Skip to main content
Molecular & Cellular Proteomics

Main menu

  • Home
  • Articles
    • Current Issue
    • Papers in Press
    • Reviews and Minireviews
    • Special Issues
    • Editorials
    • Archive
    • Letters to the Editor (eLetters)
  • Info for
    • Authors
      • Editorial Policies
      • How to Submit
      • Manuscript Contents & Organization
      • Data Reporting Requirements
      • Publication Charges
    • Reviewers
    • Librarians
    • Advertisers
    • Subscribers
  • Guidelines
    • Proteomic Identification
      • Checklist (PDF)
      • Instructions for Annotated Spectra
      • Tutorial (PDF)
    • Clinical Proteomics
      • Checklist (PDF)
    • Glycomic Identification
      • Checklist (PDF)
    • Targeted Proteomics
      • Checklist (PDF)
    • Data-Independent Acquisition
      • Checklist (PDF)
    • Frequently Asked Questions
  • About
    • Mission Statement and Scope
    • Editorial Policies
    • Editorial Board
    • MCP Lectureships
    • Permissions and Licensing
    • Partners
    • Alerts
    • Contact Us

Submit

  • Submit
  • Publications
    • ASBMB
    • Molecular & Cellular Proteomics
    • Journal of Biological Chemistry
    • Journal of Lipid Research

User menu

  • Register
  • Subscribe
  • My alerts
  • Log in
  • My Cart

Search

  • Advanced search
  • Publications
    • ASBMB
    • Molecular & Cellular Proteomics
    • Journal of Biological Chemistry
    • Journal of Lipid Research
  • Register
  • Subscribe
  • My alerts
  • Log in
  • My Cart
Molecular & Cellular Proteomics

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Papers in Press
    • Reviews and Minireviews
    • Special Issues
    • Editorials
    • Archive
    • Letters to the Editor (eLetters)
  • Info for
    • Authors
      • Editorial Policies
      • How to Submit
      • Manuscript Contents & Organization
      • Data Reporting Requirements
      • Publication Charges
    • Reviewers
    • Librarians
    • Advertisers
    • Subscribers
  • Guidelines
    • Proteomic Identification
      • Checklist (PDF)
      • Instructions for Annotated Spectra
      • Tutorial (PDF)
    • Clinical Proteomics
      • Checklist (PDF)
    • Glycomic Identification
      • Checklist (PDF)
    • Targeted Proteomics
      • Checklist (PDF)
    • Data-Independent Acquisition
      • Checklist (PDF)
    • Frequently Asked Questions
  • About
    • Mission Statement and Scope
    • Editorial Policies
    • Editorial Board
    • MCP Lectureships
    • Permissions and Licensing
    • Partners
    • Alerts
    • Contact Us
  • Submit
Research

Regulation Dynamics of Leishmania Differentiation: Deconvoluting Signals and Identifying Phosphorylation Trends

Polina Tsigankov, Pier Federico Gherardini, Manuela Helmer-Citterich, Gerald F. Späth, Peter J. Myler and Dan Zilberstein
Molecular & Cellular Proteomics July 1, 2014, First published on April 16, 2014, 13 (7) 1787-1799; https://doi.org/10.1074/mcp.M114.037705
Polina Tsigankov
From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Pier Federico Gherardini
§Center for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Manuela Helmer-Citterich
§Center for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gerald F. Späth
¶Institut Pasteur, CNRS URA2581, Unité de Parasitologie moléculaire et Signalisation, 75015 Paris, France;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter J. Myler
‖Seattle Biomedical Research Institute, Seattle, Washington 98109; **Department of Global Health, University of Washington, Seattle, Washington 98195; ‡‡Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington 98195
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dan Zilberstein
From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: danz@bi.technion.ac.il
  • Article
  • Figures & Data
  • Info & Metrics
  • eLetters
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • Fig. 1.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 1.

    A, heatmap showing the HCL-ST clustering of Log2 fold changes in phosphopeptide abundance during the differentiation time-course. Cluster numbers assigned by MeV are shown to the left. B, graphical representation of abundance changes for peptides assigned to each cluster, with the mean values for each cluster represented as a pink line.

