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Towards the Phosphoproteome of Trypanosomatids

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Proteins and Proteomics of Leishmania and Trypanosoma

Part of the book series: Subcellular Biochemistry ((SCBI,volume 74))

Abstract

The identification and localization of protein phosphorylation sites provide clues to what proteins or pathways might be activated in a given condition, helping to improve our understanding about signaling networks. Advances in strategies for enrichment of phosphorylated peptides/proteins, mass spectrometry (MS) instrumentation, and specific MS techniques for identification and quantification of post-translational modifications have allowed for large-scale mapping of phosphorylation sites, promoting the field of phosphoproteomics. The great promise of phosphoproteomics is to unravel the dynamics of signaling networks, a layer of the emerging field of systems biology. Until a few years ago only a small number of phosphorylation sites had been described. Following large-scale trends, recent phosphoproteomic studies have reported the mapping of thousands of phosphorylation sites in trypanosomatids. However, quantitative information about the regulation of such sites in different conditions is still lacking. In this chapter, we provide a historical overview of phosphoproteomic studies for trypanosomatids and discuss some challenges and perspectives in the field.

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Abbreviations

2D-DIGE:

Two dimensional differential gel electrophoresis

2DE:

Two dimensional electrophoresis

AGC:

Kinases containing PKA, PKG, and PKC

ALK:

Anaplastic lymphoma kinase

aPK:

Atypical protein kinase

CAMK:

Group of kinases containing calcium/calmodulin-dependent kinases

CaMKK:

Calmodulin-dependent protein kinase kinase

CDK1:

Cyclin-dependent kinase 1

CID:

Collision-induced dissociation

CK:

Casein-kinase

CMGC:

Group of kinases containing cyclin-dependent kinases, mitogen-activated protein kinases, Glycogen synthase kinases, and CDK-like kinases.

CRK:

CT10 regulator of kinase

DGF:

Dispersed gene family

DHB:

2,5-dihydroxybenzoic acid

DYRK:

Dual-specificity tyrosine-regulated kinase

ECD:

Electron capture dissociation

EGFR:

Epidermal growth factor receptor

ePK:

Eukaryotic protein kinase

ERK:

Extracellular signal-regulated kinase

ERLIC:

Electrostatic repulsion- hydrophilic interaction chromatography

ESI:

Electron spray ionization

ETD:

Electron transfer dissociation

FRAP:

FKBP12-rapamycin-associated protein

GMD:

Glycosomal malate dehydrogenase

GSK3:

Glycogen synthase kinase 3

HCD:

Higher-energy C-trap dissociation

HILIC:

Hydrophilic interaction chromatography

HOP:

HSP organizing protein

HSP:

Heat shock protein

IDA:

Iminodiacetic acid

IgE-HRF:

Immunoglobulin E-dependent histamine-releasing factor

IMAC:

Immobilized metal affinity chromatography

iTRAQ:

Isobaric tag for relative and absolute quantification

LC:

Liquid chromatography

m/z:

Mass-to-charge-ratio

MALDI:

Matrix-assisted laser desorption/ionization

MAP kinase:

Mitogen-activated protein kinase

MOAC:

Metal oxide affinity chromatography

mRNA:

Messenger RNA

MS:

Mass spectrometry

MSA:

Multi-stage activation

NEK:

NimA related kinase

NTA:

Nitrilotriacetic acid

PEK:

Pancreatic eukaryotic initiation factor-2alpha kinase

Pf2αS:

Prostaglandin F2-alpha synthase

PK:

Protein kinase

PKA:

Protein kinase A

PP:

Protein phosphatase

PTM:

Post-translational modification

PTP:

Tyrosine-specific phosphatase

RIO2:

Right open reading frame 2

RP:

Reverse phase

SAX:

Strong anion exchange

SCX:

Strong cation exchange

SH2:

Src homology 2

SILAC:

Stable isotope labeling by amino acids in cell culture

SIMAC:

Sequential elution from IMAC

STE:

Group of kinases homolog of Sterile

STI:

Stress inducible protein

STP:

Serine/threonine phosphatase

TCTP:

Translationally controlled-tumor-protein

TED:

Tris-(carbomethyl)-ethylendiamine

TFA:

Trifluoroacetic acid

TGF-β:

Transforming growth factor beta

TOF:

Time of flight

TPR:

Tetratricopeptide repeat

ULK:

UNC-51-like kinases

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Authors and Affiliations

  1. Functional Genomics Laboratory, Fiocruz – Parana, Brazil

    Fabricio K. Marchini, Lyris Martins Franco de Godoy, Michel Batista, Fernanda G. Kugeratski & Marco A. Krieger

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  1. Fabricio K. Marchini
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  2. Lyris Martins Franco de Godoy
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  3. Michel Batista
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  4. Fernanda G. Kugeratski
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  5. Marco A. Krieger
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Correspondence to Marco A. Krieger .

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Editors and Affiliations

  1. Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil

    André L.S. Santos

  2. Departamento de Microbiologia Geral, Ins. de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil

    Marta H. Branquinha

  3. Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil

    Claudia M. d’Avila-Levy

  4. Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil

    Lucimar F. Kneipp

  5. Departamento de Biologia Celular e Molecular, Instituto de Biologia Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil

    Cátia L. Sodré

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Marchini, F.K., de Godoy, L.M.F., Batista, M., Kugeratski, F.G., Krieger, M.A. (2014). Towards the Phosphoproteome of Trypanosomatids. In: Santos, A., Branquinha, M., d’Avila-Levy, C., Kneipp, L., Sodré, C. (eds) Proteins and Proteomics of Leishmania and Trypanosoma. Subcellular Biochemistry, vol 74. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7305-9_15

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