PROBING AGE-RELATED CHANGES IN LEGUME NODULE PROTEOME BY PROTEOMICS AND METABOLOMICS APPROACHES

Andrej Frolov, Tatiana Bilova, Christian Ihling, Ahyoung Kim, Alexander Tsarev, Veronika Chantseva, Tatiana Mamontova, Elena Lukasheva, Julia Shumilina, Anna Chekina, Ekaterina Romanovskaya, Tatiana Grishina, Kirill Demchenko, Viktor Tsyganov, Andrea Sinz, Vladimir A. Zhukov, Manuel Becana, Manuel Matamoros, Igor A. Tikhonovich, Ludger A. Wessjohann

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Abstract

Proteomics and metabolomics represent powerful tools of functional genomics, giving direct access to the molecular mechanisms underlying plant response on developmental signals, metabolic pathways, and regulatory networks. The combination of these approaches might give deeper insights into the molecular mechanisms contributing on mutualistic plant-microbial interactions, in particular, legume-rhizobial symbiosis. Here we address age-related changes in determinate and indeterminate root nodules of common bean (Phaseolus vulgaris) and pea (Pisum sativum). Juvenile, flowering, and senescent plants were harvested, the proteins were isolated by phenol extraction and digested with trypsin, isolating metabolites by a multi-step extraction with solvents of different polarity. Protein hydrolyzates were analyzed by nanoLC-ESI-Q- and LIT-Orbitrap-MS in data-dependent acquisition (DDA) mode. Database search and annotation of PTMs were based on the SEQUEST algorithm; quantification was performed using a label-free strategy. Functions and localization of the proteins were annotated by an in-house developed workflow, combined with MapMan, Mercator, LocTree3 and String tools. Analysis of primary metabolome relied on the combination of GC-MS and IP-RP-UHPLC-MS, with a secondary metabolite profiling by RP-UHPLC-MS. The analysis revealed 656 and 92 differentially regulated proteins in common bean and pea nodules, respectively. Plant proteins were mostly down-regulated and represented by the molecules involved in signaling and protein metabolism, while most of the bacterial polypeptides were up-regulated and found to be involved in energy metabolism and nitrogen fixation. Agedependent changes in metabolite profiles were characterized based on the accumulation of carbohydrates and amino acids. Interestingly, mutation in the gene sym27 resulted in the suppression of signaling and protein biosynthesis in both symbiosis partners. Remarkably, nodule ageing was accompanied with enhanced glycation and carbonylation. In total, 36 age-related glycation hotspots were identified in the P. vulgaris nodule proteome. This project was supported by the Russian Science Foundation (project 17-16-01042).
Original languageRussian
Title of host publicationII Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»
Subtitle of host publicationНаучные труды
Place of PublicationМ.
PublisherИздательство «Перо»
Pages152
Volume2
ISBN (Print)9785001505211 (Т. 2), 9785001505198
Publication statusPublished - Sep 2019
EventII ОБЪЕДИНЕННЫЙ НАУЧНЫЙ ФОРУМ, VI СЪЕЗД ФИЗИОЛОГОВ СНГ,
VI СЪЕЗД БИОХИМИКОВ РОССИИ, IX РОССИЙСКИЙ СИМПОЗИУМ «БЕЛКИ И ПЕПТИДЫ»
- Гостиничный комплекс «Дагомыс», Сочи-Дагомыс
Duration: 1 Oct 20196 Oct 2019
Conference number: VI
http://www.rusbiochem.org/page206.html

Publication series

NameACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ)
ISSN (Print)2075-8243

Conference

ConferenceII ОБЪЕДИНЕННЫЙ НАУЧНЫЙ ФОРУМ, VI СЪЕЗД ФИЗИОЛОГОВ СНГ,
VI СЪЕЗД БИОХИМИКОВ РОССИИ, IX РОССИЙСКИЙ СИМПОЗИУМ «БЕЛКИ И ПЕПТИДЫ»
CountryRussian Federation
CityСочи-Дагомыс
Period1/10/196/10/19
Internet address

