Amino acid and lactate catabolism in trimethylamine oxide respiration of Alteromonas putrefaciens NCMB 1735

Flux-Balance Analysis and Mobile CRISPRi-Guided Deletion of a Conditionally Essential Gene in Shewanella oneidensis MR-1

Carbon-neutral production of valuable bioproducts is critical to sustainable development but remains limited by the slow engineering of photosynthetic organisms. Improving existing synthetic biology tools to engineer model organisms to fix carbon dioxide is one route to overcoming the limitations of photosynthetic organisms. In this work, we describe a pipeline that enabled the deletion of a conditionally essential gene from the Shewanella oneidensis MR-1 genome. S. oneidensis is a simple bacterial host that could be used for electricity-driven conversion of carbon dioxide in the future with further genetic engineering. We used Flux Balance Analysis (FBA) to model carbon and energy flows in central metabolism and assess the effects of single and double gene deletions. We modeled the growth of deletion strains under several alternative conditions to identify substrates that restore viability to an otherwise lethal gene knockout. These predictions were tested in vivo using a Mobile-CRISPRi gene knockdown system. The information learned from FBA and knockdown experiments informed our strategy for gene deletion, allowing us to successfully delete an "expected essential" gene, gpmA. FBA predicted, knockdown experiments supported, and deletion confirmed that the "essential" gene gpmA is not needed for survival, dependent on the medium used. Removal of gpmA is a first step toward driving electrode-powered CO2 fixation via RuBisCO. This work demonstrates the potential for broadening the scope of genetic engineering in S. oneidensis as a synthetic biology chassis. By combining computational analysis with a CRISPRi knockdown system in this way, one can systematically assess the impact of conditionally essential genes and use this knowledge to generate mutations previously thought unachievable.

1-(4-Amino-2-Hydroxyphenyl)Ethenone Suppresses Agrobacterium tumefaciens Virulence and Metabolism

The impact of 1-(4-amino-2-hydroxyphenyl)ethanone (AHPE) from the metabolites of endophytic fungus Phomopsis liquidambari on quorum sensing (QS) of Agrobacterium tumefaciens was evaluated for the first time in this study. Exposure to AHPE at concentrations ranging from 12.5 to 50 μg/mL, the β-galactosidase activity, acyl-homoserine lactone level, swimming motility, chemotaxis, and flagella formation were significantly inhibited. qRT-PCR quantification combined with the docking analysis demonstrated that AHPE affected the QS system of A. tumefaciens by repressing the transcriptional levels of traI and traR rather than signal mimicry. ¹H NMR-based metabolic analysis indicated that the metabolism of A. tumefaciens was notably disturbed with AHPE treatment. AHPE treatment also resulted in the enhanced oxidative stress in A. tumefaciens. The enhanced oxidative stress lead to the disorder of energy supply, protein synthesis, and nucleotide metabolism, and ultimately attenuated the pathogenicity of A. tumefaciens. Our study indicated that AHPE can serve as a potential pesticide to defend against A. tumefaciens.

Selective Detection of Nitrogen-Containing Compound Gases

N-containing gaseous compounds, such as trimethylamine (TMA), triethylamine (TEA), ammonia (NH₃), nitrogen monoxide (NO), and nitrogen dioxide (NO₂) exude irritating odors and are harmful to the human respiratory system at high concentrations. In this study, we investigated the sensing responses of five sensor materials—Al-doped ZnO (AZO) nanoparticles (NPs), Pt-loaded AZO NPs, a Pt-loaded WO₃ (Pt-WO₃) thin film, an Au-loaded WO₃ (Au-WO₃) thin film, and N-doped graphene—to the five aforementioned gases at a concentration of 10 parts per million (ppm). The ZnO- and WO₃-based materials exhibited n-type semiconducting behavior, and their responses to tertiary amines were significantly higher than those of nitric oxides. The N-doped graphene exhibited p-type semiconducting behavior and responded only to nitric oxides. The Au- and Pt-WO₃ thin films exhibited extremely high responses of approximately 100,000 for 10 ppm of triethylamine (TEA) and approximately −2700 for 10 ppm of NO₂, respectively. These sensing responses are superior to those of previously reported sensors based on semiconducting metal oxides. On the basis of the sensing response results, we drew radar plots, which indicated that selective pattern recognition could be achieved by using the five sensing materials together. Thus, we demonstrated the possibility to distinguish each type of gas by applying the patterns to recognition techniques.