  • Fig. 2.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 2.

    A, Log2 fold abundance changes for phosphopeptides that display transient phosphorylation during differentiation. The numbers after the “_” indicate the residue number of the phosphorylation site(s) in the respective protein. B, phosphopeptides that display transient dephosphorylation.

  • Fig. 3.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 3.

    The number of phosphopeptides per protein in the time-course experiment. Different colors indicate whether different phosphopeptides from the same protein show the same (blue) or different (red, green, or purple) kinetics.

  • Fig. 4.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 4.

    Initiation of peptide phosphorylation and dephosphorylation events at different phases of differentiation.

  • Fig. 5.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 5.

    Log2 fold-change values for the 319 phosphopeptides that were detected in all three conditions of the signal-dependent phosphorylation experiment (supplemental Table S2). The values for each phosphopeptide after 2.5 h of exposure to 37 °C (red), pH (blue), and both (green) are represented by different positions along the x-axis of the graph. “Full response” indicates a change when exposed to both signals; “partial response” indicates a change when exposed to the temperature or pH signal alone. Changes that occurred in response to only temperature or pH are indicated at the top by “temp” or “pH,” “temp & pH” indicates a change in response to both temperature and pH separately, and “temp+pH” indicates a change in response to only the complete signal (both temperature and pH together).

  • Fig. 6.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 6.

    A, phosphopeptides that showed >2-fold change in phosphorylation only in response to the full signal. B, phosphopeptides that showed >2-fold change in phosphorylation in response to the full signal and were also affected by temperature. C, phosphopeptides that showed >2-fold change in phosphorylation in response to the full signal and were also affected by pH. D, phosphopeptides that showed >2-fold change in phosphorylation in response to the full signal and were also affected by temperature and pH separately. Values are presented as Log2 fold change from promastigotes.

  • Fig. 7.
    • Download figure
    • Open in new tab
    • Download powerpoint
    Fig. 7.

    A, protein kinases and phosphatase that were phosphorylated during phase I and remained phosphorylated throughout differentiation. B, protein kinases and a phosphatase that were transiently phosphorylated. C, phosphorylation kinetics of different sites in the multiply phosphorylated protein kinase A regulatory subunit like-protein (PKAR'). Values are presented as Log2 fold change from promastigotes.

Tables

  • Figures
  • Additional Files
    • View popup
    Table I Classes of proteins that were enriched for phosphorylation changes at different time points
    Trend of phosphorylationTime point
    2.5 h5 h10 h15 h24 hAmastigotes (120 h)
    UpProtein kinaseMetabolismTranslationChaperoneChaperone
    Metabolism
    Protein kinase
    DownRibosomalRibosomal transporterRibosomal transporterRibosomal transporter
    Phase IPhase IIPhase IIIPhase IV
    • “Up” denotes an increase in phosphorylation, and “down” denotes an increase in dephosphorylation.

    • View popup
    Table II Summary of log2 fold-change values for the 317 phosphopeptides that were detected in all three conditions of the signal-dependent phosphorylation experiment (supplemental Table S2 and Fig. 5)
    A, abundance changes were coded as “up” or “down” if they changed by more than 1.34-fold (log2 ≥ 0.42), and each phosphopeptide was manually assigned to 1 of 27 possible patterns.
    PatternCodeTemperaturepHpH + temperatureCount
    1UUUUpUpUp20
    2NUU–UpUp20
    3DUUDownUpUp2
    4UNUUp–Up25
    5NNU––Up56
    6DNUDown–Up4
    7UDUUpDownUp2
    8NDU–DownUp13
    9DDUDownDownUp1
    10UUNUpUp–4
    11NUN–Up–8
    12DUNDownUp–0
    13UNNUp––16
    14NNN–––85
    15DNNDown––10
    16UDNUpDown–4
    17NDN–Down–24
    18DDNDownDown–11
    19UUDUpUpDown0
    20NUD–UpDown1
    21DUDDownUpDown0
    22UNDUp–Down0
    23NND––Down3
    24DNDDown–Down3
    25UDDUpDownDown0
    26NDD–DownDown4
    27DDDDownDownDown1
    Up7155143
    No change214202162
    Down326012
    B, these patterns were used to ascribe a signal-dependent response to each phosphopeptide.
    ResponseSignalPattern(s)Number of peptides
    FullTemperature alone4 + 7 + 21 + 2430155
    pH only2 + 3 + 25 + 2626
    Temperature and pH1 + 2721
    Temperature + pH5 + 6 + 8 + 9 + 19 + 20 + 22 + 2378
    PartialTemperature only13 + 152677
    pH only11 + 1732
    Temperature and pH only10 + 12 + 16 + 1819
    No changeNone148585

