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Deciphering putative protein profile of a photomorphogenic high pigment mutant of Solanum lycopersicum (hp-1) by high-throughput LC–MS/MS analysis

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Abstract

The mutant hp-1 is a photomorphogenic high pigment tomato mutant. It has high commercial significance as a source of non-transgenic lycopene-rich mutants. The putative effect of the hp-1 mutation on the alteration of proteomic behavior remains elusive. We put effort into giving an insight mechanism underlying this high pigmentation by high-throughput LC/MS/MS analysis. The bioinformatics interpretation of the results expressed a large number of proteins specific to the hp-1 mutant. The identified proteins in the pericarp tissue were involved in physiologic processes: including photosynthesis: stress and defense: protein synthesis: processing: and folding: Carbohydrate metabolism and respiratory cycle: RO reaction and oxidative damage: ethylene biosynthesis: and cell wall metabolism with enhanced expression of ACO: NDPK: ATP synthase: MDH 1: TPM 1: OSML 13: PR10: HSP 70: STH 1: peroxidase: SOP: Gly-rich RBP: OEE 1: PSII OECP. The modulation of the accumulation scale of proteins showed the integrated functioning of light-interacting factors and fruit ripening. This report unravels the proteomic regulatory network for high pigmentation and will strengthen future research on fruit pigment development and metabolism.

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Data availability

Data sharing does not apply to this article as no datasets were generated or analyzed during the current study.

Abbreviations

ACC:

1-Aminocyclopropane-1-carboxylic acid

ACN:

Acetonitrile

ACO:

1-Aminocyclopropane-1-carboxylic Acid Oxidase

AL:

Ailsa craig

BL4:

Bell-like homeodomain 4

BR:

Breaker stage

BZR:

Brassinosteroid signaling positive regulator

CAB:

Chlorophyll a/b-binding Protein

CD:

Cutin deficient

CID:

Collision induced dissociation

CHS:

Chalcone synthase

CTAB:

Cetyl trimethyl ammonium bromide

CTRs:

Constitutive triple response

CyP:

Peptidyl-prolyl cis–trans isomerase

DAP:

Days after pollination

DAVID:

Database for annotation, visualization and integrated discovery

DDB1:

Damaged DNA binding protein 1

DEPs:

Differentially expressed proteins

DET:

De-Etiolated

DHAR:

Dehydroascorbate reductase

DHAP:

Dihydroxyacetone phosphate

DTT:

Di-thio threitol

eIF:

Eukaryotic translation initiation factor

EIN2:

Ethylene insensitive 2

F-1,6-BP:

Fructose-1,6-bisphosphate

FBA:

Fructose bisphosphate aldolase

Glu6P:

Glucose 6-phosphate

G3P:

Glyceraldehyde 3-phosphate

GGPP:

GeranylGeranyl pyrophosphate

GO:

Gene ontology

Gly-rich RBP:

Glycine-rich RNA binding proteins

GRP2:

Glycine-rich protein 2

HPLC:

High performance liquid chromatography

HSP:

Heat shock protein

iTRAQ:

Isobaric tag for relative and absolute quantitation

KEGG:

Kyoto encyclopedia of genes and genomes

LRT:

Lycopene rich tomatoes

MEP:

2-C-methyl-D-erythritol 4-phosphate

MDH:

Malate dehydrogenase

MG:

Mature green

MSR:

Methionine sulphoxide reductase

NDP:

Nucleotide diphosphate

NDPK:

Nucleoside diphosphate kinase

OAA:

Oxaloacetate

2-ODD:

2-Oxoglutarate dependent dioxygenase

OECP:

Oxygen-evolving complex proteins

OEE:

Oxygen evolving enhancer

OG:

Oxoglutarate

OSML:

Osmotin like protein: full form

PE:

Pectinesterase

PDI:

Protein disulfide isomerase

PGH:

2-Phospho-D-glycerate hydro-lyase

PGIP:

Polygalacturonase-inhibiting protein

PMSF:

Phenyl methyl sulfonyl fluoride

PPI:

Protein–protein interaction

PR:

Pathogenesis related

PRP:

Pathogenesis-related protein

PSII:

Photosystem II

PSY:

Phytoene synthase

RBCS-2A:

Ribulose bisphosphate carboxylase small chain 2A

RBP:

RNA binding proteins

RH:

Relative humidity

RO:

Reactive oxygen

RR:

Red ripe

RuBisCO:

Ribulose-1:5-bisphosphate carboxylase/oxygenase

SAPKs:

Stress activated protein kinases

SDS:

Sodium dodecyl suphate

SOD:

Superoxide dismutase

SOP:

Sulfate of potash

TAA:

Tri-chloro acetic acid

TF:

Transcription factor

TIL:

Temperature-induced lipocalin

TPI:

Triosephosphate isomerase

TPM:

Tropomyosin

TPT:

Triose phosphate transporter

UBA:

Ubiquitin associated

UBX:

Ubiquitin like

WDS:

Water deficit stress

XEG:

Xyloglucan-specific endoglucanase

XEGIP:

Xyloglucan-specific fungal endoglucanase inhibitor protein

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Acknowledgements

This research was funded through the DBT Bio-CARe Women Scientists project (BT/Bio-CARe/02/315/2011-2012 & 10/10/2013: Department of Biotechnology: Ministry of Science and Technology: Government of India). We thank C- CAMP (DBT: Govt. of India) for providing the service in the LC/MS/MS analysis of the extracted protein samples. We also appreciate Prof. Dibyendu Narayan Sengupta (Bose Institute: Kolkata) for his motivation and cooperation during the preliminary development of the project. I also would like to thank Dr. Souvik Ghatak for supporting with bioinformatics analysis for subcellular localization study.

Funding

This study was supported through the DBT Bio-CARe Women Scientists project (BT/Bio-CARe/02/315/2011–2012 & 10/10/2013: Department of Biotechnology: Ministry of Science and Technology: Government of India).

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Authors and Affiliations

  1. Amity Institute of Biotechnology, Amity University Kolkata, Major Arterial Road (South-East): Action Area II, Newtown, Kolkata, West Bengal, 700135, India

    Harshata Pal, Somali Dhal & Tahsin Khan

  2. Department of Vegetable Crops: Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, India

    Harshata Pal & Pranab Hazra

  3. Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, India

    Avinash Sethi

  4. ITC Infotech India Limited, Bangalore, India

    Avinash Sethi

  5. Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela, Odisha, India

    Somali Dhal

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Harshata Pal -All wet lab analysis and manuscript writing. Avinash Sethi -Bioinformatics data analysis and editing. Pranab Hazra -Provided experimental materials. Somali Dhal—Reference management: revision and editing. Tahsin Khan – Revision and editing.

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Pal, H., Sethi, A., Dhal, S. et al. Deciphering putative protein profile of a photomorphogenic high pigment mutant of Solanum lycopersicum (hp-1) by high-throughput LC–MS/MS analysis. J Proteins Proteom (2024). https://doi.org/10.1007/s42485-024-00153-9

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