scholarly journals (R)-1-hydroxy-2-aminoethylphosphonate ammonia-lyase, a new PLP-dependent enzyme involved in bacterial phosphonate degradation

2020 ◽  
Author(s):  
Erika Zangelmi ◽  
Toda Stankovic ◽  
Marco Malatesta ◽  
Domenico Acquotti ◽  
Katharina Pallitsch ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Elimination Reaction ◽  
Stable Carbon ◽  
Bacterial Gene ◽  
Naturally Occurring ◽  
Number Of Microorganisms

Phosphonates contain a particularly stable carbon-phosphorus bond, yet a number of microorganisms possess pathways to degrade these molecules and use them as source of phosphorus. One example is the widespread hydrolytic route for the breakdown of 2-aminoethylphosphonate (AEP). In this pathway, the aminotransferase PhnW initially converts AEP into phosphonoacetaldehyde (PAA), which is then cleaved by the hydrolase PhnX to yield acetaldehyde and phosphate. This work focuses on a novel enzyme (hereby termed PbfA), which is often encoded in bacterial gene clusters containing the phnW-phnX combination. Although PbfA is annotated as a transaminase, we report that it catalyzes an elimination reaction on the naturally occurring compound (R)-1-hydroxy-2-aminoethylphosphonate (R-HAEP). The reaction releases ammonia and generates PAA, which can be subsequently hydrolyzed by PhnX. Overall, the PbfA reaction represents a frequent accessory branch in the hydrolytic pathway for AEP degradation, which expands the scope and versatility of the pathway itself.

Stable carbon and nitrogen isotope patterns in baleen from eastern Arctic bowhead whales (Balaena mysticetus)

1998 ◽  
Vol 55 (12) ◽  
pp. 2601-2607 ◽  
Author(s):  
Keith A Hobson ◽  
Don M Schell
Keyword(s):  
Nutritional Ecology ◽  
Nitrogen Isotope ◽  
Protein Catabolism ◽  
Stable Carbon ◽  
Balaena Mysticetus ◽  
Bowhead Whales ◽  
Carbon And Nitrogen ◽  
Naturally Occurring ◽  
Western Arctic ◽  
Periodic Fluctuations

Previous measurements of naturally occurring stable isotopes of carbon (delta13C) and nitrogen (delta15N) along the baleen plates of western Arctic bowhead whales (Balaena mysticetus) have provided a continuous lifetime record of the feeding or nutritional ecology of these animals that migrate annually between isotopically different foodwebs. However, virtually nothing was known about isotopic patterns of eastern Arctic bowheads. We measured delta13C and delta15N values along the baleen plates of three eastern and one western Arctic bowhead whales taken from Canadian waters in 1988 and 1996. In contrast to western Arctic animals, we found strong evidence for periodic fluctuations in delta15N but not delta13C values in the eastern Arctic specimens. We interpret these results as evidence that eastern Arctic animals do not move between foodwebs that differ in delta13C signature and suggest that these whales either (i) move annually between areas isotopically enriched in 15N but not 13C, (ii) shift diet annually by about one third of a trophic level, or (iii) undergo seasonal fasting that results in enrichment of baleen delta15N resulting from protein catabolism.

scholarly journals Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters

2011 ◽  
Vol 27 (20) ◽  
pp. 2905-2906 ◽  
Author(s):  
A. Despalins ◽  
S. Marsit ◽  
J. Oberto
Keyword(s):  
Gene Clusters ◽  
Web Tool ◽  
Bacterial Gene

scholarly journals A widespread family of bacterial gene clusters produces ClpP inhibitors

2021 ◽  
Author(s):  
Gerry Wright ◽  
Elizabeth Culp ◽  
David Sychantha ◽  
Christian Hobson ◽  
Andrew Pawlowski ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Genome Mining ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Biosynthetic Gene Clusters ◽  
Bacterial Gene ◽  
Clinical Potential ◽  
Novel Scaffold

Abstract Intracellular proteolytic complexes play an essential role in modeling the proteome in both bacteria and eukaryotes. ClpP is the protease subunit of one such highly conserved proteolytic complex that, despite its potential, remains unexploited as a drug target. Here we describe a target-directed genome mining strategy to identify ClpP targeting compounds from the bacterial order Actinomycetales. By searching for biosynthetic gene clusters that contain duplicated copies of ClpP as putative antibiotic resistance genes, we identify a family of ClpP-associated clusters that are widespread across phyla, including environmental and pathogenic bacteria. While numerous bacterial pyrrolizidine alkaloids produced by these gene clusters are known, their connection to ClpP has never been made. We show that these previously characterized molecules do not affect ClpP function but are shunt metabolites derived from the genuine product of these gene clusters, a reactive covalent ClpP inhibitor. Focusing on one such cryptic gene cluster from Streptomyces cattleya DSM 46488, we use heterologous expression to purify the relevant ClpP inhibitor, which we name clipibicyclene. We show in vitro and in vivo that clipibicyclene is a potent covalent inhibitor of ClpP and that cluster-associated ClpPs provide resistance. ClpP inhibition results in antibacterial activity against actinobacteria, including Mycobacterium smegmatis, and inhibition of virulence factor production by Staphylococcus aureus. Finally, we solve the crystal structure of clipibicyclene-modified Escherichia coli ClpP. Clipibicyclene’s discovery deconvolutes the actual function of a family of natural products widespread in nature. It provides a novel scaffold for therapeutic ClpP inhibitor development, making these findings significant from the perspective of their discovery and their clinical potential.

