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Analysis of institutional authors

Marcet-Houben MAuthorGabaldon TCorresponding Author

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Widespread inter- and intra-domain horizontal gene transfer of D-amino acid metabolism enzymes in eukaryotes

Publicated to:Frontiers In Microbiology. 7 2001- - 2016-12-20 7(), DOI: 10.3389/fmicb.2016.02001

Authors: Naranjo-Ortíz, MA; Brock, M; Brunke, S; Hube, B; Marcet-Houben, M; Gabaldón, T

Affiliations

Barcelona Inst Sci & Technol, Ctr Genom Regulat, Barcelona, Spain - Author
Barcelona Institute of Science and Technology (BIST) - Author
Friedrich Schiller Univ, Jena, Germany - Author
Friedrich Schiller Universitat Jena - Author
Hans Knoell Inst Jena, Dept Microbial Pathogen Mech, Jena, Germany - Author
Hans-Knoll-Institute (HKI) - Author
ICREA, Barcelona, Spain - Author
Institució Catalana de Recerca i Estudis Avançats - Author
Univ Hosp, Ctr Sepsis Control & Care, Jena, Germany - Author
Univ Nottingham, Sch Life Sci, Fungal Genet & Biol Grp, Nottingham, England - Author
Univ Pompeu Fabra, Barcelona, Spain - Author
Universitat Pompeu Fabra Barcelona - Author
Universitatsklinikum Jena und Medizinische Fakultat - Author
University of Nottingham - Author
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Abstract

© 2016 Naranjo-Ortíz, Brock, Brunke, Hube, Marcet-Houben and Gabaldón. Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that D-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether D-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role.

Keywords

abaccusamino acid racemasecandida glabratad-amino acid metabolismd-amino acid oxidasefungiAbaccusAlanine racemaseAmino acid racemaseCandida glabrataD-amino acid metabolismD-amino acid oxidaseD-serineEvolutionFungalFungiHorizontal gene transferInfectionLipid-metabolismMultiple sequence alignmentPerformanceProline racemaseProtein

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Frontiers In Microbiology due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2016, it was in position 26/125, thus managing to position itself as a Q1 (Primer Cuartil), in the category Microbiology.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 1.91, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jun 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-06-13, the following number of citations:

  • WoS: 12
  • Scopus: 16
  • Europe PMC: 10
  • OpenCitations: 18

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-06-13:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 41.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 41 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 5.35.
  • The number of mentions on the social network X (formerly Twitter): 9 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Germany; United Kingdom.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Naranjo-Ortíz M) and Last Author (Gabaldon Esteban, Toni).

the author responsible for correspondence tasks has been Gabaldon Esteban, Toni.