Electron Donor Utilization and Secondary Mineral Formation during the Bioreduction of Lepidocrocite by Shewanella putrefaciens CN32

The bioreduction of Fe(III) oxides by dissimilatory iron reducing bacteria (DIRB) may result in the production of a suite of Fe(II)-bearing secondary minerals, including magnetite, siderite, vivianite, green rusts, and chukanovite; the formation of specific phases controlled by the interaction of various physiological and geochemical factors. In an effort to better understand the effects of individual electron donors on the formation of specific Fe(II)-bearing secondary minerals, we examined the effects of a series of potential electron donors on the bioreduction of lepidocrocite (γ-FeOOH) by Shewanella putrefaciens CN32. Biomineralization products were identified by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. Acetate, citrate, ethanol, glucose, glutamate, glycerol, malate, and succinate were not effectively utilized for the bioreduction of lepidocrocite by S. putrefaciens CN32; however, substantial Fe(II) production was observed when formate, lactate, H2, pyruvate, serine, or N acetylglucosamine (NAG) was provided as an electron donor. Carbonate or sulfate green rust was the dominant Fe(II)-bearing secondary mineral when formate, H2, lactate, or NAG was provided, however, siderite formed with pyruvate or serine. Geochemical modeling indicated that pH and carbonate concentration are the key factors determining the prevalence of carbonate green rust verses siderite.

1H NMR-Based Global Metabolic Studies of Pseudomonas aeruginosa upon Exposure of the Quorum Sensing Inhibitor Resveratrol

Quorum sensing (QS) is a process of bacterial communication that has been a novel target for drug discovery. Pyocyanin quantification assay confirmed that resveratrol was an effective quorum sensing inhibitor (QSI) against Pseudomonas aeruginosa PAO1. In this study, the global metabolite changes of P. aeruginosa PAO1 exposed to QSI resveratrol were investigated by ¹H NMR spectroscopy. A total of 40 metabolites containing amino acids, organic acid, organic amine, and energy storage compounds were identified. The changed metabolic profile indicated that resveratrol influenced pathways including oxidative stress, protein synthesis, and energy metabolism. Oxidative stress could upregulate the expression of genes related to QS in P. aeruginosa. It suggested that resveratrol could inhibit the QS systems in P. aeruginosa PAO1 by relieving oxidative stress due to its antioxidant activity. On the other hand, resveratrol could attenuate the pathogenicity of P. aeruginosa PAO1 by disturbing the TCA cycle so that anaerobic respiration could suppress the virulence because anaerobiosis could induce the loss of cytotoxicity regulated by QS in P. aeruginosa. These findings deepened our comprehending of the metabolic responses of P. aeruginosa PAO1 to resveratrol and pinpointed the possible underlying mechanism of resveratrol's inhibition effect on QS in P. aeruginosa PAO1.

Trimethylamine and Trimethylamine N-Oxide, a Flavin-Containing Monooxygenase 3 (FMO3)-Mediated Host-Microbiome Metabolic Axis Implicated in Health and Disease

Flavin-containing monooxygenase 3 (FMO3) is known primarily as an enzyme involved in the metabolism of therapeutic drugs. On a daily basis, however, we are exposed to one of the most abundant substrates of the enzyme trimethylamine (TMA), which is released from various dietary components by the action of gut bacteria. FMO3 converts the odorous TMA to nonodorous TMA N-oxide (TMAO), which is excreted in urine. Impaired FMO3 activity gives rise to the inherited disorder primary trimethylaminuria (TMAU). Affected individuals cannot produce TMAO and, consequently, excrete large amounts of TMA. A dysbiosis in gut bacteria can give rise to secondary TMAU. Recently, there has been much interest in FMO3 and its catalytic product, TMAO, because TMAO has been implicated in various conditions affecting health, including cardiovascular disease, reverse cholesterol transport, and glucose and lipid homeostasis. In this review, we consider the dietary components that can give rise to TMA, the gut bacteria involved in the production of TMA from dietary precursors, the metabolic reactions by which bacteria produce and use TMA, and the enzymes that catalyze the reactions. Also included is information on bacteria that produce TMA in the oral cavity and vagina, two key microbiome niches that can influence health. Finally, we discuss the importance of the TMA/TMAO microbiome-host axis in health and disease, considering factors that affect bacterial production and host metabolism of TMA, the involvement of TMAO and FMO3 in disease, and the implications of the host-microbiome axis for management of TMAU.

