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Timm J, Brochier-Armanet C, Perard J, Zambelli B, Ollagnier-de-Choudens S, Ciurli S, Cavazza C. The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein. Metallomics 2018; 9:575-583. [PMID: 28447092 DOI: 10.1039/c7mt00063d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In Rhodospirillum rubrum, maturation of Carbon Monoxide Dehydrogenase (CODH) requires three accessory proteins, CooC, CooT and CooJ, dedicated to nickel insertion into the active site, which is constituted by a distorted [NiFe3S4] cubane coordinated with a mononuclear Fe site. CooC is an ATPase proposed to provide the energy required for the maturation process, while CooJ is described as a metallochaperone with 16 histidines and 2 cysteines at the C-terminus, likely involved in metal binding and/or storage. Prior to the present study, no information was available on CooT at the molecular level. Here, the X-ray structure of RrCooT was obtained, which revealed that this protein is a homodimer featuring a fold that resembles an Sm-like domain, suggesting a role in RNA metabolism that was however not supported by experimental observations. Biochemical and biophysical evidence based on circular dichroism spectroscopy, light scattering, isothermal titration calorimetry and site-directed mutagenesis showed that RrCooT specifically binds a single Ni(ii) per dimer, with a dissociation constant of 9 nM, through the pair of Cys2, highly conserved residues, located at the dimer interface. Despite its role in the activation of RrCODH in vivo, CooT was thought to be a unique protein, found only in R. rubrum, with an unclear function. In this study, we extended the biological impact of CooT, establishing that this protein is a member of a novel Ni(ii)-binding protein family with 111 homologues, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH.
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Affiliation(s)
- J Timm
- Université Grenoble Alpes, Laboratoire de Chimie et Biologie des Métaux, BioCat, F-Grenoble, France
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Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, Gressent F, Sivignon C, Rahioui I, Kahn D, Brochier-Armanet C, Rahbé Y, Royer C. Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC Plant Biol 2016; 16:63. [PMID: 26964738 PMCID: PMC4785745 DOI: 10.1186/s12870-016-0745-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/25/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Albumin 1b peptides (A1b) are small disulfide-knotted insecticidal peptides produced by Fabaceae (also called Leguminosae). To date, their diversity among this plant family has been essentially investigated through biochemical and PCR-based approaches. The availability of high-quality genomic resources for several fabaceae species, among which the model species Medicago truncatula (Mtr), allowed for a genomic analysis of this protein family aimed at i) deciphering the evolutionary history of A1b proteins and their links with A1b-nodulins that are short non-insecticidal disulfide-bonded peptides involved in root nodule signaling and ii) exploring the functional diversity of A1b for novel bioactive molecules. RESULTS Investigating the Mtr genome revealed a remarkable expansion, mainly through tandem duplications, of albumin1 (A1) genes, retaining nearly all of the same canonical structure at both gene and protein levels. Phylogenetic analysis revealed that the ancestral molecule was most probably insecticidal giving rise to, among others, A1b-nodulins. Expression meta-analysis revealed that many A1b coding genes are silent and a wide tissue distribution of the A1 transcripts/peptides within plant organs. Evolutionary rate analyses highlighted branches and sites with positive selection signatures, including two sites shown to be critical for insecticidal activity. Seven peptides were chemically synthesized and folded in vitro, then assayed for their biological activity. Among these, AG41 (aka MtrA1013 isoform, encoded by the orphan TA24778 contig.), showed an unexpectedly high insecticidal activity. The study highlights the unique burst of diversity of A1 peptides within the Medicago genus compared to the other taxa for which full-genomes are available: no A1 member in Lotus, or in red clover to date, while only a few are present in chick pea, soybean or pigeon pea genomes. CONCLUSION The expansion of the A1 family in the Medicago genus is reminiscent of the situation described for another disulfide-rich peptide family, the "Nodule-specific Cysteine-Rich" (NCR), discovered within the same species. The oldest insecticidal A1b toxin was described from the Sophorae, dating the birth of this seed-defense function to more than 58 million years, and making this model of plant/insect toxin/receptor (A1b/insect v-ATPase) one of the oldest known.
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Affiliation(s)
- L. Karaki
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
- />Université de Lyon, F-69000 Lyon, France
| | - P. Da Silva
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Rizk
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
| | - C. Chouabe
- />Université de Lyon, F-69000 Lyon, France
- />UCBL, CarMeN Laboratory, INSERM UMR-1060, Cardioprotection Team, Faculté de Médecine, Univ Lyon-1, Université Claude Bernard Lyon1, 8 Avenue Rockefeller, 69373 Lyon Cedex 08, France
| | - N. Chantret
- />INRA, UMR1334 AGAP, 2 Place Pierre Viala, 34060 Montpellier, France
- />Supagro Montpellier, 2 Place Pierre Viala, 34060 Montpellier, France
| | - V. Eyraud
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Gressent
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Sivignon
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - I. Rahioui
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - D. Kahn
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - C. Brochier-Armanet
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Y. Rahbé
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Royer
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
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