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Chapter 16 : Proteomic Approaches To Study Lactic Acid Bacteria

Authors: David P. A. Cohen1, Elaine E. Vaughan2, Willem M. de Vos3, Erwin G. Zoetendal4
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Affiliations: 1: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands; 2: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands; 3: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands; 4: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
Content Type: Monograph
Publication Year: 2008

Category: Clinical Microbiology

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Abstract:

Biology aims to describe, understand, and predict the functionality of living cells, tissues, organisms, and ecosystems. High-throughput approaches that allow simultaneous investigation of more than one parameter will ultimately lead to better understanding of the organism’s behavior. Examples of such high-throughput approaches are genomics, transcriptomics, proteomics, and metabolomics. This chapter focuses on the application of proteomics in microbiological research in which special attention is given to the lactic acid bacteria (LAB). Proteomics has been used to investigate the functionality of LAB during preparation or fermentation of foods or their responses towards certain stress conditions (e.g., bile salts and acid) that these organisms encounter during passage through the human gastrointestinal tract. Proteomic approaches make it possible to gain insights into the relative abundance of proteins under certain conditions, and this knowledge may help predict which proteins of LAB are involved in survival under harsh conditions. Following an introduction regarding recent developments in proteomics, the chapter describes major findings obtained by studying the proteomes of LAB, especially under physiological stress conditions. It highlights the major results that were obtained by studying the proteomes of LAB under various conditions. Two separate proteomic research strategies have been applied frequently to LAB. These approaches include the construction of protein reference maps, systematic indexing of proteins, and analyses of bacterial stress responses culminating in induced changes in different proteomes.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
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Proteomic Approaches To Study Lactic Acid Bacteria
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Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16fig01
Figure 1
The gel-based proteomic method can be divided into two main parts, separation of protein complexes and identification of individual proteins. The separation of proteins in mixtures is based on the protein’s isoelectric point and its molecular weight. Identification of the proteins is commonly achieved using MALDI-TOF MS and mass fingerprinting prior to database searching.
10.1128/9781555815462/ch16fig1_thmb.gif
10.1128/9781555815462/ch16fig1.gif
Image of Figure 1
Figure 1

The gel-based proteomic method can be divided into two main parts, separation of protein complexes and identification of individual proteins. The separation of proteins in mixtures is based on the protein’s isoelectric point and its molecular weight. Identification of the proteins is commonly achieved using MALDI-TOF MS and mass fingerprinting prior to database searching.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
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Figure 2
A schematic overview of stress responses in LAB (based on , and ). Proteins within the dashed circles are associated with several stress responses visualized by two-dimensional gel electrophoresis. DnaK and GroES/EL are induced during specific stress challenges, while Clp is a general stress protein. The third group consists of proteins found to be differentially regulated during stress, changing the metabolism of the bacterium towards adaptation to the stress inducer.
10.1128/9781555815462/ch16fig2_thmb.gif
10.1128/9781555815462/ch16fig2.gif
Image of Figure 2
Figure 2

A schematic overview of stress responses in LAB (based on , and ). Proteins within the dashed circles are associated with several stress responses visualized by two-dimensional gel electrophoresis. DnaK and GroES/EL are induced during specific stress challenges, while Clp is a general stress protein. The third group consists of proteins found to be differentially regulated during stress, changing the metabolism of the bacterium towards adaptation to the stress inducer.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
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Figure 3
A schematic diagram combines metagenomic and metaproteomic data sets in order to address gut functionality of LAB. With metagenomics, identification of bacterial genes is feasible. Protein predictions of active genes by metagenomics will facilitate protein identification by metaproteomics.
10.1128/9781555815462/ch16fig3_thmb.gif
10.1128/9781555815462/ch16fig3.gif
Image of Figure 3
Figure 3

A schematic diagram combines metagenomic and metaproteomic data sets in order to address gut functionality of LAB. With metagenomics, identification of bacterial genes is feasible. Protein predictions of active genes by metagenomics will facilitate protein identification by metaproteomics.

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
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Tables

Proteomic Approaches To Study Lactic Acid Bacteria
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Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table01
Table 1
Methods used to visualize proteins by two-dimensional gel electrophoresis
Generic image for table
Table 1

Methods used to visualize proteins by two-dimensional gel electrophoresis

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table02
Table 2
Ionization methods and available mass spectrometers commonly used in proteomics studies
Generic image for table
Table 2

Ionization methods and available mass spectrometers commonly used in proteomics studies

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table03
Table 3
Proteome reference map of lactic acid bacteria
Generic image for table
Table 3

Proteome reference map of lactic acid bacteria

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16
/content/10.1128/9781555815462.ch16.ch16table04
Table 4
Proteins produced by LAB as responses to different stress challenges
Generic image for table
Table 4

Proteins produced by LAB as responses to different stress challenges

Citation: Cohen D, Vaughan E, de Vos W, Zoetendal E. 2008. Proteomic Approaches To Study Lactic Acid Bacteria, p 205-221. In Versalovic J, Wilson M (ed), Therapeutic Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815462.ch16

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