Role of Post-translational Modifications in Crop

Improvement

Dr. Hamid ManzoorSheeba Rauf (BS-BT-

19)Faraz Ahmad(BS-BT-

11)

Institute of Molecular Biology & Biotechnology (IMBB)B.Z.U. Multan

Proteome

Proteomics is the study of proteins on a genome-wide scale.

Analyze protein features. Scope of Proteomics research Critical to understand

“Post-translational Modifications is the Chemical Modification of Protein after its Translation”

OR “The Chemical Modification that takes place at

certain amino acids residues after the protein is synthesized by translation”

PTMs increases the functional diversity of the proteome by

Covalent addition of functional groups to proteins

Proteolytic cleavage of regulatory subunits, Degradation of entire proteins, Altering protein functions (Stabilizing and

localizing) by binding to amino acids

PTM

“Post-translational Modifications is the Chemical Modification of Protein after its Translation”

OR “The Chemical Modification that takes place at

certain amino acids residues after the protein is synthesized by translation”

PTMS occur mostly in E.R and golgi apparatus. Stability of protein Biochemical activity (activity regulation) Protein targeting (protein localization) Protein signaling (protein-protein interaction)

PTM

Post-translational modification

Modification Involving Peptide Bonds

Modification of amino acids

Subunit aggregation

Protein folding and chaperones

6

Protein Splicing

These modifications include: Phosphorylation Glycosylation Ubiquitination Nitrosylation Methylation Acetylation Lipidation Proteolysis

Modifications

Types

Ref: Google images

Influence all aspects of cell biologyIdentifying and understanding PTMs is critical in: Study of cell biologyDisease treatmentPreventionCrop ImprovementCell response to stress

PTM

Can occur at any Step in life CycleTagging of Target ProteinMono-modification or Poly-modificationModulation of Stress Related genesFormation of Transgenic plants over-expressing

regulators of Stress ResponseImproves tolerance to single or multiple stress

factors.

PTM

Metal Stress Flooding Stress Chill Stress Heat Stress Water Stress Some Biotic Factors

Stress Factors

Ref: Google Images

One of Most ordinary Mechanism Mediated by “Kinase” Reversible protein modification It effects following aspects of Protein

Function: Catalytic activity Subcellular localization, Stability Interaction with other proteins

Phosphorylat

ion

Phosphorylation depends upon kinase and phosphatase activities acting on proteins

Phosphatases are classified by their substrate preferences as Serine/Threonine, Tyrosine.

The Serine/Threonine subclass is associated with low temperature signaling and the regulation of cold stress response.

The inhibition of Serine/Threonine phosphatase activity induces cold-responsive genes in different species, including Arabidopsis, alfalfa, potato and tomato.

PP2A

MAPKs CDPKs CIPKs RLPKs ACS6 ZAT10 TMT1 Dehydrins

Protein Kinases

Ref: Google Images

Protein phosphorylation affects Metabolism The cell cycle, Stress, Hormonal responses, Stomatal closure Apoptosis Signal transduction pathways. Pathogen response, for example, plant–

pathogen interactions, gene expression, and defense signaling in plants.

Advantages

Ubiquitin is a small polypeptide attached to a lysine residue

Tagging of proteins Process Action of three enzymes: Ubiquitin activating enzyme

(E1) Ubiquitin conjugating

enzyme (E2) Ubiquitin ligase (E3). 26S proteasome, a

multisubunit ATP-dependent protease

Ubiquination

Ref: Google Images

1400 genes in the Arabidopsis genome encoding E3 ubiquitin ligases

Abiotic stresses alter the expression of more than 500 E3-ubiquitin ligase genes,

ubiquitin-dependent protein degradation in stress-related signalling and response mechanisms

Flower buds of Arabidopsis plants carrying a mutation in the ASK1 gene. In ASK1, the impairment of the SCF ligase-mediated ubiquitination and the resulting accumulation of SCF targets allowed the identification of ubiquitination targets.

SUMOylation is another important type of post-translational modification in which SUMO (Small Ubiquitin-related Modifier), a small polypeptide very similar to ubiquitin, is covalently bound to a lysine residue of a target protein. Same Enzymes except “SUMO needs to be

proteolytically processed by the Sentrin-specific Protease (SENPs) to expose the C-terminal”.

Action of three enzymes: SUMO activating enzyme (E1) SUMO conjugating enzyme (E2) SUMO ligase (E3).

SUMOylatio

n

Sumoylation alters protein function Biological consequences of sumoylation are: Sub-cellular re-localization, Changes in enzymatic activity Response to environmental signals.

Advantage

s

Ref: Google Images

SIZ1 is one of the three E3 SUMO ligases encoded by the Arabidopsis genome

Responsible for augmentation in SUMO conjugates

The loss of function causes a reduction in cold-induced freezing tolerance.

SIZ 1

SUMOylation is involved in: Transcriptional regulation, DNA repair, Nuclear transport, Mitochondrial fission Regulation of receptors at the plasma

membrane. Arabidopsis SIZ1

Crop Improvent

Phosphorylation

Glycosylation

Acylation

Alkylation

Hydroxylation

Pro, Lys Ser, Thr, Tyr

Asn, Ser, Thr

Asn, Gln, Lys

Lys, Arg

Glycosylation can be N-linked or O-linked, which is determined by the transfer of glycosidase and glycosyl between the Golgi apparatus and the endoplasmic reticulum.

Proteins at the endomembrane systemN-glycosylation is involved in Stability,

Activity and Subcellular localization of proteins.

The N-glycosylation pattern of 22 rice proteins is modified, whose Arabidopsis homolog, named LOS2, is an important regulator of cold acclimation.

Glycosylati

on

Acetylation and deacetylation in N-terminal and K-residue are suggested as rival to phosphorylation.

Modify a variety of proteins including: Transcription factors, Nuclear factors Alpha-tubulin DNA recognition Protein-protein interaction Protein stability

Acetylation

The transfer of one-carbon methyl group of nitrogen or oxygen (N- and O-methylation, respectively) to amino acid side chains increases the hydrophobicity of the protein and can neutralize a negative amino acid charge when bound to carboxylic acids.

Methylation is mediated by methyl-transferases, and S-adenosyl methionine (SAM) is the primary methyl group donor.

Methylatio

n

Ref: Proteome changes for crop improvement

References

Post-Translational Modifications of Nuclear Proteins in the Response of Plant Cells to Abiotic Stresses

REVIEW: Post-translational 1 regulation of cold acclimation response

Co- and post-translational modifications in Rubisco

Genomics and Bioinformatics Resources for Crop Improvement

References

Functional Proteomics of Arabidopsis thaliana Guard Cells Uncovers New Stomatal Signaling Pathways

Advances in Proteomics and Bioinformatics in Agriculture Research and Crop Improvement

Abiotic stress response in plants: When post-transcriptional and post-translational regulations control transcription

Proteome changes for crop improvement