Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology
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Establishing the roles of conserved gene products in bacteria is of fundamental importance to our understanding of the core protein complement necessary to sustain cellular life. P-loop GTPases and related ATPases represent an abundant and remarkable group of proteins in bacteria that, in many cases, have evaded characterization. Here, efforts aimed at understanding the cellular function of a group of 8 conserved, poorly characterized genes encoding P-loop GTPases, era, obg, trmE, yjeQ, engA, yihA, hflX, ychF, and a related ATPase, yjeE, are reviewed in considerable detail. While concrete cellular roles remain elusive for all of these genes and considerable pleiotropy has plagued their study, experiments to date have frequently implicated the ribosome. In the case of era, obg, yjeQ, and engA, the evidence is most consistent with roles in ribosome biogenesis, though the prediction is necessarily putative. While the protein encoded in trmE clearly has a catalytic function in tRNA modification, the participation of its GTPase domain remains obscure, as do the functions of the remaining proteins. A full understanding of the cellular functions of all of these important proteins remains the goal of ongoing studies of cellular phenotype and protein biochemistry.Key words: GTPase, unknown function, essential gene, P-loop.Keywords:
ribosome biogenesis
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Bacterial ribosome biogenesis is poorly understood especially in terms of the role of ribosomal RNA (rRNA) maturation in vivo. A major problem in addressing these questions are asynchronous biogenesis, a large population of mature particles and the lack of techniques to isolated in vivo formed ribosome biogenesis intermediates. Our group has taken multiple approaches to allow study of ribosome biogenesis in Escherichia coli. We have used genetic manipulation to discover that for specific biogenesis factors, there is a delicate balance that is necessary for viability. Additionally, we have pioneered an affinity purification approach to allow for isolation of in vivo formed intermediates. Data will be present on our findings for the role of rRNA maturation in biogenesis, subsequent ribosome function, and cell viability. Our findings may result in identification of novel targets for antimicrobial development.
ribosome biogenesis
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Archaea is a group of single-cell, microscopic organisms that have no nucleus or other membrane-bound organelles. They have many similar structural and metabolic features with bacteria, but they also have several critical differences. Many archaea and bacteria have a syntrophic relationship where they coexist and benefit each other in floc particles, biofilm, and sludge. Archaea that survive in low pH conditions are known as acidophiles, while those that survive in high pH conditions are known as alkalophiles. Sulfolobus is an example of an archaea that prefers high temperatures and extremely low pH. There are two major archaeal kingdoms with species that contribute to the stabilization of wastes: Crenarchaeota and Euryarchaeota. Crenarchaeota contains thermophilic organisms, acidophilic organisms, and ammonia-oxidizing archaea. Euryarchaeota contains halophilic organisms, thermophilic organisms, and methanogens. Archaea also have novel enzymes and metabolic pathways including sulfur pathways involved in a variety of dissimilatory and assimilatory forms of sulfur metabolism.
Crenarchaeota
Euryarchaeota
Thaumarchaeota
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GTPases are important regulatory proteins that hydrolyze GTP to GDP. A novel GTP-hydrolysis mechanism is employed by MnmE, YqeH and FeoB, where a potassium ion plays a role analogous to the Arginine finger of the Ras-RasGAP system, to accelerate otherwise slow GTP hydrolysis rates. In these proteins, two conserved asparagines and a 'K-loop' present in switch-I, were suggested as attributes of GTPases employing a K(+)-mediated mechanism. Based on their conservation, a similar mechanism was suggested for TEES family GTPases. Recently, in Dynamin, Fzo1 and RbgA, which also conserve these attributes, a similar mechanism was shown to be operative. Here, we probe K(+)-activated GTP hydrolysis in TEES (TrmE-Era-EngA-YihA-Septin) GTPases - Era, EngB and the two contiguous G-domains, GD1 and GD2 of YphC (EngA homologue) - and also in HflX, another GTPase that also conserves the same attributes. While GD1-YphC and Era exhibit a K(+)-mediated activation of GTP hydrolysis, surprisingly GD2-YphC, EngB and HflX do not. Therefore, the attributes identified thus far, do not necessarily predict a K(+)-mechanism in GTPases and hence warrant extensive structural investigations.
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Psychrophile
Extremophile
Cold-shock domain
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Archaea that live at high salt concentrations are a phylogenetically diverse group of microorganisms. They include the heterotrophic haloarchaea (class Halobacteria) and some methanogenic Archaea, and they inhabit both oxic and anoxic environments. In spite of their common hypersaline environment, halophilic archaea are surprisingly diverse in their nutritional demands, range of carbon sources degraded (including hydrocarbons and aromatic compounds) and metabolic pathways. The recent discovery of a new group of extremely halophilic Euryarchaeota, the yet uncultured Nanohaloarchaea, shows that the archaeal diversity and metabolic variability in hypersaline environments is higher than hitherto estimated.
Haloarchaea
Euryarchaeota
Crenarchaeota
Extremophile
Phylogenetic diversity
Extreme environment
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Ribosomes are vital for cell growth and survival. Until recently, it was believed that mutations in ribosomes or ribosome biogenesis factors would be lethal, due to the essential nature of these complexes. However, in the last few decades, a number of diseases of ribosome biogenesis have been discovered. It remains a challenge in the field to elucidate the molecular mechanisms underlying them.
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Abstract The Archaea are a group of microbes that form one of three domains of life on Earth. Studies with isolated strains have revealed an archaeal metabolic diversity rivaling that found within the domain Bacteria, and molecular surveys have revealed that archaea occupy a broader range of environments than was suspected based on the physiology of isolates. Archaea are also the most abundant and active microbial component in some environments, typically where their adaptations to chronic energy stress provide selective advantage over bacteria. Ongoing studies of uncultured archaea are likely to reveal important impacts on Earth's elemental and energy cycles. Key concepts Comparison of small subunit ribosomal RNA (16S rRNA) gene sequences and other cellular characteristics revealed that Archaea are a distinct group of microbes and one of three domains of life on Earth. The majority of archaeal diversity is composed of two kingdoms: the Crenarchaeota and Euryarchaeota. Most of the cultured archaea are ‘extremophiles’, or organisms that are adapted to living under extreme environmental conditions. The common ecological factor among the Archaea is their propensity to thrive under conditions of chronic energy stress. The ‘uncultured majority’ refers to the abundant, widespread, and highly diverse groups of archaea that currently lack cultured isolates. The metabolic functions of some uncultured archaea have been revealed by combining molecular, biochemical and geochemical techniques.
Euryarchaeota
Crenarchaeota
Three-domain system
Thaumarchaeota
Extreme environment
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Abstract Iron–sulfur (Fe–S) clusters are key cofactors required for the activity of essential metalloproteins. Biogenesis of Fe–S clusters is carried out by multiple proteins that work together to mobilize iron and sulfide, assemble nascent clusters, and traffic them to target metalloproteins. While the Isc, Nif, and Suf pathways are the most well‐studied Fe–S cluster biogenesis systems, it is clear that a variety of accessory proteins and metabolites cooperate with these systems for cluster assembly. Here, we review the current status of Fe–S cluster biogenesis research in Bacteria and Archaea.
Iron–sulfur cluster
Metalloprotein
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