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Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis - PubMed

Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis

An Chi et al. Mol Cell Proteomics. 2007 Dec.

Abstract

Acidithiobacillus ferrooxidans is a chemolithoautotrophic acidophile capable of obtaining energy by oxidizing ferrous iron or sulfur compounds such as metal sulfides. Some of the proteins involved in these oxidations have been described as forming part of the periplasm of this extremophile. The detailed study of the periplasmic components constitutes an important area to understand the physiology and environmental interactions of microorganisms. Proteomics analysis of the periplasmic fraction of A. ferrooxidans ATCC 23270 was performed by using high resolution linear ion trap-FT MS. We identified a total of 131 proteins in the periplasm of the microorganism grown in thiosulfate. When possible, functional categories were assigned to the proteins: 13.8% were transport and binding proteins, 14.6% were several kinds of cell envelope proteins, 10.8% were involved in energy metabolism, 10% were related to protein fate and folding, 10% were proteins with unknown functions, and 26.1% were proteins without homologues in databases. These last proteins are most likely characteristic of A. ferrooxidans and may have important roles yet to be assigned. The majority of the periplasmic proteins from A. ferrooxidans were very basic compared with those of neutrophilic microorganisms such as Escherichia coli, suggesting a special adaptation of the chemolithoautotrophic bacterium to its very acidic environment. The high throughput proteomics approach used here not only helps to understand the physiology of this extreme acidophile but also offers an important contribution to the functional annotation for the available genomes of biomining microorganisms such as A. ferrooxidans for which no efficient genetic systems are available to disrupt genes by procedures such as homologous recombination.

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Figures

Fig. 1
Fig. 1. 2-D PAGE of the periplasmic fraction of A. ferrooxidans grown on thiosulfate

Total proteins (A) or periplasmic fraction (B and C) were separated by 2-D NEPHGE (A and B) with a pH gradient between 3.0 (right side of the gel) and 10.0 (left side of the gel) or by monodimensional SDS-PAGE (C). Spots were detected by silver stain (A and B) or by colloidal Coomassie Blue (C). Molecular mass standards (in kilodaltons) are given on the left of the gels.

Fig. 2
Fig. 2. Global analysis of periplasmic proteins from A. ferrooxidans

A, percent distribution of proteins according to their export signals. B, distribution of periplasmic proteins in functional categories according to TIGR annotation.

Fig. 3
Fig. 3. pI distribution among periplasmic proteins found in A. ferrooxidans compared with some other Gram-negative micro-organisms

A, distribution of all proteins found in the periplasmic fraction from A. ferrooxidans ATCC 23270 grown in thiosulfate according to their theoretical molecular masses and isoelectric points. B, percentage of SignalP or TatP proteins with pI values above and below 7.0 predicted in complete genomes of Gram-negative bacteria. Alkalophiles, δ-proteobacterium MLMS-1 and A. ehrlichii MLHE-1; neutrophiles, E. coli K-12, T. denitrificans ATCC 25259, and G. sulfurreducens PCA; acidophiles, C. burnetii RSA 493 and A. ferrooxidans ATCC 23270. Also included in this group for comparison is the acid-tolerant H. pylori 26695.

Fig. 4
Fig. 4. Schematic location and suggested putative functions of the majority of the proteins identified in the periplasmic fraction from A. ferrooxidans

Most of the proposed localizations and possible roles of the indicated proteins are based on previously reported studies in E. coli and other microorganisms (1, 33, 40, 43, 73). The proteins shaded in gray were identified experimentally by proteomics analysis of the periplasmic fraction. Transport functions are highlighted in the upper part, and energy metabolism is in the lower portion of the figure. The OMPs are shown in their final destination into the outer membrane. Black circles represent OMP precursors in transit to the outer membrane. The order in which the different proteins are included in this schematic is arbitrary.

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