Thermoacidophile

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A thermoacidophile is an extremophilic microorganism that is both thermophilic and acidophilic; i.e., it can grow under conditions of high temperature and low pH. [1] The large majority of thermoacidophiles are archaea (particularly the Thermoproteota and "Euryarchaeota") or bacteria, though occasional eukaryotic examples have been reported. [2] [3] Thermoacidophiles can be found in hot springs and solfataric environments, within deep sea vents, or in other environments of geothermal activity. [1] : 602  They also occur in polluted environments, such as in acid mine drainage. [4]

Contents

Hot Spring in Yellowstone : A typical environment for thermoacidophiles to inhabit Morning Glory Hot Spring.jpg
Hot Spring in Yellowstone : A typical environment for thermoacidophiles to inhabit

Biotopes that favor thermoacidophiles can be found both on land and in the sea, where the mineral composition of the water typically consists of highly reduced compounds such as various sulfides, and highly oxidized sulfates. The conversion of reduced sulfides to oxidized sulfates leads to a production of protons, lowering the pH [1] of the surrounding environment. While reduced sulfides are generally considered to be reactive, their conversion to their oxidized counterpart by abiotic natural processes (reacting with things that aren’t living organisms) is relatively low. This fact emphasizes the importance of bio-oxidizers (i.e. thermoacidophiles) in constructing and maintaining this ecological niche. [5] Most of the microbes in these harsh environments are chemolithoautotrophs [6] (they gain electrons from pre-formed inorganic compounds, and use carbon dioxide as a carbon source), which have evolved specific adaptations to inhabit and grow in such selective environments. Archaea are unique in their ability to thrive in these environments, as many bacterial and eukaryotic organisms are limited to tolerance of such acidic (pH < 3.5), thermal (T> 65 °C) environments and don’t demonstrate sustained thermoacidophilicity. [6] However, the genome of a thermoacidophilic eukaryote, the red algae Galdieria sulphuraria , revealed that its environmental adaptations likely originated from horizontal gene transfer from thermoacidophilic archaea and bacteria. [2]

An apparent tradeoff has been described between adaptation to high temperature and low pH; relatively few examples are known that are tolerant of the extremes of both environments (pH < 2, growth temperature > 80 °C). [1] Adaptations that allow them to survive in these harsh environments include proton pumps and buffering strategies, epigenetic modifications of the chromosome, and altered membrane structures. Many thermoacidophilic archaea have aerobic or microaerophilic metabolism, [1] : 602  although obligately anaerobic examples (e.g. the Acidilobales) have also been identified. [6]

Unique biological adaptations

Chromosome structure and epigenetic modifications

Most thermoacidophiles are archaeal, with Crenarchaea belonging to the Sulfolobales order serving as an model system. Many of the biological mechanisms used by Crenarchae are shared by all archaea but there are some lineage-specific differences unique to thermoacidophilic archaea. One example of the unique differences for thermoacidophilic archaea is their lack of eukaryote-like histones, which are typically involved in the packaging and reorganization of the chromosome, all Thermoplasma and Crenarchaeota lack histone like proteins. [7]

Thermoacidophillic archaea typically have single, small, circular chromosome between 1.5 and 3 Mbp in length. [8] Chromatin proteins are used to condense and organize the genome, however this is not done with histone-orthologs as in eukaryotes or some bacteria, a large evolutionary divergence that characterizes thermoacidophilic archaea. Instead of using histones, a type of protein called nucleoid associated proteins (NAPs) are expressed, however the degree of conservation between species varies from protein to protein. These proteins are typically between 7 and 10 kDa in size, are basic, and account for up to 5% of cellular protein, making them one of the most highly expressed proteins in the cell. [7]

The functionality of NAPs can be altered via post-translational modifications (PTMs). These epigenetic modifications have significant impacts on their functionality and the fitness of thermophiles in extreme environments. Methylation, a form of PTM, is a common alteration to NAP structure. It has been linked to the thermostabilization of the proteins as well as the regulation of genes in epigenetic studies. [9] An example of the impact of methylation can be seen in an adaptive laboratory evolution experiment, in which a strain of Sa. solfataricu developed a super-acid resistant phenotype, even though its genome had not changed from the reference sequence. Investigation revealed that the acid resistance was conferred by a difference in the methylation of Sso7d and Cren7, both Naps. [9] This highlights how a difference in methylation can have a significant impact on the fitness of thermophiles.