Pyruvate and lactate metabolism by Shewanella oneidensis MR-1 under fermentation, oxygen limitation, and fumarate respiration conditions

Shewanella oneidensis MR-1 is a facultative anaerobe that derives energy by coupling organic matter oxidation to the reduction of a wide range of electron acceptors. Here, we quantitatively assessed the lactate and pyruvate metabolism of MR-1 under three distinct conditions: electron acceptor-limited growth on lactate with O(2), lactate with fumarate, and pyruvate fermentation. The latter does not support growth but provides energy for cell survival. Using physiological and genetic approaches combined with flux balance analysis, we showed that the proportion of ATP produced by substrate-level phosphorylation varied from 33% to 72.5% of that needed for growth depending on the electron acceptor nature and availability. While being indispensable for growth, the respiration of fumarate does not contribute significantly to ATP generation and likely serves to remove formate, a product of pyruvate formate-lyase-catalyzed pyruvate disproportionation. Under both tested respiratory conditions, S. oneidensis MR-1 carried out incomplete substrate oxidation, whereby the tricarboxylic acid (TCA) cycle did not contribute significantly. Pyruvate dehydrogenase was not involved in lactate metabolism under conditions of O(2) limitation but was required for anaerobic growth, likely by supplying reducing equivalents for biosynthesis. The results suggest that pyruvate fermentation by S. oneidensis MR-1 cells represents a combination of substrate-level phosphorylation and respiration, where pyruvate serves as an electron donor and an electron acceptor. Pyruvate reduction to lactate at the expense of formate oxidation is catalyzed by a recently described new type of oxidative NAD(P)H-independent d-lactate dehydrogenase (Dld-II). The results further indicate that pyruvate reduction coupled to formate oxidation may be accompanied by the generation of proton motive force.

Large-scale comparative phenotypic and genomic analyses reveal ecological preferences of shewanella species and identify metabolic pathways conserved at the genus level

The use of comparative genomics for the study of different microbiological species has increased substantially as sequence technologies become more affordable. However, efforts to fully link a genotype to its phenotype remain limited to the development of one mutant at a time. In this study, we provided a high-throughput alternative to this limiting step by coupling comparative genomics to the use of phenotype arrays for five sequenced Shewanella strains. Positive phenotypes were obtained for 441 nutrients (C, N, P, and S sources), with N-based compounds being the most utilized for all strains. Many genes and pathways predicted by genome analyses were confirmed with the comparative phenotype assay, and three degradation pathways believed to be missing in Shewanella were confirmed as missing. A number of previously unknown gene products were predicted to be parts of pathways or to have a function, expanding the number of gene targets for future genetic analyses. Ecologically, the comparative high-throughput phenotype analysis provided insights into niche specialization among the five different strains. For example, Shewanella amazonensis strain SB2B, isolated from the Amazon River delta, was capable of utilizing 60 C compounds, whereas Shewanella sp. strain W3-18-1, isolated from deep marine sediment, utilized only 25 of them. In spite of the large number of nutrient sources yielding positive results, our study indicated that except for the N sources, they were not sufficiently informative to predict growth phenotypes from increasing evolutionary distances. Our results indicate the importance of phenotypic evaluation for confirming genome predictions. This strategy will accelerate the functional discovery of genes and provide an ecological framework for microbial genome sequencing projects.

Substrate-level phosphorylation is the primary source of energy conservation during anaerobic respiration of Shewanella oneidensis strain MR-1

