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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
ID Shrestha, Ankita (Avtor), ID Kumar Mishra, Ajay (Avtor), ID Matoušek, Jaroslav (Avtor), ID Steinbachová, Lenka (Avtor), ID Potěšil, David (Avtor), ID Nath, Vishnu Sukumari (Avtor), ID Awasthi, Praveen (Avtor), ID Kocábek, Tomáš (Avtor), ID Jakše, Jernej (Avtor), ID Záveská Drábková, Lenka (Avtor), ID Zdráhal, Zbyněk (Avtor), ID Honys, David (Avtor), ID Steger, Gerhard (Avtor)

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URLURL - Izvorni URL, za dostop obiščite https://www.mdpi.com/1422-0067/21/22/8700 Povezava se odpre v novem oknu

Izvleček
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.

Jezik:Angleški jezik
Ključne besede:AFCVd propagation and eradication, viroid replication, viroid degradation, Nicotiana tabacum, male gametophyte, proteome, RNA sequencing, RT qPCR
Vrsta gradiva:Članek v reviji (dk_c)
Tipologija:1.01 - Izvirni znanstveni članek
Organizacija:BF - Biotehniška fakulteta
Leto izida:2020
Status objave pri reviji:Objavljeno
Verzija članka:Založnikova različica članka
Št. strani:24 str.
Številčenje:Vol. 21, iss. 22, art. 8700
UDK:577.2
ISSN pri članku:1661-6596
DOI:10.3390/ijms21228700 Povezava se odpre v novem oknu
COBISS.SI-ID:40325635 Povezava se odpre v novem oknu
Datum objave v RUL:26.01.2022
Število ogledov:124
Število prenosov:49
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Gradivo je del revije

Naslov:International journal of molecular sciences
Skrajšan naslov:Int. j. mol. sci.
Založnik:Molecular Diversity Preservation International MDPI
ISSN:1661-6596
COBISS.SI-ID:36217605 Povezava se odpre v novem oknu

Licence

Licenca:CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
Povezava:http://creativecommons.org/licenses/by/4.0/deed.sl
Opis:To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.
Začetek licenciranja:18.11.2020

Sekundarni jezik

Jezik:Slovenski jezik
Ključne besede:Nicotiana tabacum, tobak, pelod, bolezni rastlin, viroidi, proteomska analiza, transkriptomska analiza, RNA sekvenciranje, degradacija viroidov

Gradivo je financirano iz projekta

Financer:Drugi - Drug financer ali več financerjev
Program financ.:Czech Science Foundation
Številka projekta:GACR 18-10515J

Financer:Drugi - Drug financer ali več financerjev
Program financ.:German Science Foundation
Številka projekta:DFG STE 465

Financer:Drugi - Drug financer ali več financerjev
Program financ.:Czech Science Foundation
Številka projekta:17-23183S

Financer:Drugi - Drug financer ali več financerjev
Program financ.:CR, Ministry of Education, Youth, and Sports
Številka projekta:CZ.02.1.01/0.0/0.0/16_019/0000738
Naslov:Centre for Experimental Plant Biology

Financer:EC - European Commission
Program financ.:European Regional Development Fund
Naslov:Centre for Experimental Plant Biology

Financer:Drugi - Drug financer ali več financerjev
Program financ.:CIISB

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