Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication

ABSTRACT The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity. Because of their ultrasmall size, reduced genome, and lack of core biosynthetic capabilities,...

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Autores principales:	Charles Bernard, Romain Lannes, Yanyan Li, Éric Bapteste, Philippe Lopez
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	CPR DPANN interkingdom signaling microbial communication microbiology quorum sensing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/f553c72277bb47179018c744e5a8c18c
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spelling	oai:doaj.org-article:f553c72277bb47179018c744e5a8c18c2021-12-02T19:47:33ZRich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication10.1128/mSystems.00414-202379-5077https://doaj.org/article/f553c72277bb47179018c744e5a8c18c2020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00414-20https://doaj.org/toc/2379-5077ABSTRACT The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity. Because of their ultrasmall size, reduced genome, and lack of core biosynthetic capabilities, most CPR and DPANN members are predicted to be sustained through their interactions with other species. How the few characterized CPR and DPANN symbionts achieve these critical interactions is, however, poorly understood. Here, we conducted an in silico analysis on 2,597 CPR/DPANN genomes to test whether these ultrasmall microorganisms might encode homologs of reference proteins involved in the synthesis and/or the detection of 26 different types of communication molecules (quorum sensing [QS] signals), since QS signals are well-known mediators of intra- and interorganismic relationships. We report the discovery of 5,693 variants of QS proteins distributed across 63 CPR and 6 DPANN phyla and associated with 14 distinct types of communication molecules, most of which were characterized as interspecies QS signals. IMPORTANCE The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated.Charles BernardRomain LannesYanyan LiÉric BaptestePhilippe LopezAmerican Society for MicrobiologyarticleCPRDPANNinterkingdom signalingmicrobial communicationmicrobiologyquorum sensingMicrobiologyQR1-502ENmSystems, Vol 5, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	CPR DPANN interkingdom signaling microbial communication microbiology quorum sensing Microbiology QR1-502
spellingShingle	CPR DPANN interkingdom signaling microbial communication microbiology quorum sensing Microbiology QR1-502 Charles Bernard Romain Lannes Yanyan Li Éric Bapteste Philippe Lopez Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
description	ABSTRACT The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity. Because of their ultrasmall size, reduced genome, and lack of core biosynthetic capabilities, most CPR and DPANN members are predicted to be sustained through their interactions with other species. How the few characterized CPR and DPANN symbionts achieve these critical interactions is, however, poorly understood. Here, we conducted an in silico analysis on 2,597 CPR/DPANN genomes to test whether these ultrasmall microorganisms might encode homologs of reference proteins involved in the synthesis and/or the detection of 26 different types of communication molecules (quorum sensing [QS] signals), since QS signals are well-known mediators of intra- and interorganismic relationships. We report the discovery of 5,693 variants of QS proteins distributed across 63 CPR and 6 DPANN phyla and associated with 14 distinct types of communication molecules, most of which were characterized as interspecies QS signals. IMPORTANCE The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated.
format	article
author	Charles Bernard Romain Lannes Yanyan Li Éric Bapteste Philippe Lopez
author_facet	Charles Bernard Romain Lannes Yanyan Li Éric Bapteste Philippe Lopez
author_sort	Charles Bernard
title	Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
title_short	Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
title_full	Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
title_fullStr	Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
title_full_unstemmed	Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication
title_sort	rich repertoire of quorum sensing protein coding sequences in cpr and dpann associated with interspecies and interkingdom communication
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/f553c72277bb47179018c744e5a8c18c
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_version_	1718376000709984256

Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication

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