# Presentation: 807250

## mRNA – protein correlation problem. Why in many cases we don’t see a correlation between mRNA and protein changes

- mRNA is down regulated or unchanged, protein abundance changes – did we see such cases?
- mRNA is upregulated, protein is not
-         *Biological causes*
-                  varying protein stability
-                  postranslational modifications
-         *Technological causes*
-                  intrinsic features of proteomics

## Protein Identification Strategy

- Q2

- Collision Cell

- Q3

- I

- I

- II

- II

- III

- III

- Correlative

- sequence database

- searching

- Theoretical

- Acquired

- Protein identification

- Peptides

- Separate peptides by
- reverse phase chromatography

- 200

- 400

- 600

- 800

- 1000

- 1200

*m/z*

*m/z*

- 200

- 400

- 600

- 800

- 1000

- 1200

*m/z*

*m/z*

- 200

- 400

- 600

- 800

- 1000

- 1200

*m/z*

*m/z*

- 12

- 14

- 16

- Time (min)

- Tandem mass spectrum

- Q1

- *

- *

- Protein

- mixture

- .

- By “Sequest”

##  Data-Dependent Ion Selection MS/MS

-  **Data-Dependent Ion Selection MS/MS**

## Ion selection from multiple narrow mass ranges 

**Ion selection from multiple narrow mass ranges**** **

**MS scan (survey ion scan,  peptide ion scan) **

## D. vulgaris Hildenborough     metabolic reconstruction 

**based on extensive  proteome analysis **

- Great 3D LC Ms/Ms data (Diversa) set for DvH growing in batch culture with lactate and sulfate
- 2D gel data from SANDIA will help to validate LC Ms/Ms data
- Step towards quantification
- This analysis ( publication) will facilitate
-      interpretation of the data from stress experiments
-      writing papers
-      metabolic modeling

## D. vulgaris gene cluster for lactate utilization

- ORF03980 PAS domain S-box protein

- ORF03984 sigma-54 dependent DNA-binding response regulator (atoC)

- ORF03986 pyruvate flavodoxin/ferredoxin oxidoreductase, Dd 393795

- ORF03988 L-lactate permease, putative

- ORF03990 glycolate oxidase, subunit GlcD (glcD)

- ORF03992 glycolate oxidase iron-sulfur subunit.

- ORF03994 phosphate acetyltransferase (pta)

- ORF03996 acetate kinase (ackA)

- Lactate dehydrogenase?

- 03980    3982  3984         3986           3988       3990   3992     3994     3996
-                          TIGR       3025           3026       3027   3028     3029     3030

***D. vulgaris*** gene cluster for lactate utilization

## Lactate dehydrogenase? !

- Glycolate  +  O2

- Glyoxylate  +H2O2

- H

- H

- H

- H

- 2e- + 2H+

## Desulfovibrio strains for sequencing

*    **D. fructosovorans*
-   Growth on fructose,
-  At least four dehydrogenases,
-  Three hydrogenase (periplasmic Fe, FeNi, cytoplasmic NADP reducing were charachterized and mutants were obtained
*    **Desulfovibrio termitidis*
-   Isolated from termite guts
*    **Desulfovibrio sp. PT2*
*     *isolated from bioreactor inoculated with ground water
-            where it grown in the presence of metanogenes
*     *microarray analysis showed presence of* *hydrogenases found in
-            Hildenborough strain
*    **D. vulgaris* subsp. *oxamicus*
-      Closest known relative of Hildenborugh (versus DePue?)

## Slide 9

## Gene order on chromosomes of several related species 

*Hi Rd vs P. maltocida*

*S. typhiTy2 vs C18*

*Ec 157OH vs Ec 157OH Sakai*

## HI VS HD (all) 

- HI VS HD (all)

| 1 | 3 |
| --- | --- |
| 2 |  |

## HI VS HD (+ +) 

- HI VS HD (+ +)

| 1 | 3 |
| --- | --- |
| 2 |  |

## HI VS HD (- -) 

- HI VS HD (- -)

| 1 | 3 |
| --- | --- |
| 2 |  |

## http://db.systemsbiology.net/projects/local/mhc/acgt/

_**http://db.systemsbiology.net/projects/local/mhc/acgt/**_

## Screenshot:

_**Screenshot:**_