Unique sugar metabolic pathways of bifidobacteria

Bifidobacteria have many beneficial effects for human health. The gastrointestinal tract, where natural colonization of bifidobacteria occurs, is an environment poor in nutrition and oxygen. Therefore, bifidobacteria have many unique glycosidases, transporters, and metabolic enzymes for sugar fermentation to utilize diverse carbohydrates that are not absorbed by host humans and animals. They have a unique, effective central fermentative pathway called bifid shunt. Recently, a novel metabolic pathway that utilizes both human milk oligosaccharides and host glycoconjugates was found. The galacto-N-biose/lacto-N-biose I metabolic pathway plays a key role in colonization in the infant gastrointestinal tract. These pathways involve many unique enzymes and proteins. This review focuses on their molecular mechanisms, as revealed by biochemical and crystallographic studies.     

Novel metabolic pathways in Archaea

The Archaea harbor many metabolic pathways that differ to previously recognized classical pathways. Glycolysis is carried out by modified versions of the Embden-Meyerhof and Entner-Doudoroff pathways. Thermophilic archaea have recently been found to harbor a bi-functional fructose-1,6-bisphosphate aldolase/phosphatase for gluconeogenesis. A number of novel pentose-degrading pathways have also been recently identified. In terms of anabolic metabolism, a pathway for acetate assimilation, the methylaspartate cycle, and two CO2-fixing pathways, the 3-hydroxypropionate/4-hydroxybutyrate cycle and the dicarboxylate/4-hydroxybutyrate cycle, have been elucidated. As for biosynthetic pathways, recent studies have clarified the enzymes responsible for several steps involved in the biosynthesis of inositol phospholipids, polyamine, coenzyme A, flavin adeninedinucleotide and heme. By examining the presence/absence of homologs of these enzymes on genome sequences, we have found that the majority of these enzymes and pathways are specific to the Archaea.     

Evaluation of two alternative metabolic pathways for creatinine degradation in microorganisms

The microbial decomposition of creatinine was found to proceed mainly via N-methylhydantoin or creatine as the first degradation product. Either N-methylhydantoin or urea or both were detected as metabolites derived from creatinine in various microorganisms, and creatinine deiminase and creatinine amidohydrolase activities were detected concomitantly. N-Methylhydantoin hydrolase and N-carbamoylsarcosine amidohydrolase were found to be formed inducibly in the presence of creatinine or N-methylhydantoin. Three microorganisms which decompose creatinine in different ways were screened from soil. Pseudomonas putida 77 rapidly metabolized creatinine solely via N-methylhydantoin. Degradation of creatinine proceeded with both creatine and N-methylhydantoin as the first degradation products at the same time in Pseudomonas sp. H21. Pseudomonas sp. 0114 was found to metabolize creatinine mainly via creatine and to also metabolize N-methylhydantoin. Changes in the metabolites of creatinine during a cultivation or enzyme reaction were found to be closely related to the enzyme activities of interest which are regulated by creatinine or N-methylhydantoin in different ways depending on the microbial strain.     

Production of bulk chemicals via novel metabolic pathways in microorganisms

Metabolic engineering has been playing important roles in developing high performance microorganisms capable of producing various chemicals and materials from renewable biomass in a sustainable manner. Synthetic and systems biology are also contributing significantly to the creation of novel pathways and the whole cell-wide optimization of metabolic performance, respectively. In order to expand the spectrum of chemicals that can be produced biotechnologically, it is necessary to broaden the metabolic capacities of microorganisms. Expanding the metabolic pathways for biosynthesizing the target chemicals requires not only the enumeration of a series of known enzymes, but also the identification of biochemical gaps whose corresponding enzymes might not actually exist in nature; this issue is the focus of this paper. First, pathway prediction tools, effectively combining reactions that lead to the production of a target chemical, are analyzed in terms of logics representing chemical information, and designing and ranking the proposed metabolic pathways. Then, several approaches for potentially filling in the gaps of the novel metabolic pathway are suggested along with relevant examples, including the use of promiscuous enzymes that flexibly utilize different substrates, design of novel enzymes for non-natural reactions, and exploration of hypothetical proteins. Finally, strain optimization by systems metabolic engineering in the context of novel metabolic pathways constructed is briefly described. It is hoped that this review paper will provide logical ways of efficiently utilizing ‘big’ biological data to design and develop novel metabolic pathways for the production of various bulk chemicals that are currently produced from fossil resources.     