Cite this

Frolov, A., Bilova, T., Ihling, C., Kim, A., Tsarev, A., Chantseva, V., ... Wessjohann, L. A. (2019). PROBING AGE-RELATED CHANGES IN LEGUME NODULE PROTEOME BY PROTEOMICS AND METABOLOMICS APPROACHES. In II Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»: Научные труды (Vol. 2, pp. 152). (ACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ)). М.: Издательство «Перо».
Frolov, Andrej ; Bilova, Tatiana ; Ihling, Christian ; Kim, Ahyoung ; Tsarev, Alexander ; Chantseva, Veronika ; Mamontova, Tatiana ; Lukasheva, Elena ; Shumilina, Julia ; Chekina, Anna ; Romanovskaya, Ekaterina ; Grishina, Tatiana ; Demchenko, Kirill ; Tsyganov, Viktor ; Sinz, Andrea ; Zhukov, Vladimir A. ; Becana, Manuel ; Matamoros, Manuel ; Tikhonovich, Igor A. ; Wessjohann, Ludger A. . / PROBING AGE-RELATED CHANGES IN LEGUME NODULE PROTEOME BY PROTEOMICS AND METABOLOMICS APPROACHES. II Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»: Научные труды. Vol. 2 М. : Издательство «Перо», 2019. pp. 152 (ACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ)).
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abstract = "Proteomics and metabolomics represent powerful tools of functional genomics, giving direct access to the molecular mechanisms underlying plant response on developmental signals, metabolic pathways, and regulatory networks. The combination of these approaches might give deeper insights into the molecular mechanisms contributing on mutualistic plant-microbial interactions, in particular, legume-rhizobial symbiosis. Here we address age-related changes in determinate and indeterminate root nodules of common bean (Phaseolus vulgaris) and pea (Pisum sativum). Juvenile, flowering, and senescent plants were harvested, the proteins were isolated by phenol extraction and digested with trypsin, isolating metabolites by a multi-step extraction with solvents of different polarity. Protein hydrolyzates were analyzed by nanoLC-ESI-Q- and LIT-Orbitrap-MS in data-dependent acquisition (DDA) mode. Database search and annotation of PTMs were based on the SEQUEST algorithm; quantification was performed using a label-free strategy. Functions and localization of the proteins were annotated by an in-house developed workflow, combined with MapMan, Mercator, LocTree3 and String tools. Analysis of primary metabolome relied on the combination of GC-MS and IP-RP-UHPLC-MS, with a secondary metabolite profiling by RP-UHPLC-MS. The analysis revealed 656 and 92 differentially regulated proteins in common bean and pea nodules, respectively. Plant proteins were mostly down-regulated and represented by the molecules involved in signaling and protein metabolism, while most of the bacterial polypeptides were up-regulated and found to be involved in energy metabolism and nitrogen fixation. Agedependent changes in metabolite profiles were characterized based on the accumulation of carbohydrates and amino acids. Interestingly, mutation in the gene sym27 resulted in the suppression of signaling and protein biosynthesis in both symbiosis partners. Remarkably, nodule ageing was accompanied with enhanced glycation and carbonylation. In total, 36 age-related glycation hotspots were identified in the P. vulgaris nodule proteome. This project was supported by the Russian Science Foundation (project 17-16-01042).",
author = "Andrej Frolov and Tatiana Bilova and Christian Ihling and Ahyoung Kim and Alexander Tsarev and Veronika Chantseva and Tatiana Mamontova and Elena Lukasheva and Julia Shumilina and Anna Chekina and Ekaterina Romanovskaya and Tatiana Grishina and Kirill Demchenko and Viktor Tsyganov and Andrea Sinz and Zhukov, {Vladimir A.} and Manuel Becana and Manuel Matamoros and Tikhonovich, {Igor A.} and Wessjohann, {Ludger A.}",
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month = "9",
language = "русский",
isbn = "9785001505211 (Т. 2)",
volume = "2",
series = "ACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ)",
publisher = "Издательство «Перо»",
pages = "152",
booktitle = "II Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»",
address = "Российская Федерация",

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Frolov, A, Bilova, T, Ihling, C, Kim, A, Tsarev, A, Chantseva, V, Mamontova, T, Lukasheva, E, Shumilina, J, Chekina, A, Romanovskaya, E, Grishina, T, Demchenko, K, Tsyganov, V, Sinz, A, Zhukov, VA, Becana, M, Matamoros, M, Tikhonovich, IA & Wessjohann, LA 2019, PROBING AGE-RELATED CHANGES IN LEGUME NODULE PROTEOME BY PROTEOMICS AND METABOLOMICS APPROACHES. in II Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»: Научные труды. vol. 2, ACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ), Издательство «Перо», М., pp. 152, Сочи-Дагомыс, 1/10/19.

PROBING AGE-RELATED CHANGES IN LEGUME NODULE PROTEOME BY PROTEOMICS AND METABOLOMICS APPROACHES. / Frolov, Andrej ; Bilova, Tatiana; Ihling, Christian; Kim, Ahyoung; Tsarev, Alexander; Chantseva, Veronika; Mamontova, Tatiana; Lukasheva, Elena; Shumilina, Julia; Chekina, Anna; Romanovskaya, Ekaterina; Grishina, Tatiana; Demchenko, Kirill; Tsyganov, Viktor ; Sinz, Andrea; Zhukov, Vladimir A.; Becana, Manuel ; Matamoros, Manuel ; Tikhonovich, Igor A.; Wessjohann, Ludger A. .

II Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»: Научные труды. Vol. 2 М. : Издательство «Перо», 2019. p. 152 (ACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ)).

Research output

TY - CHAP

T1 - PROBING AGE-RELATED CHANGES IN LEGUME NODULE PROTEOME BY PROTEOMICS AND METABOLOMICS APPROACHES

AU - Frolov, Andrej

AU - Bilova, Tatiana

AU - Ihling, Christian

AU - Kim, Ahyoung

AU - Tsarev, Alexander

AU - Chantseva, Veronika

AU - Mamontova, Tatiana

AU - Lukasheva, Elena

AU - Shumilina, Julia

AU - Chekina, Anna

AU - Romanovskaya, Ekaterina

AU - Grishina, Tatiana

AU - Demchenko, Kirill

AU - Tsyganov, Viktor

AU - Sinz, Andrea

AU - Zhukov, Vladimir A.

