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González-Rosales C, Vergara E, Dopson M, Valdés JH, Holmes DS. Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle. Front Microbiol 2022; 12:822229. [PMID: 35242113 PMCID: PMC8886135 DOI: 10.3389/fmicb.2021.822229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 01/22/2023] Open
Abstract
Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as "first line of defense" were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for "second line of defense" systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to "hedge bet" in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events.
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Affiliation(s)
- Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jorge H. Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
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Tanudjaja E, Hoshi N, Su YH, Hamamoto S, Uozumi N. Kup-mediated Cs + uptake and Kdp-driven K + uptake coordinate to promote cell growth during excess Cs + conditions in Escherichia coli. Sci Rep 2017; 7:2122. [PMID: 28522840 PMCID: PMC5437092 DOI: 10.1038/s41598-017-02164-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/07/2017] [Indexed: 01/05/2023] Open
Abstract
The physiological effects of caesium (Cs) on living cells are poorly understood. Here, we examined the physiological role of Cs+ on the activity of the potassium transporters in E. coli. In the absence of potassium (K+), Kup-mediated Cs+ uptake partially supported cell growth, however, at a much lower rate than with sufficient K+. In K+-limited medium (0.1 mM), the presence of Cs+ (up to 25 mM) in the medium enhanced growth as much as control medium containing 1 mM K+. This effect depended on the maintenance of basal levels of intracellular K+ by other K+ uptake transporters. Higher amounts of K+ (1 mM) in the medium eliminated the positive effect of Cs+ on growth, and revealed the inhibitory effect of high Cs+ on the growth of wild-type E. coli. Cells lacking Kdp, TrkG and TrkH but expressing Kup grew less well when Cs+ was increased in the medium. A kdp mutant contained an increased ratio of Cs+/K+ in the presence of high Cs+ in the medium and consequently was strongly inhibited in growth. Taken together, under excess Cs+ conditions Kup-mediated Cs+ influx sustains cell growth, which is supported by intracellular K+ supplied by Kdp.
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Affiliation(s)
- Ellen Tanudjaja
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, 980-8579, Japan
| | - Naomi Hoshi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, 980-8579, Japan
| | - Yi-Hsin Su
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, 980-8579, Japan
| | - Shin Hamamoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, 980-8579, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, 980-8579, Japan.
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Lundbäck AK, Müller SA, Engel A, Hebert H. Assembly of Kch, a putative potassium channel from Escherichia coli. J Struct Biol 2009; 168:288-93. [PMID: 19631752 DOI: 10.1016/j.jsb.2009.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 07/16/2009] [Accepted: 07/21/2009] [Indexed: 11/30/2022]
Abstract
Attempts to explore the structure and function of Kch, a putative potassium channel of Escherichia coli have yielded varying results; potassium-associated functions have been found in vivo but not in vitro. Here the kch gene is shown to produce two proteins, full-length Kch and the large C-terminal cytosolic domain (the RCK domain). Further, these two proteins are associated at the initial stages of purification. Previous structural studies of full-length Kch claim that the isolated protein forms large aggregates that are not suitable for analysis. The results presented here show that the purified protein sample, although heterogeneous, has one major population with a mass of about 400kDa, implying the presence of two Kch tetramers in a complex form. A three dimensional reconstruction at 25A based on electron microscopy data from negatively stained particles, revealed a 210A long and 95A wide complex in which the two tetrameric Kch units are linked by their RCK domains, giving rise to a large central ring of density. The formation of this dimer of tetramers on expression or during purification, may explain why attempts to reconstitute Kch into liposomes for activity measurements have failed.
