexity of native asRNA-mediated gene regulation. To address this issue, we present a multivariate model, based on the change in free energy of complex formation (Δ G_CF) and percent mismatch of the target binding region, which can predict synthetic asRNA-mediated repression efficiency in diverse contexts. First, 69 asRNAs that bind to multiple target mRNAs were designed and tested to create the predictive model. Second, we showed that the same model is effective predicting repression of target genes in both plasmids and chromosomes. Third, using our model, we designed asRNAs that simultaneously modulated expression of a toxin and its antitoxin to demonstrate tunable control of cell growth. Fourth, we tested and validated the same model in two different biotechnologically important organisms: Escherichia coli Nissle 1917 and Bacillus subtilis 168. Last, multiple parameters, including target locations, the presence of an Hfq binding site, GC contents, and gene expression levels, were revisited to define the conditions under which the multivariate model should be used for accurate prediction. Together, 434 different strain-asRNA combinations were tested, validating the predictive model in a variety of contexts, including multiple target genes and organisms. The result presented in this study is an important step toward achieving predictable tunability of asRNA-mediated repression.

Bacterial growth inhibition by amniotic fluid. VI. Evidence for a zinc-peptide antibacterial system

The zinc bacterial inhibitory activity of amniotic fluid is dependent on the presence of a second, organic component contained in amniotic fluid. The second component is heat stable, resists proteolytic digestion, and is present in amniotic fluid throughout pregnancy. Further, the component may be a peptide with a molecular weight of less than 5,000 daltons. Phosphate reversal of amniotic fluid inhibitory activity may result from interference with the organic component rather than zinc.

Regulation of dihydrodipicolinate synthase during growth and sporulation of Bacillus cereus

A four- to sixfold increase in specific activity of dihydrodipicolinic acid synthase was observed during sporulation of Bacillus cereus. The enzyme from cells harvested before and after the increase in specific activity appeared to be very similar as judged by pH optima, heat denaturation kinetics, apparent Michaelis constants, chromatography on diethylaminoethyl-cellulose and Sephadex G-200, and polyacrylamide gel electrophoresis. Studies with various combinations of amino acids and one of the enzyme substrates, pyruvate, failed to give evidence for control of the enzyme by activation, inhibition, repression, induction, or stabilization. Omission of calcium from the sporulation medium had no significant effect on the specific activity pattern of the enzyme as a function of age of culture.

Control of lysine biosynthesis in Bacillus subtilis: inhibition of diaminopimelate decarboxylase by lysine

Diaminopimelate decarboxylase has been characterized in extracts of Bacillus subtilis and resolved from aspartokinases I and II. Under certain conditions, the enzyme is specifically inhibited by physiological concentrations of L-lysine, but less specificity and altered kinetics of inhibition are observed if lower ionic strengths are employed in the assay procedure. Diaminopimelate decarboxylase can be desensitized to lysine inhibition by either lowering the pH or diluting the enzyme in Tris buffer in the absence of pyridoxal phosphate. Evidence is presented to incidate that, under proper conditions, lysine inhibition involves an interaction of the amino acid with the enzyme rather than competition for available pyridoxal phosphate in the assay. Lysine, by affecting the level of meso-diaminopimelate, may thus regulate its biosynthesis through sequential feedback inhibition. Analysis of the diaminopimelate decarboxylase of 15 revertants of mutants that had originally lacked diaminopimelate decarboxylase activity indicates that as little as 5% of the specific activity of enzyme observed in the wild-type strain is sufficient to permit normal growth rates. In the growing cell, diaminopimelate decarboxylase may therefore exist largely in an inhibited state.

Inactivation of aspartic transcarbamylase in sporulating Bacillus subtilis: demonstration of a requirement for metabolic energy

The aspartic transcarbamylase (ATCase) activity of Bacillus subtilis cells disappears rapidly from stationary-phase cells prior to sporulation. ATCase activity does not appear in the culture fluid during the stationary phase; hence the enzyme appears to be inactivated in the cells. The enzyme is inactivated normally in two different mutants lacking proteases; the activity is very stable in crude extracts of cells or in the culture fluid. These results suggest that ATCase is not inactivated by the general proteolysis that occurs in sporulating bacteria. The inactivation of ATCase can be completely inhibited after it has begun by oxygen starvation or addition of fluoroacetate. Inhibitors of oxidative phosphorylation and electron transport also interrupt the inactivation of ATCase. The inactivation of ATCase is very slow in two mutant strains that are deficient in enzymes of tricarboxylic acid cycle. Addition of gluconate to stationary cultures of the mutant strains, which is known to restore depleted adenosine 5'-triphosphate pools in these bacteria, also restores inactivation of ATCase. These experiments support the conclusion that the generation of metabolic energy is necessary for the inactivation of ATCase in stationary cells. ATCase activity is stable in growing cells in which ATCase synthesis is repressed by addition of uracil; the enzyme is inactivated normally, however, when such cells cease growing.

Isotopic study of control of the lysine biosynthetic pathway during sporulation of Bacillus cereus

The extent of incorporation of aspartate into dipicolinic acid and into various amino compounds was determined in Bacillus cereus at various times before, during, and near the end of synthesis of dipicolinic acid. The purpose of this study was to gain further information on the in vivo control of the biosynthesis of amino acids derived from aspartate. Control of the lysine biosynthetic pathway was of particular interest with regard to sporulation, owing to the important role of diaminopimelate and dipicolinate in the structure of the spore. As synthesis of dipicolinate was initiated, incorporation of carbon derived from aspartate was funneled preferentially into this compound as compared with others of the aspartate group. Incorporation into lysine essentially stopped just before the synthesis of dipicolinate began. This is consistent with the previously observed disappearance at this time of diaminopimelic acid decarboxylase in cell-free extracts. Synthesis of diaminopimelate continued during the time of synthesis of dipicolinate. The previous suggestion that diaminopimelate might exert negative control on one of the enzymes between dihydrodipicolinate and diaminopimelate is thus considered unlikely. The possibility is discussed that synthesis of dipicolinate is favored by an increase in the rate of synthesis of dihydrodipicolinate rather than by a block in its rate of utilization.