A transcriptional and proteomic survey of Arachnocampa luminosa (Diptera: Keroplatidae) lanterns gives insights into the origin of bioluminescence from the Malpighian tubules in Diptera.

Fungus-gnats of the genus Arachnocampa are unique among bioluminescent insects for displaying blue-green bioluminescence, and are responsible for one of the most beautiful bioluminescence spectacles on the roofs of the Waitomo Caves. Despite morphological studies showing that Arachnocampa larval lanterns involve specialization of the Malpighian tubules, the biochemical origin of their bioluminescence remains enigmatic. Using a cDNA library previously constructed from lanterns of the New Zealand glowworm A. luminosa, we carried out the first transcriptional analysis of ~ 500 expressed sequence tags (ESTs) to identify putative candidate proteins for light production, and to better understand the molecular physiology of the lanterns and their relationship with Malpighian tubule physiology. The analysis showed an abundance of hexamerin-like proteins, as well as luciferase-like enzymes, indicating a possible critical role for these proteins in bioluminescence. These findings were corroborated by proteomic analysis of lantern extracts, which showed the presence of hexamerins and luciferase-like enzymes. Other gene products typical of Malpighian tubules, such as detoxifying enzymes, were also found. The results support the existence of an evolutionary link between Malpighian tubule detoxification and the origin of bioluminescence in these Diptera.

The Gonyaulax clock at 50: translational control of circadian expression.

The unicellular circadian clock of Gonyaulax polyedra (now renamed Lingulodinium polyedrum) has provided important insights concerning circadian rhythmicity. Many, perhaps most, of its key systems are circadian-controlled, ranging from bioluminescence and photosynthesis to motility, cell division, and the synthesis of many proteins, favoring the "master clock" concept. But different rhythms may have different free-running periods and different phase angles under different T cycles, observations not easily accommodated in a single oscillator model. Gonyaulax has a feature significantly different from that of other known systems, namely, that clock control of protein synthesis occurs at the translational level. With one mRNA, this involves a protein binding to a 22-nucleotide region in the 3'-untranslated region (3'UTR), but no similar regions have been found in other mRNAs. Pulses of protein synthesis inhibitors cause phase shifts, whereas inhibitors of protein phosphorylation administered chronically cause period changes. In Gonyaulax and other systems, low temperature results in arrhythmicity. A return to a permissive temperature results in a reinitiation of the rhythm, with the phase established by the time of increase, similar to the effect of bright light. Evidence for cellular communication via substance(s) in the medium has been obtained.

Members of a dinoflagellate luciferase gene family differ in synonymous substitution rates.

Regulation and evolution of dinoflagellate luciferases are of particular interest since the enzyme is structurally unique and bioluminescence is under circadian control. In this study, three new members of the dinoflagellate luciferase gene family were identified and characterized from Pyrocystis lunula. These genes, lcfA, lcfB, and lcfC, also exhibit the unusual structure and organization previously reported for the luciferase gene of a related dinoflagellate, Lingulodinium polyedrum: three repeated domains, each encoding an active catalytic site, multiple gene copies, and tandem organization. The histidine residues involved in the pH regulation of L. polyedrum luciferase activity, and implicated in the regulation of flashing, are also fully conserved in P. lunula. The interspecific conservation between the individual luciferase domains of P. lunula and L. polyedrum is higher than among domains intramolecularly, indicating that this unique gene structure arose through duplication events that occurred prior to the divergence of these dinoflagellates. However, P. lunula luciferase genes differ from L. polyedrum in several respects, notably, the occurrence of an intron in one gene (lcfC), a 2.25-kb intergenic region connecting lcfA and lcfB, and, of particular interest, an invariant rate of synonymous (silent) substitutions along the repeat domains, in contrast to L. polyedrum luciferase, where the occurrence of synonymous substitutions is practically absent in the central region of the domains.

Self-protection against cell wall hydrolysis in Streptococcus milleri NMSCC 061 and analysis of the millericin B operon.

