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Grant support

We thank Dr. Christina Kiel for her comments and the Genomics, Proteomics and Protein Technologies Core Facilities at CRG. Also we thank to Dr. Marc Guell and Dr. Hinnerk Eilers for fruitful discussions. Besray Unal was co-funded by Marie Curie Actions. This work was supported by the European Research Council (ERC), the Fundacion Marcelino Botin, the Spanish Ministerio de Economia y Competitividad BIO2007-61762 and the ISCIII (PI10/01702).

Analysis of institutional authors

Lluch Senar, MaríaCorresponding AuthorDelgado Blanco, JavierAuthorLlorens-Rico, VAuthorUnal, EbAuthorYus, EAuthorMartinez, SAuthorSerrano Pubul, LuisAuthorFerrar, TonyAuthorSerrano, LAuthor

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March 25, 2020
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Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium

Publicated to:Molecular Systems Biology. 11 (1): - 2015-01-01 11(1), DOI: 10.15252/msb.20145558

Authors: Lluch-Senar, M; Delgado, J; Chen, WH; Lloréns-Rico, V; O'Reilly, FJ; Wodke, JA; Unal, EB; Yus, E; Martínez, S; Nichols, RJ; Ferrar, T; Vivancos, A; Schmeisky, A; Stülke, J; van Noort, V; Gavin, AC; Bork, P; Serrano, L

Affiliations

Ctr Genom Regulat CRG, EMBL CRG Syst Biol Res Unit, Barcelona, Spain - Author
European Mol Biol Lab, Heidelberg, Germany - Author
Humboldt Univ, D-10099 Berlin, Germany - Author
ICREA, Barcelona, Spain - Author
Inst Microbiol & Genet, Dept Gen Microbiol, Gottingen, Germany - Author
Katholieke Univ Leuven, Ctr Microbial & Plant Genet, Leuven, Belgium - Author
MDC Mol Med, Berlin, Germany - Author
Stanford Univ, Dept Genet, Stanford, CA 94305 USA - Author
UPF, Barcelona, Spain - Author
VHIO, Barcelona, Spain - Author
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Abstract

Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for 10% of all ORFs, are the most frequently essential genomic components (53%), followed by conventional ORFs (49%). Essentiality of smORFs may be explained by their function as members of protein and/or DNA/RNA complexes. In larger proteins, essentiality applied to individual domains and not entire proteins, a notion we could confirm by expression of truncated domains. The fraction of essential non-coding RNAs (ncRNAs) non-overlapping with essential genes is 5% higher than of non-transcribed regions (0.9%), pointing to the important functions of the former. We found that the minimal essential genome is comprised of 33% (269,410 bp) of the M. pneumoniae genome. Our data highlight an unexpected hidden layer of smORFs with essential functions, as well as non-coding regions, thus changing the focus when aiming to define the minimal essential genome.© 2015 The Authors. Published under the terms of the CC BY 4.0 license.

Keywords

BindingMinimal genomeNon-coding rnasNon?coding rnasNon‐coding rnasProteinsRnasSmall proteinsTranscription

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Molecular Systems Biology 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, 2015, it was in position 14/289, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 2.3. This 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: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 3.62 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 11.79 (source consulted: Dimensions Aug 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-08-02, the following number of citations:

  • WoS: 95
  • Scopus: 81
  • Europe PMC: 90

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 2025-08-02:

  • 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: 248.
  • 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: 257 (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: 17.6.
  • The number of mentions on the social network Facebook: 3 (Altmetric).
  • The number of mentions on the social network X (formerly Twitter): 15 (Altmetric).
  • The number of mentions in news outlets: 1 (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: Belgium; Germany; United States of America.

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 (LLUCH SENAR, MARÍA) and Last Author (SERRANO VERNOS, LAURA).

the author responsible for correspondence tasks has been LLUCH SENAR, MARÍA.