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Analysis of institutional authors

Sanchis-Lopez, ClaudiaCorresponding AuthorPaul Cerna-Vargas, JeanAuthorSantamaria-Hernando, SarayCorresponding AuthorRodriguez-Palenzuela, PabloAuthorLopez-Solanilla, EmiliaAuthorHuerta-Cepas, JaimeCorresponding AuthorRodriguez-Herva, Jose JCorresponding Author

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October 21, 2021
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Article

Prevalence and specificity of chemoreceptor profiles in plant-associated bacteria

Publicated to: mSystems. 6 (5): e0095121- - 2021-10-01 6(5), DOI: 10.1128/mSystems.00951-21

Authors:

Sanchis-Lopez, Claudia; Paul Cerna-Vargas, Jean; Santamaria-Hernando, Saray; Ramos, Cayo; Krell, Tino; Rodriguez-Palenzuela, Pablo; Lopez-Solanilla, Emilia; Huerta-Cepas, Jaime; Rodriguez-Herva, Jose J; Rodriguez-Herva, Jose J
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Affiliations

CSIC, Estn Expt Zaidin, Dept Environm Protect, Granada, Spain - Author
Interacciones Moleculares Planta-Patógeno. Universidad Politécnica de Madrid - Author
Univ Malaga, Fac Ciencias, Inst Hortofruticultura Subtrop & Mediterranea May, Area Genet,CSIC,IHSM UMA CSIC, Malaga, Spain - Author
Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas CBGP, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Madrid, Spain - Author
Univ Politecn Madrid UPM, Dept Biotecnol Biol Vegetal, Escuela Tecn Super Ingn Agron Alimentaria & Biosi, Madrid, Spain - Author
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Abstract

Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the ligand binding domain (LBD) of chemoreceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity. Here, we analyzed 82,277 CR sequences from 11,806 representative microbial species covering the whole prokaryotic phylogeny, and we classified them according to their LBD type using a de novo homology clustering method. Through phylogenomic analysis, we identified hundreds of LBDs that are found predominantly in plant-associated bacteria, including several LBDs specific to phytopathogens and plant symbionts. Functional annotation of our catalogue showed that many of the LBD clusters identified might constitute unknown types of LBDs. Moreover, we found that the taxonomic distribution of most LBD types that are specific to plant-associated bacteria is only partially explained by phylogeny, suggesting that lifestyle and niche adaptation are important factors in their selection. Finally, our results show that the profile of LBD types in a given genome is related to the lifestyle specialization, with plant symbionts and phytopathogens showing the highest number of niche-specific LBDs. The LBD catalogue and information on how to profile novel genomes are available at https://github.com/compgenomicslab/CRs. IMPORTANCE Considering the enormous variety of LBDs at sensor proteins, an important question resides in establishing the forces that have driven their evolution and selection. We present here the first clear demonstration that environmental factors play an important role in the selection and evolution of LBDs. We were able to demonstrate the existence of LBD families that are highly enriched in plant-associated bacteria but show a wide phylogenetic spread. These findings offer a number of research opportunities in the field of single transduction, such as the exploration of similar relationships in chemoreceptors of bacteria with a different lifestyle, like those inhabiting or infecting the human intestine. Similarly, our results raise the question whether similar LBD types might be shared by members of different sensor protein families. Lastly, we provide a comprehensive catalogue of CRs classified by their LBD region that includes a large number of putative new LBD types.
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Keywords

amino-acidaspartatechemoreceptorchemotaxisclassificationidentificationmethyl-accepting chemotaxis proteinplant-associated bacteriareceptorsreconstructionsystemvirulenceChemoreceptorChemotaxisDickeya-dadantii 3937Life on landMcpMethyl-accepting chemotaxis proteinPlant-associated bacteria

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal mSystems 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, 2021, it was in position 27/137, 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 World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 2.39. 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 13, 2025)

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: 3.33 (source consulted: FECYT Mar 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2026-04-28, the following number of citations:

  • WoS: 38
  • Scopus: 37
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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 2026-04-28:

  • 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: 37.
  • 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: 35 (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: 22.
  • The number of mentions on the social network X (formerly Twitter): 20 (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.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://oa.upm.es/92729/

As a result of the publication of the work in the institutional repository, statistical usage data has been obtained that reflects its impact. In terms of dissemination, we can state that, as of

  • Views: 47
  • Downloads: 12
Continuing with the social impact of the work, it is important to emphasize that, due to its content, it can be assigned to the area of interest of ODS 15 - Life on land, with a probability of 43% according to the mBERT algorithm developed by Aurora University.
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Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Sudan.

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 (LOPEZ SOLANILLA, EMILIA ANTONIA) and Last Author (RODRIGUEZ HERVA, JOSE JUAN).

the authors responsible for correspondence tasks have been LOPEZ SOLANILLA, EMILIA ANTONIA, SANTAMARIA HERNANDO, SARAY, HUERTA CEPAS, JAIME and RODRIGUEZ HERVA, JOSE JUAN.

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Project objectives

Los objetivos perseguidos en esta aportación se centran en profundizar en el conocimiento sobre los perfiles de quimiorreceptores en bacterias asociadas a plantas. Se pretende analizar 82,277 secuencias de quimiorreceptores de 11,806 especies microbianas representativas para clasificar sus dominios de unión a ligandos (LBD) mediante un método de agrupamiento homólogo de novo. Además, se busca identificar y caracterizar LBDs específicos de bacterias asociadas a plantas, incluyendo fitopatógenos y simbiontes. Se pretende evaluar la distribución taxonómica de estos LBDs para determinar la influencia de la filogenia y la adaptación al nicho ecológico. Finalmente, se aspira a relacionar los perfiles de LBD con la especialización del estilo de vida bacteriano y proporcionar un catálogo funcional y accesible de estos dominios.
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Most relevant results

El estudio presenta un análisis exhaustivo de 82,277 secuencias de receptores quimiorreceptores (CR) de 11,806 especies microbianas representativas. Se identificaron cientos de dominios de unión a ligandos (LBD) predominantes en bacterias asociadas a plantas, incluyendo LBDs específicos de fitopatógenos y simbiontes vegetales. La anotación funcional reveló numerosos grupos de LBD posiblemente desconocidos hasta ahora. La distribución taxonómica de la mayoría de los LBD específicos de bacterias asociadas a plantas no se explica completamente por la filogenia, indicando que la adaptación al nicho y estilo de vida influyen en su selección. Finalmente, el perfil de LBD en un genoma está relacionado con la especialización del estilo de vida, destacando fitopatógenos y simbiontes con mayor número de LBDs específicos.
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