Streptococcus milleri NMSCC 061 produces an endopeptidase, millericin B, which hydrolyzes the peptide moiety of susceptible cell wall peptidoglycan. The nucleotide sequence of a 4.9-kb chromosomal region showed three open reading frames (ORFs) and a putative tRNA(Leu) sequence. The three ORFs encode a millericin B preprotein (MilB), a putative immunity protein (MilF), and a putative transporter protein (MilT). The milB gene encodes a 277-amino-acid preprotein with an 18-amino-acid signal peptide with a consensus IIGG cleavage motif. The predicted protein encoded by milT is homologous to ABC (ATP-binding cassette) transporters of several bacteriocin systems and to proteins implicated in the signal-sequence-independent export of Escherichia coli hemolysin A. These similarities strongly suggest that the milT gene product is involved in the translocation of millericin B. The gene milF encodes a protein of 302 amino acids that shows similarities to the FemA and FemB proteins of Staphylococcus aureus, which are involved in the addition of glycine to a pentapeptide peptidoglycan precursor. Comparisons of the cell wall mucopeptide of S. milleri NMSCC 061(resistant to lysis by millericin B) and S. milleri NMSCC 051(sensitive) showed a single amino acid difference. Serial growth of S. milleri NMSCC 051 in a cell wall minimal medium containing an increased concentration of leucine resulted in the in vivo substitution of leucine for threonine in the mucopeptide of the cell wall. A cell wall variant of S. milleri NMSCC 051 (sensitive) that contained an amino acid substitution (leucine for threonine) within its peptidoglycan cross bridge showed partial susceptibility to millericin B. The putative tRNA(Leu) sequence located upstream of milB may be a cell wall-specific tRNA and could together with the milF protein, play a potential role in the addition of leucine to the pentapeptide peptidoglycan precursor and thereby, contributing to self-protection to millericin B in the producer strain.

N-terminal intramolecularly conserved histidines of three domains in Gonyaulax luciferase are responsible for loss of activity in the alkaline region.

Gonyaulax luciferase is a single-chain ( approximately 137 kDa) polypeptide comprising 111 N-terminal amino acids followed by three contiguous homologous domains (377 amino acids each). Each domain has luciferase activity, accounting for the earlier observation that proteolytic fragments ( approximately 35 kDa) of luciferase are active. The activity of the full-length native enzyme is maximal at pH 6.3, dropping to near zero at pH 8; the activity of fragments also peaks at pH 6.3 but remains high at 8. While the activity loss at higher pH might be thought to be associated with the conformation of the full-length protein, we show here that this is a property of individual domains. The three intramolecularly homologous domains, separately cloned and expressed in Escherichia coli as fusion proteins, exhibit pH-activity curves similar to that of the full-length enzyme. For each domain the removal of approximately 50 N-terminal amino acids resulted in an increase in the ratio of luciferase activity at pH 8 relative to that at pH 6.3, such that their pH-activity profiles mimicked that of the proteolytic fragments reported earlier. Replacement of N-terminal histidines by alanine by site-directed mutagenesis identified four that are involved in the loss of activity at high pH. This system illustrates an unusual, possibly unique mechanism for pH regulation of enzyme activity, which has been postulated to be responsible for the control of the characteristic flashes of bioluminescence.

Genotypic analysis of Escherichia coli strains from poultry carcasses and their susceptibilities to antimicrobial agents.

Plasmid profiling and amplified fragment length polymorphism (AFLP) analysis were used to genotype 50 Escherichia coli strains from poultry carcasses. Thirty different plasmid profiles were evident, and clustering of the AFLP data showed that they were a distinctly heterogeneous group of strains. Susceptibility testing against five antimicrobial agents used in the South African poultry industry showed all strains to be susceptible to danofloxacin and colistin, while the majority (96%) were resistant to two tetracyclines.

Different regulatory mechanisms modulate the expression of a dinoflagellate iron-superoxide dismutase.

Regulation of antioxidant enzymes is critical to control the levels of reactive oxygen species in cell compartments highly susceptible to oxidative stress. In this work, we studied the regulation of a chloroplastic iron superoxide dismutase (Fe-SOD) from Lingulodinium polyedrum (formerly Gonyaulax polyedra) under different physiological conditions. A cDNA-encoding Fe-SOD was isolated from this dinoflagellate, showing high sequence similarity to cyanobacterial, algal, and plant Fe-SODs. Under standard growth conditions, on a 12:12-h light-dark cycle, Lingulodinium polyedrum Fe-SOD exhibited a daily rhythm of activity and cellular abundance with the maximum occurring during the middle of the light phase. Northern analyses showed that this rhythmicity is not related to changes in Fe-SOD mRNA levels, indicative of translational regulation. By contrast, conditions of metal-induced oxidative stress resulted in higher levels of Fe-SOD transcripts, suggesting that transcriptional control is responsible for increased protein and activity levels. Daily (circadian) and metal-induced up-regulation of Fe-SOD expression in L. polyedrum are thus mediated by different regulatory pathways, allowing biochemically distinct changes appropriate to oxidative challenges.