AU - Becana, Manuel

AU - Matamoros, Manuel

AU - Tikhonovich, Igor A.

AU - Wessjohann, Ludger A.

PY - 2019/9

Y1 - 2019/9

N2 - Proteomics and metabolomics represent powerful tools of functional genomics, giving direct access to the molecular mechanisms underlying plant response on developmental signals, metabolic pathways, and regulatory networks. The combination of these approaches might give deeper insights into the molecular mechanisms contributing on mutualistic plant-microbial interactions, in particular, legume-rhizobial symbiosis. Here we address age-related changes in determinate and indeterminate root nodules of common bean (Phaseolus vulgaris) and pea (Pisum sativum). Juvenile, flowering, and senescent plants were harvested, the proteins were isolated by phenol extraction and digested with trypsin, isolating metabolites by a multi-step extraction with solvents of different polarity. Protein hydrolyzates were analyzed by nanoLC-ESI-Q- and LIT-Orbitrap-MS in data-dependent acquisition (DDA) mode. Database search and annotation of PTMs were based on the SEQUEST algorithm; quantification was performed using a label-free strategy. Functions and localization of the proteins were annotated by an in-house developed workflow, combined with MapMan, Mercator, LocTree3 and String tools. Analysis of primary metabolome relied on the combination of GC-MS and IP-RP-UHPLC-MS, with a secondary metabolite profiling by RP-UHPLC-MS. The analysis revealed 656 and 92 differentially regulated proteins in common bean and pea nodules, respectively. Plant proteins were mostly down-regulated and represented by the molecules involved in signaling and protein metabolism, while most of the bacterial polypeptides were up-regulated and found to be involved in energy metabolism and nitrogen fixation. Agedependent changes in metabolite profiles were characterized based on the accumulation of carbohydrates and amino acids. Interestingly, mutation in the gene sym27 resulted in the suppression of signaling and protein biosynthesis in both symbiosis partners. Remarkably, nodule ageing was accompanied with enhanced glycation and carbonylation. In total, 36 age-related glycation hotspots were identified in the P. vulgaris nodule proteome. This project was supported by the Russian Science Foundation (project 17-16-01042).

AB - Proteomics and metabolomics represent powerful tools of functional genomics, giving direct access to the molecular mechanisms underlying plant response on developmental signals, metabolic pathways, and regulatory networks. The combination of these approaches might give deeper insights into the molecular mechanisms contributing on mutualistic plant-microbial interactions, in particular, legume-rhizobial symbiosis. Here we address age-related changes in determinate and indeterminate root nodules of common bean (Phaseolus vulgaris) and pea (Pisum sativum). Juvenile, flowering, and senescent plants were harvested, the proteins were isolated by phenol extraction and digested with trypsin, isolating metabolites by a multi-step extraction with solvents of different polarity. Protein hydrolyzates were analyzed by nanoLC-ESI-Q- and LIT-Orbitrap-MS in data-dependent acquisition (DDA) mode. Database search and annotation of PTMs were based on the SEQUEST algorithm; quantification was performed using a label-free strategy. Functions and localization of the proteins were annotated by an in-house developed workflow, combined with MapMan, Mercator, LocTree3 and String tools. Analysis of primary metabolome relied on the combination of GC-MS and IP-RP-UHPLC-MS, with a secondary metabolite profiling by RP-UHPLC-MS. The analysis revealed 656 and 92 differentially regulated proteins in common bean and pea nodules, respectively. Plant proteins were mostly down-regulated and represented by the molecules involved in signaling and protein metabolism, while most of the bacterial polypeptides were up-regulated and found to be involved in energy metabolism and nitrogen fixation. Agedependent changes in metabolite profiles were characterized based on the accumulation of carbohydrates and amino acids. Interestingly, mutation in the gene sym27 resulted in the suppression of signaling and protein biosynthesis in both symbiosis partners. Remarkably, nodule ageing was accompanied with enhanced glycation and carbonylation. In total, 36 age-related glycation hotspots were identified in the P. vulgaris nodule proteome. This project was supported by the Russian Science Foundation (project 17-16-01042).

UR - https://pure.spbu.ru/admin/files/48615932/_2_II_1_6_2019_.pdf

M3 - иная часть книжной публикации

SN - 9785001505211 (Т. 2)

SN - 9785001505198

VL - 2

T3 - ACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ)

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BT - II Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»

PB - Издательство «Перо»

CY - М.

ER -

Frolov A, Bilova T, Ihling C, Kim A, Tsarev A, Chantseva V et al. PROBING AGE-RELATED CHANGES IN LEGUME NODULE PROTEOME BY PROTEOMICS AND METABOLOMICS APPROACHES. In II Объединенный научный форум: VI Съезд биохимиков России и IX Российский симпозиум «Белки и пептиды»: Научные труды. Vol. 2. М.: Издательство «Перо». 2019. p. 152. (ACTA NATURAE (РУССКОЯЗЫЧНАЯ ВЕРСИЯ)).