Integrated Proteo-Transcriptomic Analyses Reveal Insights into
Regulation of Pollen Development Stages and Dynamics of
Cellular Response to Apple Fruit Crinkle Viroid
(AFCVd)-Infection in Nicotiana tabacum

J 2020

Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum

SHRESTHA, Ankita, Ajay Kumar MISHRA, Jaroslav MATOUŠEK, Lenka STEINBACHOVÁ, David POTĚŠIL et. al.

Basic information

Original name

Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum

Authors

SHRESTHA, Ankita (203 Czech Republic), Ajay Kumar MISHRA (203 Czech Republic), Jaroslav MATOUŠEK (203 Czech Republic), Lenka STEINBACHOVÁ (203 Czech Republic), David POTĚŠIL (203 Czech Republic, belonging to the institution), Vishnu Sukumari NATH (203 Czech Republic), Praveen AVASTHI (203 Czech Republic), Tomáš KOCÁBEK (203 Czech Republic), Jernej JAKSE (705 Slovenia), Lenka ZÁVESKÁ DRÁBKOVÁ (203 Czech Republic), Zbyněk ZDRÁHAL (203 Czech Republic, guarantor, belonging to the institution), David HONYS (203 Czech Republic) and Gerhard STEGER (276 Germany)

Edition

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2020, 1661-6596

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

fulltext

Impact factor

Impact factor: 2.598 in 2011

RIV identification code

RIV/00216224:14740/20:00118234

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.3390/ijms21228700

UT WoS

000594293400001

Keywords in English

AFCVd propagation and eradication; viroid replication; viroid degradation; Nicotiana tabacum; male gametophyte; Proteome; RNA sequencing; RT qPCR

Abstract

V originále

Tobacco (Nicotiana tabacum) pollen is a well-suited model for studying many fundamental biological processes owing to its well-defined and distinct development stages. It is also one of the major agents involved in the transmission of infectious viroids, which is the primary mechanism of viroid pathogenicity in plants. However, some viroids are non-transmissible and may be possibly degraded or eliminated during the gradual process of pollen development maturation. The molecular details behind the response of developing pollen against the apple fruit crinkle viroid (AFCVd) infection and viroid eradication is largely unknown. In this study, we performed an integrative analysis of the transcriptome and proteome profiles to disentangle the molecular cascade of events governing the three pollen development stages: early bicellular pollen (stage 3, S3), late bicellular pollen (stage 5, S5), and 6 h-pollen tube (PT6). The integrated analysis delivered the molecular portraits of the developing pollen against AFCVd infection, including mechanistic insights into the viroid eradication during the last steps of pollen development. The isobaric tags for label-free relative quantification (iTRAQ) with digital gene expression (DGE) experiments led us to reliably identify subsets of 5321, 5286, and 6923 proteins and 64,033, 60,597, and 46,640 expressed genes in S3, S5, and PT6, respectively. In these subsets, 2234, 2108 proteins and 9207 and 14,065 mRNAs were differentially expressed in pairwise comparisons of three stages S5 vs. S3 and PT6 vs. S5 of control pollen in tobacco. Correlation analysis between the abundance of differentially expressed mRNAs (DEGs) and differentially expressed proteins (DEPs) in pairwise comparisons of three stages of pollen revealed numerous discordant changes in mRNA/protein pairs. Only a modest correlation was observed, indicative of divergent transcription, and its regulation and importance of post-transcriptional events in the determination of the fate of early and late pollen development in tobacco. The functional and enrichment analysis of correlated DEGs/DEPs revealed the activation in pathways involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, and cofactor as well as vitamin metabolism, which points to the importance of these metabolic pathways in pollen development. Furthermore, the detailed picture of AFCVd-infected correlated DEGs/DEPs was obtained in pairwise comparisons of three stages of infected pollen. The AFCVd infection caused the modulation of several genes involved in protein degradation, nuclear transport, phytohormone signaling, defense response, and phosphorylation. Intriguingly, we also identified several factors including, DNA-dependent RNA-polymerase, ribosomal protein, Argonaute (AGO) proteins, nucleotide binding proteins, and RNA exonucleases, which may plausibly involve in viroid stabilization and eradication during the last steps of pollen development. The present study provides essential insights into the transcriptional and translational dynamics of tobacco pollen, which further strengthens our understanding of plant-viroid interactions and support for future mechanistic studies directed at delineating the functional role of candidate factors involved in viroid elimination.

Links

EF16_019/0000738, research and development project

Name: Centrum experimentální biologie rostlin

90127, large research infrastructures

Name: CIISB II

Citovat

SHRESTHA, Ankita, Ajay Kumar MISHRA, Jaroslav MATOUŠEK, Lenka STEINBACHOVÁ, David POTĚŠIL, Vishnu Sukumari NATH, Praveen AVASTHI, Tomáš KOCÁBEK, Jernej JAKSE, Lenka ZÁVESKÁ DRÁBKOVÁ, Zbyněk ZDRÁHAL, David HONYS and Gerhard STEGER. Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2020, vol. 21, No 22, p. "8700", 24 pp. ISSN 1661-6596. Available from: https://dx.doi.org/10.3390/ijms21228700.