It is well established that respiratory organisms use proton motive force to produce ATP via F-type ATP synthase aerobically and that this process may reverse during anaerobiosis to produce proton motive force. Here, we show that Shewanella oneidensis strain MR-1, a nonfermentative, facultative anaerobe known to respire exogenous electron acceptors, generates ATP primarily from substrate-level phosphorylation under anaerobic conditions. Mutant strains lacking ackA (SO2915) and pta (SO2916), genes required for acetate production and a significant portion of substrate-level ATP produced anaerobically, were tested for growth. These mutant strains were unable to grow anaerobically with lactate and fumarate as the electron acceptor, consistent with substrate-level phosphorylation yielding a significant amount of ATP. Mutant strains lacking ackA and pta were also shown to grow slowly using N-acetylglucosamine as the carbon source and fumarate as the electron acceptor, consistent with some ATP generation deriving from the Entner-Doudoroff pathway with this substrate. A deletion strain lacking the sole F-type ATP synthase (SO4746 to SO4754) demonstrated enhanced growth on N-acetylglucosamine and a minor defect with lactate under anaerobic conditions. ATP synthase mutants grown anaerobically on lactate while expressing proteorhodopsin, a light-dependent proton pump, exhibited restored growth when exposed to light, consistent with a proton-pumping role for ATP synthase under anaerobic conditions. Although S. oneidensis requires external electron acceptors to balance redox reactions and is not fermentative, we find that substrate-level phosphorylation is its primary anaerobic energy conservation strategy. Phenotypic characterization of an ackA deletion in Shewanella sp. strain MR-4 and genomic analysis of other sequenced strains suggest that this strategy is a common feature of Shewanella.

Determination of trimethylamine in fish by capillary electrophoresis with electrogenerated tris(2,2′-bipyridyl)ruthenium(II) chemiluminescence detection

A capillary electrophoresis with electrogenerated chemiluminescence (CE-ECL) method for the determination of trimethylamine (TMA) in fish was studied. In the presence of TMA, ECL from the reaction of analyte and in situ generated tris(2,2'-bipyridyl)ruthenium(III) [Ru(bpy)(3) (3+)] at electrode surface could be produced. The ECL detection was performed using a Pt working electrode biased at 1.23 V (vs. Ag/AgCl) potential in a 10 mmol/L sodium borate buffer solution, pH 9.2, containing 3 mmol/L Ru(bpy)(3) (2+). A linear calibration curve (correlation coefficient = 0.9996) was obtained in the range 8 x 10(-5)-4 x 10(-8) mol/L for TMA concentration. Recoveries obtained were in the range 98.78-101.46%. The method was successfully applied for the assay of TMA in fish, in combination with solid phase extraction (SPE) disks for sample clean-up and enrichment.

Anaerobic central metabolic pathways in Shewanella oneidensis MR-1 reinterpreted in the light of isotopic metabolite labeling

It has been proposed that during growth under anaerobic or oxygen-limited conditions, Shewanella oneidensis MR-1 uses the serine-isocitrate lyase pathway common to many methylotrophic anaerobes, in which formaldehyde produced from pyruvate is condensed with glycine to form serine. The serine is then transformed through hydroxypyruvate and glycerate to enter central metabolism at phosphoglycerate. To examine its use of the serine-isocitrate lyase pathway under anaerobic conditions, we grew S. oneidensis MR-1 on [1-13C]lactate as the sole carbon source, with either trimethylamine N-oxide (TMAO) or fumarate as an electron acceptor. Analysis of cellular metabolites indicated that a large percentage (>70%) of lactate was partially oxidized to either acetate or pyruvate. The 13C isotope distributions in amino acids and other key metabolites indicate that under anaerobic conditions, although glyoxylate synthesized from the isocitrate lyase reaction can be converted to glycine, a complete serine-isocitrate pathway is not present and serine/glycine is, in fact, oxidized via a highly reversible degradation pathway. The labeling data also suggest significant activity in the anapleurotic (malic enzyme and phosphoenolpyruvate carboxylase) reactions. Although the tricarboxylic acid (TCA) cycle is often observed to be incomplete in many other anaerobes (absence of 2-oxoglutarate dehydrogenase activity), isotopic labeling supports the existence of a complete TCA cycle in S. oneidensis MR-1 under certain anaerobic conditions, e.g., TMAO-reducing conditions.