In addition to local structuring by NAPs, the Sulfolobales genome is also globally compartmentalized into two sub-Mbp compartments. Each compartment, often referred to as the A and B compartment respectively, is populated by specific sets of genes that vary in their level of transcription. [10] The A compartment generally contains genes involved in essential biological processes such as the creation of metabolic proteins, which are highly expressed in the cell. The B compartment holds genes related to environmental stress responses, CRISPR-Cas clusters and fatty acid metabolism. The exact mechanism regarding the global restructuring of the genome is not currently known, however a protein known as coalescin has been found to play a critical role in the restructuring, with an inverse correlation observed between the occurrence of coalescin and the transcriptional activity of genes in the B compartment. [10]

Thermostability and stress responses

Thermoacidophiles have adapted to the extreme environments they inhabit by evolving specific mechanisms to deal with the high temperature and low pH environment. While these mechanisms aren’t necessarily unique to thermoacidophiles and can be found in thermophiles and acidophiles respectively, their incorporation into a single organism can lead to synergistic effects. For example, while DNA stability doesn’t necessarily depend solely on its base pair composition, some thermoacidophiles favor the AGG and AGA codons over CGN for arginine.  The trend of favoring the heat-stabile nucleotides adenine and guanine has been observed throughout thermoacidophile genomes. Additionally, thermoacidophiles tend to avoid using amino acids that participate in unwanted side reactions at high temperatures, including histidine, glutamine and threonine. [11] Proteins in thermoacidophiles are also smaller on average than those found in mesophiles, with the former having an average length of 283 amino acids and the latter being 340, a difference of ~20%. [11] This is theorized to occur because smaller proteins are more heat stabile than larger proteins. The use of reverse DNA gyrase is another thermal adaptation, it introduces positive DNA supercoiling to increase the heat stability of the genome, and is a protein unique to hyperthermophiles.[ citation needed ]

While some thermoacidophiles can grow optimally at a pH close to 0, their cytoplasm is often near neutral pH. This results in a massive pH difference across the membrane. Thermoacidophiles have several mechanisms to deal with this. The first of which is a reversed membrane potential, where the intracellular side of the membrane is positively charged and the extracellular membrane is negatively charged. The reversed membrane potential is created by the active transport of potassium ions into the cell, which prevents the passive diffusion of protons across the membrane. [12] Cytosolic buffering strategies are also implemented, such as using basic amino acids such as arginine, lysine and histidine. The structure of the membrane also contributes to the thermoacidophilicity of Sulfoluobales, as their membranes consist of ether linked lipids that aren’t as susceptible to acid hydrolysis and the increase of porosity that leads to thermal leakage as normal lipid bilayers. Some archaea also have cyclopentyl rings attached to their lipids that have been shown to increase the thermostability of the membrane. [13]

Despite all of the previously mentioned adaptations that allow thermoacidophiles to survive harsh environments, it is inevitable that conditions in the cell reach a point where a protein is damaged by the extreme environment they inhabit. The thermosome is a common tool in thermoacidophilic archaea. It generally consists of multiple alpha and beta subunits, the proportions of which in the structure vary with temperature. [14] The structure of the thermosome resembles a capsule with openings at each end. Unlike bacterial thermosomes, which have a separate subunit that closes off the internal space, the archaeal thermosome undergoes a conformational change to close the openings at each end via the hydrolysis of ATP. The thermosome closes around the protein and offers a more stable environment for the protein to refold properly. If the thermosome cannot refold the denatured protein, the protein is tagged by ubiquitin for degradation by the proteasome. [14]

Related Research Articles

<span class="mw-page-title-main">Thermoproteota</span> Phylum of archaea

The Thermoproteota are prokaryotes that have been classified as a phylum of the domain Archaea. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Thermoproteota environmental rRNA indicating the organisms may be the most abundant archaea in the marine environment. Originally, they were separated from the other archaea based on rRNA sequences; other physiological features, such as lack of histones, have supported this division, although some crenarchaea were found to have histones. Until 2005 all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells. Recent evidence shows that some members of the Thermoproteota are methanogens.

<i>Sulfolobus</i> Genus of archaea

Sulfolobus is a genus of microorganism in the family Sulfolobaceae. It belongs to the archaea domain.

Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.

Acidophiles or acidophilic organisms are those that thrive under highly acidic conditions. These organisms can be found in different branches of the tree of life, including Archaea, Bacteria, and Eukarya.

<span class="mw-page-title-main">Sulfolobaceae</span> Family of archaea

Sulfolobaceae are a family of the Sulfolobales belonging to the domain Archaea. The family consists of several genera adapted to survive environmental niches with extreme temperature and low pH conditions.

Icerudivirus is a genus of viruses in the family Rudiviridae. These viruses are non-enveloped, stiff-rod-shaped viruses with linear dsDNA genomes, that infect hyperthermophilic archaea of the species Sulfolobus islandicus. There are three species in the genus.

Archaeocin is the name given to a new type of potentially useful antibiotic that is derived from the Archaea group of organisms. Eight archaeocins have been partially or fully characterized, but hundreds of archaeocins are believed to exist, especially within the haloarchaea. Production of these archaeal proteinaceous antimicrobials is a nearly universal feature of the rod-shaped haloarchaea.