Additional Files

  • Figures
  • Tables
  • Supplemental Data

    Files in this Data Supplement:

    • Supplemental figure S1 - LinJ.05.0140 phosphopeptides.
    • Supplemental figure S2 - Initiation of phosphorylation/dephosphorylation events at different time-points during differentiation.
    • Legends for supplemental data - Legends for supplemental tables and figures
    • Supplemental Table S1 - Leishmania donovani phosphopeptide abundance during promastigote-to-amastigote differentiation.
    • Supplemental Table S2 - Signal-dependent phosphopeptide abundance at 2.5 hours of Leishmania donovani differentiation.
PreviousNext
Back to top
Print
Download PDF
Article Alerts
Sign In to Email Alerts with your Email Address
Email Article

Thank you for your interest in spreading the word on Molecular & Cellular Proteomics.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Regulation Dynamics of Leishmania Differentiation: Deconvoluting Signals and Identifying Phosphorylation Trends
(Your Name) has sent you a message from Molecular & Cellular Proteomics
(Your Name) thought you would like to see the Molecular & Cellular Proteomics web site.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Citation Tools
Regulation Dynamics of Leishmania Differentiation: Deconvoluting Signals and Identifying Phosphorylation Trends
Polina Tsigankov, Pier Federico Gherardini, Manuela Helmer-Citterich, Gerald F. Späth, Peter J. Myler, Dan Zilberstein
Molecular & Cellular Proteomics July 1, 2014, First published on April 16, 2014, 13 (7) 1787-1799; DOI: 10.1074/mcp.M114.037705

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero

Request Permissions

Share
Regulation Dynamics of Leishmania Differentiation: Deconvoluting Signals and Identifying Phosphorylation Trends
Polina Tsigankov, Pier Federico Gherardini, Manuela Helmer-Citterich, Gerald F. Späth, Peter J. Myler, Dan Zilberstein
Molecular & Cellular Proteomics July 1, 2014, First published on April 16, 2014, 13 (7) 1787-1799; DOI: 10.1074/mcp.M114.037705
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

In this issue

Molecular & Cellular Proteomics: 13 (7)
Molecular & Cellular Proteomics
Vol. 13, Issue 7
1 Jul 2014
  • Table of Contents
  • Table of Contents (PDF)
  • Cover (PDF)
  • About the Cover
  • Index by author
  • Ed Board (PDF)

View this article with LENS

Jump to section

  • Article
    • Abstract
    • EXPERIMENTAL PROCEDURES
    • RESULTS
    • DISCUSSION
    • Acknowledgments
    • Footnotes
    • REFERENCES
  • Figures & Data
  • eLetters
  • Info & Metrics
  • PDF

  • Follow MCP on Twitter
  • RSS feeds
  • Email

Articles

  • Current Issue
  • Papers in Press
  • Archive

For Authors

  • Submit a Manuscript
  • Info for Authors

Guidelines

  • Proteomic Identification
  • Clinical Proteomics
  • Glycomic Identification
  • Targeted Proteomics
  • Frequently Asked Questions

About MCP

  • About the Journal
  • Permissions and Licensing
  • Advertisers
  • Subscribers

ASBMB Publications

  • Molecular & Cellular Proteomics
  • Journal of Biological Chemistry
  • Journal of Lipid Research
  • ASBMB Today

© 2019 American Society for Biochemistry and Molecular Biology | Privacy Policy

MCP Print ISSN 1535-9476 Online ISSN 1535-9484

Powered by HighWire