Shewanella oneidensis MR-1 fluxome under various oxygen conditions

The central metabolic fluxes of Shewanella oneidensis MR-1 were examined under carbon-limited (aerobic) and oxygen-limited (microaerobic) chemostat conditions, using 13C-labeled lactate as the sole carbon source. The carbon labeling patterns of key amino acids in biomass were probed using both gas chromatography-mass spectrometry (GC-MS) and 13C nuclear magnetic resonance (NMR). Based on the genome annotation, a metabolic pathway model was constructed to quantify the central metabolic flux distributions. The model showed that the tricarboxylic acid (TCA) cycle is the major carbon metabolism route under both conditions. The Entner-Doudoroff and pentose phosphate pathways were utilized primarily for biomass synthesis (with a flux below 5% of the lactate uptake rate). The anaplerotic reactions (pyruvate to malate and oxaloacetate to phosphoenolpyruvate) and the glyoxylate shunt were active. Under carbon-limited conditions, a substantial amount (9% of the lactate uptake rate) of carbon entered the highly reversible serine metabolic pathway. Under microaerobic conditions, fluxes through the TCA cycle decreased and acetate production increased compared to what was found for carbon-limited conditions, and the flux from glyoxylate to glycine (serine-glyoxylate aminotransferase) became measurable. Although the flux distributions under aerobic, microaerobic, and shake flask culture conditions were different, the relative flux ratios for some central metabolic reactions did not differ significantly (in particular, between the shake flask and aerobic-chemostat groups). Hence, the central metabolism of S. oneidensis appears to be robust to environmental changes. Our study also demonstrates the merit of coupling GC-MS with 13C NMR for metabolic flux analysis to reduce the use of 13C-labeled substrates and to obtain more-accurate flux values.

Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments

Genomic sequences have been used to find the genetic foundation for carbon source metabolism in Shewanella oneidensis MR-1. Annotated S. oneidensis MR-1 gene products were examined for their sequence similarity to enzymes participating in pathways for utilization of carbon and energy as described in the BioCyc database (http://www.biocyc.org/) or in the primary literature. A picture emerges that relegates five- and six-carbon sugars to minor roles as carbon sources, whereas multiple pathways for utilization of up to three-carbon carbohydrates seem to be present. Capacity to utilize amino acids for carbon and energy is also present. A few contradictions emerged in which enzymes appear to be present by annotations but are not active in the cell according to physiological experiments. Annotations are based on close sequence similarity and will not reveal inactivity due to deleterious mutations or due to lack of coordination of regulation and transport. Genes for a few enzymes known by experiment to be active are not found in the genome. This may be due to extensive divergence after duplication or convergence of function in separate lines in evolution rendering activities undetectable by sequence similarity. To minimize false predictions from protein sequences, we have been conservative in predicting pathways. We did not predict any pathway when, although a partial pathway was seen it was composed largely of enzymes already accounted for in any other complete pathway. This is an example of how a biochemically oriented sequence analysis can generate questions and direct further experimental investigation.

Influence of the freshness grade of raw fish on the formation of volatile and biogenic amines during the manufacture and storage of vinegar-marinated anchovies

Volatile and biogenic amines from three batches of anchovies, marinated in vinegar, were studied. The anchovies had been vacuum-packed and kept in refrigerated storage for 3 months. Trimethylamine and total volatile basic nitrogen levels were very low and constant throughout marinating and storage process: less than 1 and 10 mg/100 g, respectively. Certain amine levels, mainly those of tyramine and serotonin, increased slightly, particularly during storage. However, even the highest recorded levels were much lower than those considered to be hazardous for human consumption. To study the influence of raw material freshness in the amine profile, two laboratory trials using fresh and spoiled anchovies and simulating the industry standard marinating process were carried out. Levels for both volatile and biogenic amines were dependent on raw material quality, proving consistently higher in those deriving from nonfresh fish. Vinegar marinating leads to a decrease in the accumulation of amines in anchovy while their concentration in the vinegar solution increases due to the vinegar effect as solvent extractor.

Influence of acetate and CO2 on the TMAO-reduction reaction by Shewanella baltica

