-
Nature Communications Nov 2018A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome...
A fundamental question in microbiology is whether there is continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) help address this question by facilitating high resolution taxonomic analysis of thousands of genomes from diverse phylogenetic lineages. To scale to available genomes and beyond, we present FastANI, a new method to estimate ANI using alignment-free approximate sequence mapping. FastANI is accurate for both finished and draft genomes, and is up to three orders of magnitude faster compared to alignment-based approaches. We leverage FastANI to compute pairwise ANI values among all prokaryotic genomes available in the NCBI database. Our results reveal clear genetic discontinuity, with 99.8% of the total 8 billion genome pairs analyzed conforming to >95% intra-species and <83% inter-species ANI values. This discontinuity is manifested with or without the most frequently sequenced species, and is robust to historic additions in the genome databases.
Topics: Databases, Factual; Genetic Variation; Genome, Bacterial; Phylogeny; Prokaryotic Cells; Sequence Analysis, DNA
PubMed: 30504855
DOI: 10.1038/s41467-018-07641-9 -
Cold Spring Harbor Perspectives in... Oct 2010Mounting evidence in recent years has challenged the dogma that prokaryotes are simple and undefined cells devoid of an organized subcellular architecture. In fact,... (Review)
Review
Mounting evidence in recent years has challenged the dogma that prokaryotes are simple and undefined cells devoid of an organized subcellular architecture. In fact, proteins once thought to be the purely eukaryotic inventions, including relatives of actin and tubulin control prokaryotic cell shape, DNA segregation, and cytokinesis. Similarly, compartmentalization, commonly noted as a distinguishing feature of eukaryotic cells, is also prevalent in the prokaryotic world in the form of protein-bounded and lipid-bounded organelles. In this article we highlight some of these prokaryotic organelles and discuss the current knowledge on their ultrastructure and the molecular mechanisms of their biogenesis and maintenance.
Topics: Cytoskeleton; Lipid Bilayers; Magnetosomes; Magnetospirillum; Organelles; Prokaryotic Cells
PubMed: 20739411
DOI: 10.1101/cshperspect.a000422 -
Philosophical Transactions of the Royal... Mar 2021The premise of this two-part theme issue is simple: the cognitive sciences should join the rest of the life sciences in how they approach the quarry within their...
The premise of this two-part theme issue is simple: the cognitive sciences should join the rest of the life sciences in how they approach the quarry within their research domain. Specifically, understanding how organisms on the lower branches of the phylogenetic tree become familiar with, value and exploit elements of an ecological niche while avoiding harm can be expected to aid understanding of how organisms that evolved later (including ) do the same or similar things. We call this approach basal cognition. In this introductory essay, we explain what the approach involves. Because no definition of cognition exists that reflects its biological basis, we advance a working definition that can be operationalized; introduce a behaviour-generating toolkit of capacities that comprise the function (e.g. sensing/perception, memory, valence, learning, decision making, communication), each element of which can be studied relatively independently; and identify a (necessarily incomplete) suite of common biophysical mechanisms found throughout the domains of life involved in implementing the toolkit. The articles in this collection illuminate different aspects of basal cognition across different forms of biological organization, from prokaryotes and single-celled eukaryotes-the focus of Part 1-to plants and finally to animals, without and with nervous systems, the focus of Part 2. By showcasing work in diverse, currently disconnected fields, we hope to sketch the outline of a new multidisciplinary approach for comprehending cognition, arguably the most fascinating and hard-to-fathom evolved function on this planet. Doing so has the potential to shed light on problems in a wide variety of research domains, including microbiology, immunology, zoology, biophysics, botany, developmental biology, neurobiology/science, regenerative medicine, computational biology, artificial life and synthetic bioengineering. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.
Topics: Animals; Cognition; Cognitive Science; Eukaryotic Cells; Invertebrates; Plant Physiological Phenomena; Prokaryotic Cells; Vertebrates
PubMed: 33487107
DOI: 10.1098/rstb.2019.0750 -
Proceedings of the National Academy of... Jun 1998The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4-6 x 10(30) cells and 350-550 Pg of C (1 Pg = 10(15) g),... (Review)
Review
The number of prokaryotes and the total amount of their cellular carbon on earth are estimated to be 4-6 x 10(30) cells and 350-550 Pg of C (1 Pg = 10(15) g), respectively. Thus, the total amount of prokaryotic carbon is 60-100% of the estimated total carbon in plants, and inclusion of prokaryotic carbon in global models will almost double estimates of the amount of carbon stored in living organisms. In addition, the earth's prokaryotes contain 85-130 Pg of N and 9-14 Pg of P, or about 10-fold more of these nutrients than do plants, and represent the largest pool of these nutrients in living organisms. Most of the earth's prokaryotes occur in the open ocean, in soil, and in oceanic and terrestrial subsurfaces, where the numbers of cells are 1.2 x 10(29), 2.6 x 10(29), 3.5 x 10(30), and 0. 25-2.5 x 10(30), respectively. The numbers of heterotrophic prokaryotes in the upper 200 m of the open ocean, the ocean below 200 m, and soil are consistent with average turnover times of 6-25 days, 0.8 yr, and 2.5 yr, respectively. Although subject to a great deal of uncertainty, the estimate for the average turnover time of prokaryotes in the subsurface is on the order of 1-2 x 10(3) yr. The cellular production rate for all prokaryotes on earth is estimated at 1.7 x 10(30) cells/yr and is highest in the open ocean. The large population size and rapid growth of prokaryotes provides an enormous capacity for genetic diversity.
