Pathway alignment: application to the comparative analysis of glycolytic enzymes

Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described.

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Comparative Analysis of Protein Glycosylation Pathways in Humans and the Fungal PathogenCandida albicans

International Journal of Microbiology ◽

10.1155/2014/267497 ◽

2014 ◽

Vol 2014 ◽

pp. 1-16 ◽

Cited By ~ 11

Author(s):

Iván Martínez-Duncker ◽

Diana F. Díaz-Jímenez ◽

Héctor M. Mora-Montes

Keyword(s):

Candida Albicans ◽

Comparative Analysis ◽

Metabolic Pathways ◽

Fungal Pathogen ◽

Protein Glycosylation ◽

Pharmacological Targets ◽

Species Specific

Protein glycosylation pathways are present in all kingdoms of life and are metabolic pathways found in all the life kingdoms. Despite sharing commonalities in their synthesis, glycans attached to glycoproteins have species-specific structures generated by the presence of different sets of enzymes and acceptor substrates in each organism. In this review, we present a comparative analysis of the main glycosylation pathways shared by humans and the fungal pathogenCandida albicans:N-linked glycosylation,O-linked mannosylation and glycosylphosphatidylinositol-anchorage. The knowledge of similarities and divergences between these metabolic pathways could help find new pharmacological targets forC. albicansinfection.

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General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways

Metabolites ◽

10.3390/metabo11060336 ◽

2021 ◽

Vol 11 (6) ◽

pp. 336

Author(s):

Boštjan Murovec ◽

Leon Deutsch ◽

Blaž Stres

Keyword(s):

16S Rrna ◽

Metabolic Pathways ◽

Large Scale ◽

Enzymatic Reactions ◽

Operational Taxonomic Units ◽

Biochemical Pathways ◽

Meaningful Information ◽

Novel Biomarkers ◽

Reproducible Analysis ◽

Microbiome Profiling

General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.

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Comparative genome analysis of Corynebacterium species: The underestimated pathogens with high virulence potential

Infection Genetics and Evolution ◽

10.1016/j.meegid.2021.104928 ◽

2021 ◽

pp. 104928

Author(s):

Fouzia Nasim ◽

Arijit Dey ◽

Insaf Ahmed Qureshi

Keyword(s):

Genome Analysis ◽

Comparative Genome Analysis ◽

Comparative Genome ◽

Virulence Potential ◽

Corynebacterium Species ◽

High Virulence

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Synteny Conservation and Chromosome Rearrangements During Mammalian Evolution

Genetics ◽

10.1093/genetics/147.1.289 ◽

1997 ◽

Vol 147 (1) ◽

pp. 289-296 ◽

Cited By ~ 2

Author(s):

Jason Ehrlich ◽

David Sankoff ◽

Joseph H Nadeau

Keyword(s):

Genome Analysis ◽

Systematic Errors ◽

Chromosome Rearrangements ◽

Mammalian Evolution ◽

Comparative Genome Analysis ◽

Reciprocal Translocations ◽

Comparative Genome ◽

Strong Selection ◽

Synteny Conservation

Abstract An important problem in comparative genome analysis has been defining reliable measures of synteny conservation. The published analytical measures of synteny conservation have limitations. Nonindependence of comparisons, conserved and disrupted syntenies that are as yet unidentified, and redundant rearrangements lead to systematic errors that tend to overestimate the degree of conservation. We recently derived methods to estimate the total number of conserved syntenies within the genome, counting both those that have already been described and those that remain to be discovered. With this method, we show that ~65% of the conserved syntenies have already been identified for humans and mice, that rates of synteny disruption vary ~25-fold among mammalian lineages, and that despite strong selection against reciprocal translocations, inter-chromosome rearrangements occurred approximately fourfold more often than inversions and other intra-chromosome rearrangements, at least for lineages leading to humans and mice.

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Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens

Molecules ◽

10.3390/molecules26154538 ◽

2021 ◽

Vol 26 (15) ◽

pp. 4538

Author(s):

Scarlett Puebla-Barragan ◽

Emiley Watson ◽

Charlotte van der Veer ◽

John A. Chmiel ◽

Charles Carr ◽

...

Keyword(s):

Biogenic Amines ◽

Metabolic Pathways ◽

Vaginal Microbiota ◽

Comparative Genome Analysis ◽

Genetic Traits ◽

Lactobacillus Crispatus ◽

Vaginal Swabs ◽

The Common ◽

Synthesis And Degradation

Lactobacillus crispatus is the dominant species in the vagina of many women. With the potential for strains of this species to be used as a probiotic to help prevent and treat dysbiosis, we investigated isolates from vaginal swabs with Lactobacillus-dominated and a dysbiotic microbiota. A comparative genome analysis led to the identification of metabolic pathways for synthesis and degradation of three major biogenic amines in most strains. However, targeted metabolomic analysis of the production and degradation of biogenic amines showed that certain strains have either the ability to produce or to degrade these compounds. Notably, six strains produced cadaverine, one produced putrescine, and two produced tyramine. These biogenic amines are known to raise vaginal pH, cause malodour, and make the environment more favourable to vaginal pathogens. In vitro experiments confirmed that strains isolated from women with a dysbiotic vaginal microbiota have higher antimicrobial effects against the common urogenital pathogens Escherichia coli and Enterococcus faecium. The results indicate that not all L. crispatus vaginal strains appear suitable for probiotic application and the basis for selection should not be only the overall composition of the vaginal microbiota of the host from which they came, but specific biochemical and genetic traits.

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