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Chapter 22 : Genomics of Acidophiles

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Abstract:

Acidophily is a trait of organisms referring to the ability to survive and preferentially multiply at low pH (<3). Extremely acidic environments are found in natural geothermal areas as well as in man-made habitats such as mining wastes. Acidophiles that thrive in these habitats are found among the archaeal, bacterial, and eukaryotic microorganisms. Genome sequence analysis of prokaryotic microorganisms is proceeding at an enormous pace and in the past few years has been applied to several acid-adapted microbes. Since among acidophiles most genomic information is available on representatives of the thermoacidophilic archaeal lineages and , this chapter focuses mainly on these organisms. A more comprehensive understanding of the mechanisms that underlie protein stability at harsh conditions may be accessible by a comparative analysis of protein structures. A recent study of the structure of the maltose-maltodextrin-binding protein (MBP) from gives some insights into the molecular basis for protein acidostability. The majority of acidophilic archaea, especially the extreme acidophiles of the , have a scavenging life style—they rely on the decomposition of organic matter for their nutrition and usually require yeast, meat, or bacterial extracts to grow in culture. An important metabolic feature for acidophiles, related to their life style, is the ability to efficiently metabolize weak organic acids. The secondary transporters of thermoacidophiles are believed to utilize protons and not Na as a motive force. Thermophilic and acidophilic archaea form two distinct phylogenetic groups, one belonging to the euryarchaeal and the second one to the crenarchaeal lineage.

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22

Key Concept Ranking

Bacteria and Archaea
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Major Facilitator Superfamily
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Bacterial Proteins
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Amino Acid Decarboxylase
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Figures

Image of Figure 1.
Figure 1.

Size and coding density distribution of selected archaeal genomes. The genomes included in the graph include representatives of all archaeal lineages. Organismal designations are PTO, ; TAC, ; TVO, ; STO, ; SSO, .

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22
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Image of Figure 2.
Figure 2.

Proteome isoelectric point distribution and amino acid usage based on genome data. The isoelectric point distribution graphs represent plots of the number of proteins with a certain p (-axis) in intervals of 0.1 pH units (-axis). The amino acid usage data is derived from the genome atlas database (https://www.cbs.dtu.dk/services/GenomeAtlas/index.php) ( ).

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22
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Image of Figure 3.
Figure 3.

Genome-based reconstruction of the predicted respiratory chain of the euryarchaeon . The components marked in bold are proposed to be either of bacterial or of crenarchaeal origin, based on protein similarity.

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22
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Image of Figure 4.
Figure 4.

Density of genes encoding transporter proteins in the publicly available archaeal genomes. Data were obtained from http://membranetransport.org/ ( ).

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22
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Image of Figure 5.
Figure 5.

(A) A simplified 16S rRNA phylogenetic tree of . The two thermoacidophilic groups are boxed. (B) Occurrence of homologs in , and , the criterion for homology is a minimum of 30% amino acid sequence similarity. Orthologous and paralogous sequences were counted only once. The size of the circles is proportional to the genome size. Reproduced from ) with permission from the National Academy of Sciences.

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22
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Tables

Generic image for table
Table 1.

Occurrence of homologs of the acid resistance genes among thermoacidophilic archaea

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22
Generic image for table
Table 2.

Distribution of ORFs coding for chaperones and DNA superstructure formation proteins in archaeal genomes

Citation: Angelov A, Liebl W. 2007. Genomics of Acidophiles, p 279-292. In Gerday C, Glansdorff N (ed), Physiology and Biochemistry of Extremophiles. ASM Press, Washington, DC. doi: 10.1128/9781555815813.ch22

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