Absence of a putative mannose-specific phosphotransferase system enzyme IIAB component in a leucocin A-resistant strain of Listeria monocytogenes, as shown by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Leucocin A is a class IIa bacteriocin produced by Leuconostoc spp. that has previously been shown to inhibit the growth of Listeria monocytogenes. A spontaneous resistant mutant of L. monocytogenes was isolated and found to be resistant to leucocin A at levels in excess of 2 mg/ml. The mutant showed no significant cross-resistance to nontype IIa bacteriocins including nisaplin and ESF1-7GR. However, there were no inhibition zones found on a lawn of the mutant when challenged with an extract containing 51,200 AU of pediocin PA-2 per ml as determined by a simultaneous assay on the sensitive wild-type strain. DNA and protein analysis of the resistant and susceptible strains were carried out using silver-stained amplified fragment length polymorphism (ssAFLP) and one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), respectively. Two-dimensional SDS-PAGE clearly showed a 35-kDa protein which was present in the sensitive but absent from the resistant strain. The N-terminal end of the 35-kDa protein was sequenced and found to have an 83% homology to the mannose-specific phosphotransferase system enzyme IIAB of Streptococcus salivarius.

Characterization and determination of origin of lactic acid bacteria from a sorghum-based fermented weaning food by analysis of soluble proteins and amplified fragment length polymorphism fingerprinting.

The group that includes the lactic acid bacteria is one of the most diverse groups of bacteria known, and these organisms have been characterized extensively by using different techniques. In this study, 180 lactic acid bacterial strains isolated from sorghum powder (44 strains) and from corresponding fermented (93 strains) and cooked fermented (43 strains) porridge samples that were prepared in 15 households were characterized by using biochemical and physiological methods, as well as by analyzing the electrophoretic profiles of total soluble proteins. A total of 58 of the 180 strains were Lactobacillus plantarum strains, 47 were Leuconostoc mesenteroides strains, 25 were Lactobacillus sake-Lactobacillus curvatus strains, 17 were Pediococcus pentosaceus strains, 13 were Pediococcus acidilactici strains, and 7 were Lactococcus lactis strains. L. plantarum and L. mesenteroides strains were the dominant strains during the fermentation process and were recovered from 87 and 73% of the households, respectively. The potential origins of these groups of lactic acid bacteria were assessed by amplified fragment length polymorphism fingerprint analysis.

Purification and partial characterization of a murein hydrolase, millericin B, produced by Streptococcus milleri NMSCC 061.

Streptococcus milleri NMSCC 061 was screened for antimicrobial substances and shown to produce a bacteriolytic cell wall hydrolase, termed millericin B. The enzyme was purified to homogeneity by a four-step purification procedure that consisted of ammonium sulfate precipitation followed by gel filtration, ultrafiltration, and ion-exchange chromatography. The yield following ion-exchange chromatography was 6.4%, with a greater-than-2,000-fold increase in specific activity. The molecular weight of the enzyme was 28,924 as determined by electrospray mass spectrometry. The amino acid sequences of both the N terminus of the enzyme (NH(2) SENDFSLAMVSN) and an internal fragment which was generated by cyanogen bromide cleavage (NH(2) SIQTNAPWGL) were determined by automated Edman degradation. Millericin B displayed a broad spectrum of activity against gram-positive bacteria but was not active against Bacillus subtilis W23 or Escherichia coli ATCC 486 or against the producer strain itself. N-Dinitrophenyl derivatization and hydrazine hydrolysis of free amino and free carboxyl groups liberated from peptidoglycan digested with millericin B followed by thin-layer chromatography showed millericin B to be an endopeptidase with multiple activities. It cleaves the stem peptide at the N terminus of glutamic acid as well as the N terminus of the last residue in the interpeptide cross-link of susceptible strains.

