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Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

Lehtovirta-Morley LE, Sayavedra-Soto LA, Gallois N, Schouten S, Stein LY, Prosser JI, Nicol GW - Appl. Environ. Microbiol. (2016)

Bottom Line: Instead, the genome indicates that "Ca Nitrosotalea devanaterra" contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA.Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of "Ca Nitrosotalea devanaterra" were not dominated by crenarchaeol, as found in neutrophilic AOA.This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom l.lehtovirta@abdn.ac.uk.

No MeSH data available.


Related in: MedlinePlus

Gene organization within potassium transporter (A) and pH homeostasis (B) gene clusters. Arrows indicate the relative lengths and directions of ORFs. Values inside the arrows indicate synteny E values. Values above the arrows indicate the gene name. (A) kdpABC, potassium-transporting ATPase gene; kdpD, signal transduction histidine kinase gene; PAC/PAS, PAS/PAC sensor histidine kinase gene; 1, gene for protein of unknown function; 2, signal transduction response regulator gene; 3, peptidase gene. (B) mntH, magnesium/divalent cation transporter gene; cam, carbonic anhydrase gene; uspA, universal stress protein gene; mgtA, magnesium transporting P-type ATPase gene; alsD, putative alpha-acetolactate decarboxylase gene; 1, phosphoribosyltransferase-like protein gene; 2, gene for conserved protein of unknown function; 3, Val tRNA gene; 4, adenylate/guanylate cyclase sensor protein gene; 5, gene for protein of unknown function; 6, response regulator receiver protein gene; 7, secreted copper domain-containing protein gene; 8, putative adenylate cyclase gene; 9, putative transposase gene.
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Figure 2: Gene organization within potassium transporter (A) and pH homeostasis (B) gene clusters. Arrows indicate the relative lengths and directions of ORFs. Values inside the arrows indicate synteny E values. Values above the arrows indicate the gene name. (A) kdpABC, potassium-transporting ATPase gene; kdpD, signal transduction histidine kinase gene; PAC/PAS, PAS/PAC sensor histidine kinase gene; 1, gene for protein of unknown function; 2, signal transduction response regulator gene; 3, peptidase gene. (B) mntH, magnesium/divalent cation transporter gene; cam, carbonic anhydrase gene; uspA, universal stress protein gene; mgtA, magnesium transporting P-type ATPase gene; alsD, putative alpha-acetolactate decarboxylase gene; 1, phosphoribosyltransferase-like protein gene; 2, gene for conserved protein of unknown function; 3, Val tRNA gene; 4, adenylate/guanylate cyclase sensor protein gene; 5, gene for protein of unknown function; 6, response regulator receiver protein gene; 7, secreted copper domain-containing protein gene; 8, putative adenylate cyclase gene; 9, putative transposase gene.

Mentions: The genome carries genes encoding two P-type ATPases, kdpABCD (NDEV_1461, NDEV_1460, NDEV_1459, and NDEV_1455) and mgtA (NDEV_1079), predicted for K+ and Mg2+ transport, respectively (Fig. 1 and 2). While mgtA is not found in AOA except “Ca. Nitrosotalea devanaterra” (see Table S4 in the supplemental material), the kdp gene cluster is syntenic in many prokaryotes, e.g., proteobacteria, Nitrososphaera viennensis, and acidophilic archaea (Fig. 2A). “Ca. Nitrosotalea devanaterra” also lacks the trk potassium transporter gene conserved in many AOA genomes (see Table S6 in the supplemental material). Potassium is typically a critically important solute for maintaining the reverse membrane potential in acidophiles (15), and it is therefore surprising that the “Ca. Nitrosotalea devanaterra” genome does not contain genes for potassium transporters which are absent in all neutrophilic AOA.


Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

Lehtovirta-Morley LE, Sayavedra-Soto LA, Gallois N, Schouten S, Stein LY, Prosser JI, Nicol GW - Appl. Environ. Microbiol. (2016)

Gene organization within potassium transporter (A) and pH homeostasis (B) gene clusters. Arrows indicate the relative lengths and directions of ORFs. Values inside the arrows indicate synteny E values. Values above the arrows indicate the gene name. (A) kdpABC, potassium-transporting ATPase gene; kdpD, signal transduction histidine kinase gene; PAC/PAS, PAS/PAC sensor histidine kinase gene; 1, gene for protein of unknown function; 2, signal transduction response regulator gene; 3, peptidase gene. (B) mntH, magnesium/divalent cation transporter gene; cam, carbonic anhydrase gene; uspA, universal stress protein gene; mgtA, magnesium transporting P-type ATPase gene; alsD, putative alpha-acetolactate decarboxylase gene; 1, phosphoribosyltransferase-like protein gene; 2, gene for conserved protein of unknown function; 3, Val tRNA gene; 4, adenylate/guanylate cyclase sensor protein gene; 5, gene for protein of unknown function; 6, response regulator receiver protein gene; 7, secreted copper domain-containing protein gene; 8, putative adenylate cyclase gene; 9, putative transposase gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 2: Gene organization within potassium transporter (A) and pH homeostasis (B) gene clusters. Arrows indicate the relative lengths and directions of ORFs. Values inside the arrows indicate synteny E values. Values above the arrows indicate the gene name. (A) kdpABC, potassium-transporting ATPase gene; kdpD, signal transduction histidine kinase gene; PAC/PAS, PAS/PAC sensor histidine kinase gene; 1, gene for protein of unknown function; 2, signal transduction response regulator gene; 3, peptidase gene. (B) mntH, magnesium/divalent cation transporter gene; cam, carbonic anhydrase gene; uspA, universal stress protein gene; mgtA, magnesium transporting P-type ATPase gene; alsD, putative alpha-acetolactate decarboxylase gene; 1, phosphoribosyltransferase-like protein gene; 2, gene for conserved protein of unknown function; 3, Val tRNA gene; 4, adenylate/guanylate cyclase sensor protein gene; 5, gene for protein of unknown function; 6, response regulator receiver protein gene; 7, secreted copper domain-containing protein gene; 8, putative adenylate cyclase gene; 9, putative transposase gene.
Mentions: The genome carries genes encoding two P-type ATPases, kdpABCD (NDEV_1461, NDEV_1460, NDEV_1459, and NDEV_1455) and mgtA (NDEV_1079), predicted for K+ and Mg2+ transport, respectively (Fig. 1 and 2). While mgtA is not found in AOA except “Ca. Nitrosotalea devanaterra” (see Table S4 in the supplemental material), the kdp gene cluster is syntenic in many prokaryotes, e.g., proteobacteria, Nitrososphaera viennensis, and acidophilic archaea (Fig. 2A). “Ca. Nitrosotalea devanaterra” also lacks the trk potassium transporter gene conserved in many AOA genomes (see Table S6 in the supplemental material). Potassium is typically a critically important solute for maintaining the reverse membrane potential in acidophiles (15), and it is therefore surprising that the “Ca. Nitrosotalea devanaterra” genome does not contain genes for potassium transporters which are absent in all neutrophilic AOA.

Bottom Line: Instead, the genome indicates that "Ca Nitrosotalea devanaterra" contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA.Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of "Ca Nitrosotalea devanaterra" were not dominated by crenarchaeol, as found in neutrophilic AOA.This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom l.lehtovirta@abdn.ac.uk.

No MeSH data available.


Related in: MedlinePlus