In this work, the TMAO-reduction by Shewanella baltica, one of the representative spoilage organisms in modified atmosphere packaged marine fish fillets, and the effect of acetate and CO2 on this reduction were studied in vitro. The growth of S. baltica and the corresponding evolution of some compounds (acetate, lactate, pyruvate, glucose and trimethylamine (TMA)) were followed during storage at 4 degrees C in two types of broths. The first medium was a defined medium (pH = 6.8) to which lactate or pyruvate was added as hydrogen donor. Pyruvate showed to be more efficient as H-donor for S. baltica than lactate, as growth was much faster when equimolar amounts of pyruvate instead of lactate were present. Although the growth of S. baltica, when pyruvate is used as H-donor and no acetate is added, was not much inhibited by the CO2-atmosphere, CO2 had a pronounced effect on the studied reactions as it partly inhibited the reduction of pyruvate to acetate. The effect of acetate on this reaction was, on the other hand, not significant. To simulate the reactions occurring in situ, a buffered fish extract (pH = 6.8) was used. In spite of the neutral pH, the growth of S. baltica in this medium was highly inhibited by relatively small concentrations of acetate (< 0.3%). When 0.1% of acetate was added to the fish extract, less acetate was formed and lactate was more slowly consumed in comparison to the experiments without the addition of acetate. The consumption of lactate and the production of acetate were almost completely inhibited when the fish extract contained 0.25% of acetate. Apparently, the addition of acetate inhibited the use of lactate as H-donor. After extended storage times (17 days at 4 degrees C) TMA production started. Most probably, alternative H-donors were used by S. baltica, from which the pathway seems to be less energy efficient. This can be deduced from the exceptional growth inhibition of S. baltica by small amounts of acetate. However, when practical storage times for fish (e.g. 6 days at 4 degrees C after packaging) are considered, growth and TMAO-reduction by S. baltica was completely inhibited during this period by 0.25% of acetate.

Shelf-life extension of cod fillets with an acetate buffer spray prior to packaging under modified atmospheres

Fresh cod fillets (Gadus morhua) were sprayed with a 10% acetate buffer (pH 5.6), packed with an industrial gas-flushing packaging machine under modified atmospheres (50% CO2--45% O2--5% N2, 2 cm3/1 g gas/product ratio) and stored at 7 degrees C for 12 days. Control cod fillets were directly packed and stored under the same conditions. A reduction of the aerobic plate counts was observed immediately after the cod fillets had been sprayed. During storage under modified atmospheres, there was complete inhibition of H2S-producing bacteria and Enterobacteriaceae in the treated cod fillets. Production of total volatile bases and trimethylamine (TMA) was inhibited in treated fillets for 10 days' storage under modified atmospheres. Inhibition of TMA production can be attributed to growth inhibition of H2S-producing bacteria, inhibition of the trimethylamine oxide (TMAO)-dependent metabolism of TMAO-reducing bacteria and the stable pH during storage. The shelf-life, at 7 degrees C, of treated cod fillets, based on cooked flavour score, was almost 12 days, ca 8 days more than shelf-life of the control fillets.

Chemical and sensory changes associated with microbial flora of Mediterranean boque (Boops boops) stored aerobically at 0, 3, 7, and 10 degreesC

The development of a microbial population and changes in the physicochemical and sensorial characteristics of Mediterranean boque (Boops boops), called gopa in Greece, stored aerobically at 0, 3, 7, and 10 degreesC were studied. Pseudomonads and Shewanella putrefaciens were the dominant bacteria at the end of the storage period, regardless of the temperature tested. Enterobacteria and Brochothrix thermosphacta also grew, but their population density was always 2 to 3 log10 CFU g-1 less than that of pseudomonads. The concentration of potential indicators of spoilage, glucose and lactic acid, decreased while that of the alpha-amino groups increased during storage. The concentrations of these carbon sources also decreased on sterile fish blocks inoculated with strains isolated from fish microbial flora. The organic acid profile of sterile fish blocks inoculated with the above-mentioned bacteria and that of naturally spoiled fish differed significantly. An excellent correlation (r = -0.96) between log10 counts of S. putrefaciens or Pseudomonas bacteria with freshness was observed in this study.

Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 A resolution

The periplasmic trimethylamine N-oxide (TMAO) reductase from the marine bacteria Shewanella massilia is involved in a respiratory chain, having trimethylamine N-oxide as terminal electron acceptor. This molybdoenzyme belongs to the dimethyl sulfoxide (DMSO) reductase family, but has a different substrate specificity than its homologous enzyme. While the DMSO reductases reduce a broad spectra of organic S-oxide and N-oxide compounds, TMAO reductase from Shewanella massilia reduces only TMAO as the natural compound. The crystal structure was solved by molecular replacement with the coordinates of the DMSO reductase from Rhodobacter sphaeroides. The overall fold of the protein structure is essentially the same as the DMSO reductase structures, organized into four domains. The molybdenum coordination sphere is closest to that described in the DMSO reductase of Rhodobacter capsulatus. The structural differences found in the protein environment of the active site could be related to the differences in substrate specificity of these enzymes. In close vicinity of the molybdenum ion a tyrosine residue is missing in the TMAO reductase, leaving a greater space accessible to the solvent. This tyrosine residue has contacts to the oxo groups in the DMSO reductase structures. The arrangement and number of charged residues lining the inner surface of the funnel-like entrance to the active site, is different in the TMAO reductase than in the DMSO reductases from Rhodobacter species. Furthermore a surface loop at the top of the active-site funnel, for which no density was present in the DMSO reductase structures, is well defined in the oxidized form of the TMAO reductase structure, and is located on the border of the funnel-like entrance of the active center.