Analysis of selenium granules in Aeromonas hydrophila

1991 ◽  
Vol 49 ◽  
pp. 324-325
Author(s):  
N. R. Smith ◽  
B. J. Bramlett ◽  
C. Echer ◽  
B. A. Dixon
Keyword(s):  
Aeromonas Hydrophila ◽  
Fossil Fuel ◽  
Reduction Process ◽  
Drainage Water ◽  
Agricultural Drainage ◽  
Essential Trace Element ◽  
Fossil Fuel Combustion ◽  
Naturally Occurring ◽  
Number Of Microorganisms ◽  
State Models

Selenium (Se) is a naturally occurring nonmetallic element found in the environment as a result of fossil fuel combustion and industrial and agricultural processes. Although it is an essential trace element for plants and animals, high levels of soluble Se in agricultural drainage water have had deleterious effects on fish and waterfowl. The toxic forms of Se exist as selenate (+VI) and selenite (+IV) and both valence forms can be chemically reduced to insoluble, non-toxic elemental Se (O).A number of microorganisms are capable of reducing soluble Se to the zero valence state. Models have been proposed for using indigenous bacteria in water treatment systems to remove the toxic forms of Se via the reduction process. In order to realistically utilize this procedure, it is necessary to demonstrate that indeed the soluble Se is converted to elemental Se.

scholarly journals Stable carbon and nitrogen isotopic fractionation between diet and swine tissues

2006 ◽  
Vol 63 (6) ◽  
pp. 579-582 ◽  
Author(s):  
Gabriela Bielefeld Nardoto ◽  
Patricia Barboza de Godoy ◽  
Epaminondas Sansigolo de Barros Ferraz ◽  
Jean Pierre Henry Balbaud Ometto ◽  
Luiz Antonio Martinelli
Keyword(s):  
Stable Isotope ◽  
Isotopic Fractionation ◽  
Isotope Ratios ◽  
Animal Nutrition ◽  
Stable Carbon ◽  
Carbon And Nitrogen ◽  
Dietary Reconstruction ◽  
Naturally Occurring ◽  
C And N ◽  
The One

Naturally occurring stable isotope ratios can be a powerful tool in studies of animal nutrition, provided that the assumptions required for dietary reconstruction are validated by studies such as the one presented here. The objective of this study was to document the magnitude of isotopic fractionation between swine diet and their different tissues. For this, the isotopic ratios of carbon and nitrogen of the diet and selected tissues (hair, nail, liver, muscle, fat and cartilage) were determined. The delta13C and delta15N of the diet were -15.9‰ and 1.3‰, respectively, and all delta15N of swine tissues were 2.2 to 3.0‰ enriched in 15N in relation to the diet. Little variation in delta15N occurred among tissues, with exception to liver that was less enriched in 15N than the nail. Nail and hair presented no 13C enrichment relative to diet. Cartilage was ~1.0‰ enriched in 13C as compared to diet. Liver and muscle were on average 2.1‰ more depleted in 13C in relation to diet as well as fat tissues. Some of the C and N isotope ratios of swine tissues differed in organs, but the isotopic fractionation trends among tissues appears to be similar to other mammals. Therefore our data provide a good baseline to interpret stable isotope patterns in domestic mammals (such as swine) in controlled or semi-controlled experiments.

scholarly journals Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Abdoul-Razak Tidjani ◽  
Jean-Noël Lorenzi ◽  
Maxime Toussaint ◽  
Erwin van Dijk ◽  
Delphine Naquin ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Public Goods ◽  
Significant Proportion ◽  
Gene Clusters ◽  
Recent Common Ancestor ◽  
Natural Soil ◽  
Gene Pools ◽  
Bacterial Gene ◽  
Integrative And Conjugative Elements

ABSTRACT In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations. IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.

scholarly journals Computational modelling of Chromosomally Clustering Protein Domains In Bacteria

2021 ◽  
Author(s):  
Chiara E. Cotroneo ◽  
Isobel Claire Gormley ◽  
Denis C. Shields ◽  
Michael Salter-Townshend
Keyword(s):  
Gene Ontology ◽  
Mixture Model ◽  
Computational Modelling ◽  
Protein Domains ◽  
Gene Clusters ◽  
Protein Domain ◽  
Parameter Estimates ◽  
Bacterial Gene ◽  
Wide Range ◽  
The Stability

Abstract Background: In bacteria, genes with related functions - such as those involved in the metabolism of the same compound or in infection processes - are often physically close on the genome and form groups called clusters. The enrichment of such clusters over various distantly related bacteria can be used to predict the roles of genes of unknown function that cluster with characterised genes. There is no obvious rule to define a cluster, given their variability in size and intergenic distances, and the definition of what comprises a “gene”, since genes can gain and lose domains over time. Protein domains can cluster within a gene, or in adjacent genes of related function, and in both cases these are chromosomally clustered. Here, we model the distances between pairs of protein domain coding regions across a wide range of bacteria and archaea via a probabilistic two component mixture model, without imposing arbitrary thresholds in terms of gene numbers or distances. Results: We trained our model using matched Gene Ontology terms to label functionally related pairs and assess the stability of the parameters of the model across 14, 178 archaeal and bacterial strains. We found that the parameters of our mixture model are remarkably stable across bacteria and archaea, except for endosymbionts and obligate intracellular pathogens. Obligate pathogens have smaller genomes, and although they vary, on average do not show noticeably different clustering distances; the main difference in the parameter estimates is that a far greater proportion of the genes sharing ontology terms are clustered. This may reflect that these genomes are enriched for complexes encoded by clustered core housekeeping genes, as a proportion of the total genes. Given the overall stability of the parameter estimates, we then used the mean parameter estimates across the entire dataset to investigate which gene ontology terms are most frequently associated with clustered genes. Conclusions: Given the stability of the mixture model across species, it may be used to predict bacterial gene clusters that are shared across multiple species, in addition to giving insights into the evolutionary pressures on the chromosomal locations of genes in different species.

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