Isotopes in geobiochemistry: tracing metabolic pathways in microorganisms of environmental relevance with stable isotopes

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Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic degradation in microorganisms: A review

Contemporary data on the mechanism of biodegradation of aromatic hydrocarbons and biodegradation genes (genomic organization and pathways of evolution) in diverse groups of microorganisms have been reviewed. Studies of this problem are topical, in view of the need in identification and construction of new strains degrading xenobiotics, particularly those halogenated. For this reason, emphasis is placed on specific features of explored metabolic pathways that can be used for constructing new enzymatic systems not present in nature. Sections on the mechanisms of genomic rearrangements involving biodegradation determinants are presented from the same standpoint. Part of the review is devoted to analyzing methods used for studying the population dynamics of bacterial communities involved in xenobiotic degradation in natural biotopes or industrial waste disposal plants. Particular attention is given to methods of gene systematics.     

Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic biodegradation in microorganisms: a review

Contemporary data on the mechanism of biodegradation of aromatic hydrocarbons and biodegradation genes (genomic organization and pathways of evolution) in diverse groups of microorganisms have been reviewed. Studies of this problem are topical, in view of the need in identification and construction of new strains degrading xenobiotics, particularly those halogenated. For this reason, emphasis is placed on specific features of explored metabolic pathways that can be used for constructing new enzymatic systems not present in nature. Sections on the mechanisms of genomic rearrangements involving biodegradation determinants are presented from the same standpoint. Part of the review is devoted to analyzing methods used for studying the population dynamics of bacterial communities involved in xenobiotic degradation in natural biotopes or industrial waste disposal plants. Particular attention is given to methods of gene systematics.     

甜菊糖生产污染微生物的鉴定

本课题对甜菊糖甙生产中污染渗滤液的微生物进行了形态和生理生化鉴定,得出污染渗滤液最严重的微生物是一假单胞菌．     

Signaling pathways activated by microorganisms

Invasion of viruses and bacteria is initially sensed by the host innate immune system, and evokes a rapid inflammatory response. Nucleotides from RNA viruses are recognized by retinoic-acid-inducible gene I-like helicases and Toll-like receptors, and this recognition triggers signaling cascades that induce antiviral mediators such as type I interferons. By contrast, Toll-like receptors recognizing bacterial components induce the expression of proinflammatory cytokines. Furthermore, recent studies suggest that viral and bacterial DNA also induce interferons in a Toll-independent mechanism, possibly through unidentified cytoplasmic receptor(s).     

CRISPR-based metabolic engineering in non-model microorganisms

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Novel metabolic biomarkers related to sulfur-dependent detoxification pathways in autistic patients of Saudi Arabia

Background  

Xenobiotics are neurotoxins that dramatically alter the health of the child. In addition, an inefficient detoxification system leads to oxidative stress, gut dysbiosis, and immune dysfunction. The consensus among physicians who treat autism with a biomedical approach is that those on the spectrum are burdened with oxidative stress and immune problems. In a trial to understand the role of detoxification in the etiology of autism, selected parameters related to sulfur-dependent detoxification mechanisms in plasma of autistic children from Saudi Arabia will be investigated compared to control subjects.     

Enzymes and pathways of polyamine breakdown in microorganisms

Abstract The information currently available on the breakdown of spermidine and putrescine by microorganisms is reviewed. Two major metabolic routes have been described, one for the free bases via δ¹-pyrroline (4-aminobutyraldehyde), the other via N -acetyl derivatives. In both pathways oxidases or aminotransferases are the key enzymes in removing the nitrogen atoms. The two routes converge at 4-aminobutyrate, which is then metabolized via succinate. The degradation of putrescine in Escherichia coli has been well characterized at both genetic and biochemical levels, but for other bacteria much less information is available. The C₃ moiety of spermidine is broken down via β-alanine, but the metabolism of this compound and its precursors is poorly understood. In yeasts, a catabolic route for spermidine and putrescine via N -acetyl derivatives has been described in Candida boidinii , and the evidence for its occurrence in other species is reviewed. Except for the terminal step of this pathway, the same group of enzymes can metabolize both the C₃ and C₄ moieties of spermidine. It is likely that other routes of polyamine catabolism also exist in both bacteria and yeasts.     

