ArticlemBio2014
Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
Article in mBio, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 29 citations in OpenAlex.
- Interactive tools for functional annotation of bacterial genomes.Database : the journal of biological databases and curation · 2024Article
- Choline degradation inJournal of bacteriology · 2024Article
- Exploring stachydrine: from natural occurrence to biological activities and metabolic pathways.Frontiers in plant science · 2024Review
- Second-Shell Amino Acid R266 Helps DetermineBiochemistry · 2021Article
- MtpB, a member of the MttB superfamily from the human intestinal acetogenThe Journal of biological chemistry · 2019Article
- Dynamic Analysis of Metabolic Response in Gastric Ulcer (GU) Rats with Electroacupuncture Treatment UsingEvidence-based complementary and alternative medicine : eCAM · 2019Article
- Confronting the catalytic dark matter encoded by sequenced genomes.Nucleic acids research · 2017Article
- Functional characterization of aconitase X as a cis-3-hydroxy-L-proline dehydratase.Scientific reports · 2016Article
- De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis.BMC genomics · 2015Article
- Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism.MicrobiologyOpen · 2015Article
- Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.Trends in biochemical sciences · 2014Review
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Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
unlabelledThrough the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. IMPORTANCE: At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.