Amplified fragment length polymorphism fingerprinting of Pseudomonas strains from a poultry processing plant.

Molecular typing has been used previously to identify and trace dissemination of pathogenic and spoilage bacteria associated with food processing. Amplified fragment length polymorphism (AFLP) is a novel DNA fingerprinting technique which is considered highly reproducible and has high discriminatory power. This technique was used to fingerprint 88 Pseudomonas fluorescens and Pseudomonas putida strains that were previously isolated from plate counts of carcasses at six processing stages and various equipment surfaces and environmental sources of a poultry abattoir. Clustering of the AFLP patterns revealed a high level of diversity among the strains. Six clusters (clusters I through VI) were delineated at an arbitrary Dice coefficient level of 0.65; clusters III (31 strains) and IV (28 strains) were the largest clusters. More than one-half (52.3%) of the strains obtained from carcass samples, which may have represented the resident carcass population, grouped together in cluster III. By contrast, 43.2% of the strains from most of the equipment surfaces and environmental sources grouped together in cluster IV. In most cases, the clusters in which carcass strains from processing stages grouped corresponded to the clusters in which strains from the associated equipment surfaces and/or environmental sources were found. This provided evidence that there was cross-contamination between carcasses and the abattoir environment at the DNA level. The AFLP data also showed that strains were being disseminated from the beginning to the end of the poultry processing operation, since many strains associated with carcasses at the packaging stage were members of the same clusters as strains obtained from carcasses after the defeathering stage.

Bacterial populations associated with a sorghum-based fermented weaning cereal.

Microbiological surveys, to determine the quality and safety, were conducted on 45 sorghum samples comprising dry powders (n = 15) and corresponding fermented (n = 15) and cooked fermented porridge (n = 15) samples collected from households in an informal settlement of the Gauteng Province of South Africa. Mean aerobic plate counts, Gram-negative counts and bacterial spore counts of sorghum powder samples decreased in fermented and cooked fermented porridge samples. However, mean lactic acid bacteria counts increased in fermented porridge samples, but decreased slightly in cooked fermented porridge samples. The mean pH value of sorghum powder samples decreased in fermented and cooked fermented porridge, respectively. Bacillus (B.) cereus was detected in all 15 sorghum powder samples, while Escherichia (E.) coli was detected in 53%, Clostridium perfringens in 27%, Listeria monocytogenes in 13% and Aeromonas spp., Salmonella spp., Staphylococcus aureus, Shigella spp. and Yersinia spp., each in 7% of sorghum powder samples. Of the fermented porridge samples, 40% contained B. cereus and 7% contained E. coli. None of the pathogens tested for were detected in cooked fermented porridge samples. B. cereus (53%), B. subtilis (21%), B. thuringiensis (13%), B. licheniformis (10%) and B. coagulans (3%) were identified from 120 isolates randomly selected from spore count plates of the highest dilution showing growth.

Acute and chronic effects of toxic metals on viability, encystment and bioluminescence in the dinoflagellate Gonyaulax polyedra.

Toxicity bioassays based on survival were carried out with cells of the marine dinoflagellate Gonyaulax polyedra exposed to mercury (Hg2+ ), cadmium (Cd2+), lead (Pb2+) and copper (Cu2+). The toxicity scale of these metals found was Hg2+ > Cu2+ > Cd2+ > Pb2+. Cells exposed to metals promptly underwent encystment, which is an important strategy for surviving metal exposure. Following 48 h exposure to Cu2+, complete excystment occurred within 96 h after reinoculation of cells in fresh metal-free media, and with Pb2+ partial recovery occurred in that time. Bioluminescence was affected by the metals in a dose-dependent manner primarily by increasing the frequency of flashing, but the glow emission was also altered with acute Cu2+ and Pb2+ treatments. Several physiological processes in G. polyedra are under circadian control. Chronic exposures to metals caused no substantial alterations in the circadian rhythm of bioluminescence glow, indicating that the biological clock of this dinoflagellate is not sensitive to these metals at the concentrations tested.

Circadian synthesis of a nuclear-encoded chloroplast glyceraldehyde-3-phosphate dehydrogenase in the dinoflagellate Gonyaulax polyedra is translationally controlled.