Evolution of dominance in metabolic pathways

Dominance is a form of phenotypic robustness to mutations. Understanding how such robustness can evolve provides a window into how the relation between genotype and phenotype can evolve. As such, the issue of dominance evolution is a question about the evolution of inheritance systems. Attempts at explaining the evolution of dominance have run into two problems. One is that selection for dominance is sensitive to the frequency of heterozygotes. Accordingly, dominance cannot evolve unless special conditions lead to the presence of a high frequency of mutant alleles in the population. Second, on the basis of theoretical results in metabolic control analysis, it has been proposed that metabolic systems possess inherent constraints. These hypothetical constraints imply the default manifestation of dominance of the wild type with respect to the effects of mutations at most loci. Hence, some biologists have maintained that an evolutionary explanation is not relevant to dominance. In this article, we put into question the hypothetical assumption of default metabolic constraints. We show that this assumption is based on an exclusion of important nonlinear interactions that can occur between enzymes in a pathway. With an a priori exclusion of such interactions, the possibility of epistasis and hence dominance modification is eliminated. We present a theoretical model that integrates enzyme kinetics and population genetics to address dominance evolution in metabolic pathways. In the case of mutations that decrease enzyme concentrations, and given the mechanistic constraints of Michaelis-Menten-type catalysis, it is shown that dominance of the wild type can be extensively modified in a two-enzyme pathway. Moreover, we discuss analytical results indicating that the conclusions from the two-enzyme case can be generalized to any number of enzymes. Dominance modification is achieved chiefly through changes in enzyme concentrations or kinetic parameters such as k(cat), both of which can alter saturation levels. Low saturation translates into higher levels of dominance with respect to mutations that decrease enzyme concentrations. Furthermore, it is shown that in the two-enzyme example, dominance evolves as a by-product of selection in a manner that is insensitive to the frequency of heterozygotes. Using variation in k(cat) as an example of modifier mutations, it is shown that the latter can have direct fitness effects in addition to dominance modification effects. Dominance evolution can occur in a frequency-insensitive manner as a result of selection for such dual-effects alleles. This type of selection may prove to be a common pattern for the evolution of phenotypic robustness to mutations.     

Priming xylem for stress recovery depends on coordinated activity of sugar metabolic pathways and changes in xylem sap pH

Some plant species are capable of significant reduction of xylem embolism during recovery from drought despite stem water potential remains negative. However, the functional biology underlying this process is elusive. We subjected poplar trees to drought stress followed by a period of recovery. Water potential, hydraulic conductivity, gas exchange, xylem sap pH, and carbohydrate content in sap and woody stems were monitored in combination with an analysis of carbohydrate metabolism, enzyme activity, and expression of genes involved in sugar metabolic and transport pathways. Drought resulted in an alteration of differential partitioning between starch and soluble sugars. Upon stress, an increase in the starch degradation rate and the overexpression of sugar symporter genes promoted the efflux of disaccharides (mostly maltose and sucrose) to the apoplast. In turn, the efflux activity of the sugar‐proton cotransporters caused a drop in xylem pH. The newly acidic environment induced the activity of apoplastic invertases leading to the accumulation of monosaccharides in the apoplast, thus providing the main osmoticum necessary for recovery. During drought and recovery, a complex network of coordinated molecular and biochemical signals was activated at the interface between xylem and parenchyma cells that appeared to prime the xylem for hydraulic recovery.     

Enzymes and pathways of polyamine breakdown in microorganisms.

The information currently available on the breakdown of spermidine and putrescine by microorganisms is reviewed. Two major metabolic routes have been described, one for the free bases via delta 1-pyrroline (4-aminobutyraldehyde), the other via N-acetyl derivatives. In both pathways oxidases or aminotransferases are the key enzymes in removing the nitrogen atoms. The two routes converge at 4-aminobutyrate, which is then metabolized via succinate. The degradation of putrescine in Escherichia coli has been well characterized at both genetic and biochemical levels, but for other bacteria much less information is available. The C3 moiety of spermidine is broken down via beta-alanine, but the metabolism of this compound and its precursors is poorly understood. In yeasts, a catabolic route for spermidine and putrescine via N-acetyl derivatives has been described in Candida boidinii, and the evidence for its occurrence in other species is reviewed. Except for the terminal step of this pathway, the same group of enzymes can metabolize both the C3 and C4 moieties of spermidine. It is likely that other routes of polyamine catabolism also exist in both bacteria and yeasts.