1. Plant Proteomics IB 474A/CPSC 468A
Steve Huber
197 ERML
Lecture 1 Intro and Overview
Definition of proteomics
Student Expectations Survey
Housekeeping and course objectives
Why study proteomics?

2. WHAT IS PROTEOMICS?
The analysis of complete complements of proteins: identification and quantification; modifications; interactions; and activities. FUNCTION.
AND HOW DO THESE CHANGE DURING A BIOLOGICAL RESPONSE?
Science 291 (2001) 1221.
Peck SC (2005) Update on Proteomics in Arabidopsis. Where do we go from here? Plant Physiol 138:

3. Major Proteomics Directions
PTMs
“Proteomics is an increasingly ambiguous term being applied to almost any aspect of protein expression, structure or function.”
Adapted from Human Proteome Organization (
Required Reading for Lecture 2: Rose et al.(2004) Plant J 39:

4. Tools of Functional Genomics
Colebatch et al (2002) Functional Genomics: tools of the trade. New Phytol 153:

5. Solving the Puzzle of Protein Function
Proteomics is a multipotent tool central to research efforts in many fields and disciplines. Maximum functional utility will come from joint efforts.

6. Overview of lectures—Major Topics
Lec 1 Intro and Overview
Lec 2 2-Dimensional Electrophoresis
Lec 3 Quantitative proteomics (Prof. Yau)
Lec 4 UIUC Proteomics Facility tour—meet in 307 Noyes
Lec 5 Top-Down Mass spec and IGB tour
Lec 6 Post-translational modifications (PTMs): Phosphorylation
Lec 7 PTMs-continued
Lec 8 Protein-Protein Interactions
Lec 9 Pro-Pro continued
Lec 10 Proteomes of organs and subcell compartments
Lec 11 Abiotic stress
Lec 12 Biotic stress
Lec 13 Hormone signaling
Lec 14 Hot topics; miscellaneous; student presentations?
Lec 15 In-class FINAL EXAM
FOCUS IS ON EXPERIMENTAL AND STRATEGIC CONSIDERATIONS RATHER THAN INSTRUMENTATION

7. COURSE OBJECTIVES Appreciate fundamentals of proteomic research
Understand protein abundance/PTM in relation to development, nutrition, stress, etc.
Enhance presentation skills: Critically evaluate (and present) a current proteomics paper.

8. GRADING
20% 2 homework problem sets
30% Assigned reading (4 in-class quizzes; pick top 3 of 4 scores)
20% Written essay (journal article evaluation); ‘News & Views’ style with section on application to another significant question.
20% Final exam (last class)
10% Classroom participation
100%
Class Presentation; 15 min (same article used for written evaluation); submit PowerPoint slides for distribution to the class before the talk. Instructor and students will grade talks.
10%
ATTENDANCE IS EXPECTED; CHEATING AND PLAGIARISM WILL NOT BE TOLERATED

9. Journal Article Evaluation Paper Rubric
(5 page maximum; double spaced)
I. Present background and goals of study
Background clearly presented points
Goals elaborated points
II. Describe approaches and methodology Clearly explain principles underlying the work 10 points
Identify weaknesses and strengths points
Describe general applicability of methods 10 points
III. Identify major conclusions
Conclusions concisely elaborated points
Identify any questionable points of interpretation 10 points
Identify any unresolved points points
IV. Why the proteomics approach? points
Explain unique benefit from the proteomics approach
How could this work (concept; technique; approach, etc) be applied to answer another significant biological question? (be as specific as possible; ≤ 1 page)
15 points

10. RESOURCES Optional textbooks:
Introduction to Proteomics. Tools for the New Biology. Daniel C. Liebler (2002) Humana Press, ISBN
Proteomics in Practice. A laboratory manual of proteome analysis. R. Westermeier and T. Naven (2002) Wiley-VCH, ISBN
CURRENT LITERATURE AND WEBSITES
‘Protemics Primer’ (
Assigned Reading for Lecture 2: Rose et al. (2004) Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant J. 39:

11. A Single Gene Can Produce Many Proteins
Principle:
One gene ≠ one transcript ≠ one protein
ONE Genome but MANY Proteomes!
Targeting sequence
Peck (2005) Plant Physiol 138: 591

12. Correlation between protein and mRNA in yeast
Gygi et al. (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:

13. Diurnal changes of transcript and enzyme activity in Arabidopsis
We will discuss AGPase (ADPglucose pyrophosphorylase) and NiA (nitrate reductase) later in the course.
Gibon et al. (2004) A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: comparisons of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell 16:

14. Proteomics Leads to New Biology:
Identify and quantitate post-translational modifications (e.g.,O-acetylation; O-glycosylation).
Determine localization of proteins
Identify signal transduction components (e.g., BSK1; PPDK-RP)
Understand plant responses (e.g., to stress; genotypic differences; etc)
Anything that can’t be predicted from the genome, or when responses are not controlled transcriptionally.