The circadian clock has previously been shown to restrict synthesis of several proteins in the dinoflagellate Gonyaulax polyedra to only a few hours each day. We have identified one of these proteins as glyceraldehyde-3-phosphate dehydrogenase. Two nuclear genes encoding the enzyme have been cloned, one corresponding to a cytoplasmic isoform and the other to a plastid targeted protein. On the basis of protein microsequence data, we conclude that the synthesis of the plastid isoform is clock-regulated. This regulation is not related to mRNA levels, which remain constant throughout the cycle, suggesting a translational control mechanism, in contrast to the transcriptional regulation of GAPDH that has been demonstrated in Neurospora. Although the rhythm of synthesis has a high amplitude, the abundance and activity rhythms are greatly attenuated, which is attributed to the long half-life of the protein.

Novel effects on the Gonyaulax circadian system produced by the protein kinase inhibitor staurosporine.

The protein kinase inhibitor staurosporine was found to cause a dramatic increase in the free-running period (FRP) of circadian rhythms in the dinoflagellate Gonyaulax polyedra, and its effect was similar when added at different phases of the circadian cycle. Chronic exposure to staurosporine lengthened the FRP by as much as 7 h without significantly affecting the amplitude or waveform of the bioluminescence rhythm. The effect on the length of the FRP occurred only above a threshold concentration, and it lasted for a limited number of cycles that depended on the dose of the drug. The FRP lengthening was not evident until 23 to 26 h after staurosporine addition, even though the drug entered Gonyaulax cells in 1 h or less. When tested in combination with bright light pulses, staurosporine was found to enhance both light-induced phase advances and delays, indicating that the drug acts on circadian phototransduction. At concentrations that alter the FRP and the response to light pulses, staurosporine appears to act on a small number of protein kinases, attenuating the activity of two individual protein kinases without affecting overall phosphate incorporation into proteins in vitro.

Structural variations in nisin associated with different membrane mimicking and pH environments.

Nisin is a membrane active antimicrobial peptide containing unusual dehydrated amino acid residues. The secondary structure of nisin in aqueous solution, membrane mimicking solvents and at various pH values was investigated using circular dichroism. In aqueous solution nisin is largely randomly coiled. In liposomes and at pH 6 and above, however, the presence of a maximum at 195 nm and a minimum at 190 nm was notable and indicative of beta-turn formation in these environments. This change in structure was speculated to result in an increasing unavailability of the site for initial reaction of peptide and membrane at higher pH.

Modification of a synthetic antimicrobial peptide (ESF1) for improved inhibitory activity.

Rational modification of an existing cationic alpha-helical antimicrobial peptide (ESF1) for improved activity by increasing amphipathicity was undertaken. ESF1 and two variants (GR7 and SA3) were synthesized and tested for activity range, minimum inhibitory concentration, and hemolytic activity. Biological activity was related to structure as determined by circular dichroism. The substitution of arginine for glycine in position seven was found to increase antimicrobial activity without effecting hemolysis. Increased activity was related to stronger alpha-helix formation in buffer. Increased beta-sheet formation in micellar SDS was observed and speculated to be due to a stronger ability of the variants to form multimolecule complexes, a feature consistent with existing models of cationic peptide activity.

Flow cytometry demonstrates bacteriocin-induced injury to Listeria monocytogenes.

Flow cytometry was used to study the effect of the bacteriocin leucocin B-TA11a on Listeria (L.) monocytogenes. Mixed proportions of dead and live control populations were analyzed by flow cytometry to determine detection limits of the Dead/Live Baclight Bacterial Viability KitTM. High correlations for flow cytometric detection of defined proportions of live or dead cells in mixtures between 10 and 100% of dead (r2 = 0.97) or live (r2 = 0.99) cells were obtained. However, mixtures containing less than 10% of either live or dead control cells gave correlations below 0.72. The growth of L. monocytogenes in the absence and presence of leucocin B-TA11a was analyzed by flow cytometry with Baclight, plate counts, and optical density measurements. Although leucocin B-TA11a initially inhibited listerial growth, the uptake of both Baclight dyes suggested that cells remained viable but became leaky, possibly indicating bacteriocin-induced pore formation in the target membranes.