In vitro study of TMAO reduction by Shewanella putrefaciens isolated from cod fillets packed in modified atmosphere

A strain of Shewanella putrefaciens was isolated from cod fillets in a modified atmosphere (60% CO2, 30% O2, 10% N2). The effect of pH on the growth of Shewanella putrefaciens and TMAO reduction was studied in fish extract with citrate buffer systems at pH values from 5.8 to 6.8. The effect of the modified atmosphere (CO2, O2) on the growth of S. putrefaciens and on the reduction of TMAO to TMA was studied using solid media from fish extract packed under variable mixtures of CO2, O2 and N2. All the samples were incubated at 7 degrees C for 7 days. Slow development of S. putrefaciens and no production of TMA was observed in fish extract buffered at pH 5.8. Inclusion of O2 in packaging atmosphere of solid fish extract, even at small proportions (10%), was inhibitory for the reduction of TMAO, while there was no effect of O2 on the growth of S. putrefaciens. Increased levels of CO2 (> or = 50%) in the atmosphere were inhibiting the growth of S. putrefaciens and consequently the production of TMA.

Microbiological spoilage of fish and fish products

Spoilage of fresh and lightly preserved fish products is caused by microbial action. This paper reviews the current knowledge in terms of the microbiology of fish and fish products with particular emphasis on identification of specific spoilage bacteria and the qualitative and quantitative biochemical indicators of spoilage. Shewanella putrefaciens and Pseudomonas spp. are the specific spoilage bacteria of iced fresh fish regardless of the origin of the fish. Modified atmosphere stored marine fish from temperate waters are spoiled by the CO2 resistant Photobacterium phosphoreum whereas Gram-positive bacteria are likely spoilers of CO2 packed fish from fresh or tropical waters. Fish products with high salt contents may spoil due to growth of halophilic bacteria (salted fish) or growth of anaerobic bacteria and yeasts (barrel salted fish). Whilst the spoilage of fresh and highly salted fish is well understood, much less is known about spoilage of lightly preserved fish products. It is concluded that the spoilage is probably caused by lactic acid bacteria, certain psychotrophic Enterobacteriaceae and/or Photobacterium phosphoreum. However, more work is needed in this area.

A biochemical study of the intermediary carbon metabolism of Shewanella putrefaciens

Cell extracts were used to determine the enzymes involved in the intermediary carbon metabolism of several strains of Shewanella putrefaciens. Enzymes of the Entner-Doudoroff pathway (6-phosphogluconate dehydratase and 2-keto-3-deoxy-6-phosphogluconate aldolase) were detected, but those of the Embden-Meyerhof-Parnas pathway were not. While several tricarboxylic acid cycle enzymes were present under both aerobic and anaerobic conditions, two key enzymes (2-oxoglutarate dehydrogenase and pyruvate dehydrogenase) were greatly diminished under anaerobic conditions. Extracts of cell grown anaerobically on formate as the sole source of carbon and energy were positive for hydroxypyruvate reductase, the key enzyme of the serine pathway in other methylotrophs, while no hexulose synthase activity was seen.

Spoilage and shelf-life of cod fillets packed in vacuum or modified atmospheres

Microbial growth, sensory and chemical changes and composition of gas atmosphere were studied in vacuum packed (VP) and modified atmosphere packed (MAP) cod fillets stored at 0 degree C. Contrary to previous studies, coccobacilli and pleomorphic Gram-negative microorganisms (2-4 by 2-5 microns) and not Shewanella putrefaciens were found most likely to be the main spoilage organisms. These microorganisms, which may be Photobacterium phosphoreum, can explain the short shelf-life extension of VP and MAP fish products compared to meat products. It is suggested that they may inhibit the typical H2S-producing fish spoilage bacteria, S. putrefaciens, as the maximum concentration of H2S-producing bacteria found in MAP fish products is very low. Compared to VP, a shelf-life extension of 6-7 days was obtained with 48% CO2 in MAP. However, with pure CO2 the shelf life was only extended by 2-3 days. Poor texture and high drip loss indicated that the shelf life of these fillets was limited by chemical reactions and not only by microbial activity.