<span class="mw-page-title-main">Prokaryote</span> Unicellular organism lacking a membrane-bound nucleus

A prokaryote is a single-cell organism whose cell lacks a nucleus and other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό (pró), meaning 'before', and κάρυον (káruon), meaning 'nut' or 'kernel'. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. However in the three-domain system, based upon molecular analysis, prokaryotes are divided into two domains: Bacteria and Archaea. Organisms with nuclei are placed in a third domain: Eukaryota.

<span class="mw-page-title-main">Archaea</span> Domain of organisms

Archaea is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic, as eukaryotes are now known to have evolved from archaea. Even though the domain Archaea includes eukaryotes, the term "archaea" in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

<span class="mw-page-title-main">Acidophiles in acid mine drainage</span>

The outflow of acidic liquids and other pollutants from mines is often catalysed by acid-loving microorganisms; these are the acidophiles in acid mine drainage.

The archaellum is a unique structure on the cell surface of many archaea that allows for swimming motility. The archaellum consists of a rigid helical filament that is attached to the cell membrane by a molecular motor. This molecular motor – composed of cytosolic, membrane, and pseudo-periplasmic proteins – is responsible for the assembly of the filament and, once assembled, for its rotation. The rotation of the filament propels archaeal cells in liquid medium, in a manner similar to the propeller of a boat. The bacterial analog of the archaellum is the flagellum, which is also responsible for their swimming motility and can also be compared to a rotating corkscrew. Although the movement of archaella and flagella is sometimes described as "whip-like", this is incorrect, as only cilia from Eukaryotes move in this manner. Indeed, even "flagellum" is a misnomer, as bacterial flagella also work as propeller-like structures.

Thermoplasma volcanium is a moderate thermoacidophilic archaea isolated from acidic hydrothermal vents and solfatara fields. It contains no cell wall and is motile. It is a facultative anaerobic chemoorganoheterotroph. No previous phylogenetic classifications have been made for this organism. Thermoplasma volcanium reproduces asexually via binary fission and is nonpathogenic.

Sulfolobus metallicus is a coccoid shaped thermophilic archaeon. It is a strict chemolithoautotroph gaining energy by oxidation of sulphur and sulphidic ores into sulfuric acid. Its type strain is Kra 23. It has many uses that take advantage of its ability to grow on metal media under acidic and hot environments.

Saccharolobus solfataricus is a species of thermophilic archaeon. It was transferred from the genus Sulfolobus to the new genus Saccharolobus with the description of Saccharolobus caldissimus in 2018.

<span class="mw-page-title-main">Lokiarchaeota</span> Phylum of archaea

Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group, also known as Marine Benthic Group B. Lokiarchaeota is part of the superphylum Asgard containing the phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota, and Helarchaeota. A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes. The analysis revealed several genes with cell membrane-related functions. The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.

Acidilobus saccharovorans is a thermoacidophilic species of anaerobic archaea. The species was originally described in 2009 after being isolated from hot springs in Kamchatka.

<span class="mw-page-title-main">Aciduliprofundum boonei</span> Species of archaeon

"Candidatus Aciduliprofundum boonei" is an obligate thermoacidophilic candidate species of archaea belonging to the phylum "Euryarchaeota". Isolated from acidic hydrothermal vent environments, "Ca. A. boonei" is the first cultured representative of a biogeochemically significant clade of thermoacidophilic archaea known as the "Deep-Sea Hydrothermal Vent Euryarchaeota 2 (DHVE2)".

<span class="mw-page-title-main">Archaeal virus</span> Type of virus that infects the domain of unicellular, prokaryotic organisms or Archaea

An archaeal virus is a virus that infects and replicates in archaea, a domain of unicellular, prokaryotic organisms. Archaeal viruses, like their hosts, are found worldwide, including in extreme environments inhospitable to most life such as acidic hot springs, highly saline bodies of water, and at the bottom of the ocean. They have been also found in the human body. The first known archaeal virus was described in 1974 and since then, a large diversity of archaeal viruses have been discovered, many possessing unique characteristics not found in other viruses. Little is known about their biological processes, such as how they replicate, but they are believed to have many independent origins, some of which likely predate the last archaeal common ancestor (LACA).

Christa Schleper is a German microbiologist known for her work on the evolution and ecology of Archaea. Schleper is Head of the Department of Functional and Evolutionary Biology at the University of Vienna in Austria.

<i>Adnaviria</i> Realm of viruses

Adnaviria is a realm of viruses that includes archaeal viruses that have a filamentous virion and a linear, double-stranded DNA genome. The genome exists in A-form (A-DNA) and encodes a dimeric major capsid protein (MCP) that contains the SIRV2 fold, a type of alpha-helix bundle containing four helices. The virion consists of the genome encased in capsid proteins to form a helical nucleoprotein complex. For some viruses, this helix is surrounded by a lipid membrane called an envelope. Some contain an additional protein layer between the nucleoprotein helix and the envelope. Complete virions are long and thin and may be flexible or a stiff like a rod.

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