@article{1745100,
   author = {Shrestha, Ankita and Mishra, Ajay Kumar and Matoušek, Jaroslav and Steinbachová, Lenka and Potěšil, David and Nath, Vishnu Sukumari and Avasthi, Praveen and Kocábek, Tomáš and Jakse, Jernej and Záveská Drábková, Lenka and Zdráhal, Zbyněk and Honys, David and Steger, Gerhard},
   article_number = {22},
   doi = {http://dx.doi.org/10.3390/ijms21228700},
   keywords = {AFCVd propagation and eradication; viroid replication; viroid degradation; Nicotiana tabacum; male gametophyte; Proteome; RNA sequencing; RT qPCR},
   language = {eng},
   issn = {1661-6596},
   journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
   title = {Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum},
   url = {https://www.mdpi.com/1422-0067/21/22/8700},
   volume = {21},
   year = {2020}
}

TY  - JOUR
ID  - 1745100
AU  - Shrestha, Ankita - Mishra, Ajay Kumar - Matoušek, Jaroslav - Steinbachová, Lenka - Potěšil, David - Nath, Vishnu Sukumari - Avasthi, Praveen - Kocábek, Tomáš - Jakse, Jernej - Záveská Drábková, Lenka - Zdráhal, Zbyněk - Honys, David - Steger, Gerhard
PY  - 2020
TI  - Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum
JF  - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
VL  - 21
IS  - 22
SP  - "8700"
EP  - "8700"
SN  - 16616596
KW  - AFCVd propagation and eradication
KW  - viroid replication
KW  - viroid degradation
KW  - Nicotiana tabacum
KW  - male gametophyte
KW  - Proteome
KW  - RNA sequencing
KW  - RT qPCR
UR  - https://www.mdpi.com/1422-0067/21/22/8700
N2  - Tobacco (Nicotiana tabacum) pollen is a well-suited model for studying many fundamental biological processes owing to its well-defined and distinct development stages. It is also one of the major agents involved in the transmission of infectious viroids, which is the primary mechanism of viroid pathogenicity in plants. However, some viroids are non-transmissible and may be possibly degraded or eliminated during the gradual process of pollen development maturation. The molecular details behind the response of developing pollen against the apple fruit crinkle viroid (AFCVd) infection and viroid eradication is largely unknown. In this study, we performed an integrative analysis of the transcriptome and proteome profiles to disentangle the molecular cascade of events governing the three pollen development stages: early bicellular pollen (stage 3, S3), late bicellular pollen (stage 5, S5), and 6 h-pollen tube (PT6). The integrated analysis delivered the molecular portraits of the developing pollen against AFCVd infection, including mechanistic insights into the viroid eradication during the last steps of pollen development. The isobaric tags for label-free relative quantification (iTRAQ) with digital gene expression (DGE) experiments led us to reliably identify subsets of 5321, 5286, and 6923 proteins and 64,033, 60,597, and 46,640 expressed genes in S3, S5, and PT6, respectively. In these subsets, 2234, 2108 proteins and 9207 and 14,065 mRNAs were differentially expressed in pairwise comparisons of three stages S5 vs. S3 and PT6 vs. S5 of control pollen in tobacco. Correlation analysis between the abundance of differentially expressed mRNAs (DEGs) and differentially expressed proteins (DEPs) in pairwise comparisons of three stages of pollen revealed numerous discordant changes in mRNA/protein pairs. Only a modest correlation was observed, indicative of divergent transcription, and its regulation and importance of post-transcriptional events in the determination of the fate of early and late pollen development in tobacco. The functional and enrichment analysis of correlated DEGs/DEPs revealed the activation in pathways involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, and cofactor as well as vitamin metabolism, which points to the importance of these metabolic pathways in pollen development. Furthermore, the detailed picture of AFCVd-infected correlated DEGs/DEPs was obtained in pairwise comparisons of three stages of infected pollen. The AFCVd infection caused the modulation of several genes involved in protein degradation, nuclear transport, phytohormone signaling, defense response, and phosphorylation. Intriguingly, we also identified several factors including, DNA-dependent RNA-polymerase, ribosomal protein, Argonaute (AGO) proteins, nucleotide binding proteins, and RNA exonucleases, which may plausibly involve in viroid stabilization and eradication during the last steps of pollen development. The present study provides essential insights into the transcriptional and translational dynamics of tobacco pollen, which further strengthens our understanding of plant-viroid interactions and support for future mechanistic studies directed at delineating the functional role of candidate factors involved in viroid elimination.
ER  -

SHRESTHA, Ankita, Ajay Kumar MISHRA, Jaroslav MATOUŠEK, Lenka STEINBACHOVÁ, David POTĚŠIL, Vishnu Sukumari NATH, Praveen AVASTHI, Tomáš KOCÁBEK, Jernej JAKSE, Lenka ZÁVESKÁ DRÁBKOVÁ, Zbyněk ZDRÁHAL, David HONYS and Gerhard STEGER. Integrated Proteo-Transcriptomic Analyses Reveal Insights into Regulation of Pollen Development Stages and Dynamics of Cellular Response to Apple Fruit Crinkle Viroid (AFCVd)-Infection in Nicotiana tabacum. \textit{INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}. 2020, vol.~21, No~22, p.~''8700'', 24 pp. ISSN~1661-6596. Available from: https://dx.doi.org/10.3390/ijms21228700.

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