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Affiliation(s)
- Anna-Karin Lundbäck
- Karolinska Institutet, Department of Biosciences and Nutrition and Royal Institute of Technology, Novum, Huddinge, Sweden
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Polen T, Krämer M, Bongaerts J, Wubbolts M, Wendisch VF. The global gene expression response of Escherichia coli to l-phenylalanine. J Biotechnol 2005; 115:221-37. [PMID: 15639085 DOI: 10.1016/j.jbiotec.2004.08.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 07/29/2004] [Accepted: 08/19/2004] [Indexed: 10/26/2022]
Abstract
We investigated the global gene expression changes of Escherichia coli due to the presence of different concentrations of phenylalanine or shikimate in the growth medium. The response to 0.5 g l(-1) phenylalanine primarily reflected a perturbed aromatic amino acid metabolism, in particular due to TyrR-mediated regulation. The addition of 5g l(-1) phenylalanine reduced the growth rate by half and elicited a great number of likely indirect effects on genes regulated in response to changed pH, nitrogen or carbon availability. Consistent with the observed gene expression changes, supplementation with shikimate, tyrosine and tryptophan relieved growth inhibition by phenylalanine. In contrast to the wild-type, a tyrR disruption strain showed increased expression of pckA and of tktB in the presence of phenylalanine, but its growth was not affected by phenylalanine at the concentrations tested. The absence of growth inhibition by phenylalanine suggested that at high phenylalanine concentrations TyrR-defective strains might perform better in phenylalanine production.
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Affiliation(s)
- T Polen
- Institut für Biotechnologie 1, Forschungszentrum Jülich, D-52425 Jülich, Germany.
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Kuo MMC, Saimi Y, Kung C. Gain-of-function mutations indicate that Escherichia coli Kch forms a functional K+ conduit in vivo. EMBO J 2003; 22:4049-58. [PMID: 12912904 PMCID: PMC175798 DOI: 10.1093/emboj/cdg409] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although Kch of Escherichia coli is thought to be a K(+) channel by sequence homology, there is little evidence that it actually conducts K(+) ions in vitro or in vivo. We isolated gain-of-function (GOF) Kch mutations that render bacteria specifically sensitive to K(+) ions. Millimolar added K(+), but not Na(+) or sorbitol, blocks the initiation or continuation of mutant growth in liquid media. The mutations are mapped at the RCK (or KTN) domain, which is considered to be the cytoplasmic sensor controlling the gate. Additional mutations directed to the K(+)-filter sequence rescue the GOF mutant. The apparent K(+)-specific conduction through the 'loose-cannon' mutant channel suggests that the wild-type Kch channel also conducts, albeit in a regulated manner. Changing the internal ATG does not erase the GOF toxicity, but removes kch's short second product, suggesting that it is not required for channel function in vivo. The mutant phenotypes are better explained by a perturbation of membrane potential instead of internal K(+) concentration. Possible implications on the normal function of Kch are discussed.
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Affiliation(s)
- Mario Meng-Chiang Kuo
- Laboratory of Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706, USA
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Epstein W. The roles and regulation of potassium in bacteria. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2003; 75:293-320. [PMID: 14604015 DOI: 10.1016/s0079-6603(03)75008-9] [Citation(s) in RCA: 341] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Potassium is the major intracellular cation in bacteria as well as in eucaryotic cells. Bacteria accumulate K+ by a number of different transport systems that vary in kinetics, energy coupling, and regulation. The Trk and Kdp systems of enteric organisms have been well studied and are found in many distantly related species. The Ktr system, resembling Trk in many ways, is also found in many bacteria. In most species two or more independent saturable K(+)-transport systems are present. The KefB and KefC type of system that is activated by treatment of cells with toxic electrophiles is the only specific K(+)-efflux system that has been well characterized. Pressure-activated channels of at least three types are found in bacteria; these represent nonspecific paths of efflux when turgor pressure is dangerously high. A close homolog of eucaryotic K+ channels is found in many bacteria, but its role remains obscure. K+ transporters are regulated both by ion concentrations and turgor. A very general property is activation of K+ uptake by an increase in medium osmolarity. This response is modulated by both internal and external concentrations of K+. Kdp is the only K(+)-transport system whose expression is regulated by environmental conditions. Decrease in turgor pressure and/or reduction in external K+ rapidly increase expression of Kdp. The signal created by these changes, inferred to be reduced turgor, is transmitted by the KdpD sensor kinase to the KdpE-response regulator that in turn stimulates transcription of the kdp genes. K+ acts as a cytoplasmic-signaling molecule, activating and/or inducing enzymes and transport systems that allow the cell to adapt to elevated osmolarity. The signal could be ionic strength or specifically K+. This signaling response is probably mediated by a direct sensing of internal ionic strength by each particular system and not by a component or system that coordinates this response by different systems to elevated K+.
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Affiliation(s)
- Wolfgang Epstein
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
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