Production and specificity of poly- and monoclonal antibodies raised against Shewanella putrefaciens

Polyclonal antibodies were raised in rabbits and mice against Shewanella putrefaciens. Murine monoclonal antibodies were produced against the type strain (ATCC 8071) as well as wild type strains isolated from fish products. The specificities of four polyclonal and 12 monoclonal antibodies were tested by dot-blotting, an indirect and a competitive ELISA against 16 Gram-negative strains; including six strains of S. putrefaciens and one strain of Pseudomonas rubescens (NC 10695). All polyclonal antibodies reacted strongly with S. putrefaciens and with Ps. rubescens and cross-reacted with the nine other bacteria (Pseudomonas spp., Aeromonas spp. and Vibrio anguillarum). The monoclonal antibodies could be divided into three groups with different patterns of specificity. The largest group (8 monoclonal antibodies) reacted strongly with S. putrefaciens and with Ps. rubescens and showed only weak reactions with the other strains. The results confirm that Ps. rubescens should be classified as S. putrefaciens.

Evaluation of the bacteriological quality of seafood

Bacteria largely determine the quality of fresh and lightly preserved fish products. This paper surveys traditional and rapid methods for estimation of bacterial levels in seafood. The use of traditional agar techniques is discussed with reference to development of substrates and procedures suited for fish and fish products. This includes estimation of the bacteria specifically involved in the spoilage process. During the last decade, several microbiological rapid methods or principles (DEFT, microcolonies, Limulus lysate, ATP, conductance, microcalorimetry, reduction of trimethylamine oxide (TMAO)) have been suggested for estimating the bacteriological quality of seafoods. A brief survey of these methods and the results obtained is given. Preliminary results on development of poly- and monoclonal antibodies against Shewanella putrefaciens are mentioned. Future research may involve the development of DNA-probes against genes coding for specific spoilage reactions.

Growth and activity of Shewanella putrefaciens isolated from spoiling fish

A total of 101 cultures of H2S-producing organisms isolated from spoiling cod was studied. All cultures were identified as Shewanella putrefaciens. Two groups were distinguished on the basis of pattern of trimethylamine oxide reduction determined by conductance measurement, generation time at 25 degrees C and salt tolerance. The S. putrefaciens cultures were further characterized in a number of model experiments in order to examine the spoilage activity under various conditions. A good correlation between bacterial counts, detection time in conductance measurements and production of trimethylamine and off-odour was found. There were no differences in spoilage potential between strains of S. putrefaciens, and neither initial level of inoculum nor batch of cod used as substrate influenced the levels of bacterial count corresponding to a certain production of trimethylamine and off-odour.

Trimethylamine oxide respiration of Alteromonas putrefaciens NCMB 1735: Na+-stimulated anaerobic transport in cells and membrane vesicles

Alteromonas putrefaciens NCMB 1735 required the presence of NaCl for anaerobic growth with serine, cysteine, and formate as substrate and trimethylamine oxide ( TMAO ) as external electron acceptor. When lactate was substrate, the organism grew equally well in the absence of NaCl. Anaerobic uptake of glutamate, aspartate, serine, cysteine, and lactate in resting cells was strongly stimulated with NaCl, and cytoplasmic membrane vesicles energized by electron transfer from formate to TMAO displayed active Na+-dependent uptake of serine. The data suggested that participation in transport processes was the only vital function of Na+ in A. putrefaciens. Formate- and TMAO -dependent anaerobic serine uptake in vesicles was sensitive to the protonophore carbonyl cyanide m-chlorophenyl-hydrazone and the ionophores valinomycin and gramicidin. Transport-active vesicles contained cytochromes of b and c type, and both serine uptake and TMAO reduction with formate were inhibited with the electron transfer inhibitor 2-heptyl-4-hydroxyquinoline N-oxide. Thus, reduction of TMAO to trimethylamine in A. putrefaciens appeared to be coupled with a chemiosmotic mechanism of energy conversion.