Topics: Prokaryotic Cells
PubMed: 9618454
DOI: 10.1073/pnas.95.12.6578 -
Journal of Genetics Jun 2017An analysis has been performed on implications existing between the presence/absence of the evolutionary stage of the prokaryote, that is to say, the presence/absence of...
An analysis has been performed on implications existing between the presence/absence of the evolutionary stage of the prokaryote, that is to say, the presence/absence of common characteristics between archaea and bacteria, and the monophyletic/polyphyletic origin of genes of proteins. Thereafter, a theorem stating that: 'the polyphyletic origin of proteins would imply the absence of common characteristics between bacteria and archaea and therefore the lack of the evolutionary stage of the prokaryote, and vice versa that the indefinable prokaryote stage implies a polyphyletic origin of proteins', has been made and validated. The conclusion is that given the absence of truth in common characteristics between archaea and bacteria, the origin of genes of proteins should have been polyphyletic.
Topics: Archaea; Bacteria; Evolution, Molecular; Phylogeny; Prokaryotic Cells; Proteins
PubMed: 28674242
DOI: 10.1007/s12041-017-0775-x -
Antioxidants & Redox Signaling Jun 2015An ancient anionic phospholipid, cardiolipin (CL), ubiquitously present in prokaryotic and eukaryotic membranes, is essential for several structural and functional... (Review)
Review
SIGNIFICANCE
An ancient anionic phospholipid, cardiolipin (CL), ubiquitously present in prokaryotic and eukaryotic membranes, is essential for several structural and functional purposes.
RECENT ADVANCES
The emerging role of CLs in signaling has become the focus of many studies.
CRITICAL ISSUES
In this work, we describe two major pathways through which mitochondrial CLs may fulfill the signaling functions via utilization of their (i) asymmetric distribution across membranes and translocations, leading to the surface externalization and (ii) ability to undergo oxidation reactions to yield the signature products recognizable by the executionary machinery of cells.
FUTURE DIRECTIONS
We present a concept that CLs and their oxidation/hydrolysis products constitute a rich communication language utilized by mitochondria of eukaryotic cells for diversified regulation of cell physiology and metabolism as well as for inter-cellular interactions.
Topics: Animals; Apoptosis; Cardiolipins; Humans; Hydrolysis; Lipid Metabolism; Mitochondria; Mitochondrial Membranes; Oxidation-Reduction; Prokaryotic Cells; Signal Transduction
PubMed: 25566681
DOI: 10.1089/ars.2014.6219 -
Microbiology and Molecular Biology... Jun 2013In its early history, life appeared to depend on pyrophosphate rather than ATP as the source of energy. Ancient membrane pyrophosphatases that couple pyrophosphate... (Review)
Review
In its early history, life appeared to depend on pyrophosphate rather than ATP as the source of energy. Ancient membrane pyrophosphatases that couple pyrophosphate hydrolysis to active H(+) transport across biological membranes (H(+)-pyrophosphatases) have long been known in prokaryotes, plants, and protists. Recent studies have identified two evolutionarily related and widespread prokaryotic relics that can pump Na(+) (Na(+)-pyrophosphatase) or both Na(+) and H(+) (Na(+),H(+)-pyrophosphatase). Both these transporters require Na(+) for pyrophosphate hydrolysis and are further activated by K(+). The determination of the three-dimensional structures of H(+)- and Na(+)-pyrophosphatases has been another recent breakthrough in the studies of these cation pumps. Structural and functional studies have highlighted the major determinants of the cation specificities of membrane pyrophosphatases and their potential use in constructing transgenic stress-resistant organisms.
Topics: Animals; Biological Transport; Cation Transport Proteins; Cell Membrane; Diphosphates; Hydrolysis; Phylogeny; Prokaryotic Cells; Protons; Pyrophosphatases; Sodium
PubMed: 23699258
DOI: 10.1128/MMBR.00003-13 -
The Journal of Physiology Jun 2024Origins research currently rests on a vitalistic foundation and requires reconceptualization. From a cellular perspective, prokaryotic cells grow and divide in stable,... (Review)
Review
Origins research currently rests on a vitalistic foundation and requires reconceptualization. From a cellular perspective, prokaryotic cells grow and divide in stable, colloidal processes, throughout which the cytoplasm remains crowded (concentrated) with closely interacting proteins and nucleic acids. Their functional stability is ensured by repulsive and attractive non-covalent forces, especially van der Waals forces, screened electrostatic forces, and hydrogen bonding (hydration and the hydrophobic effect). On average, biomacromolecules are crowded at above 15% volume fraction, surrounded by up to 3 nm layer of aqueous electrolyte at ionic strength above 0.01 molar; they are energized by biochemical reactions coupled to nutrient environments. During cellular growth, non-covalent molecular forces and biochemical reactions stabilize the cytoplasm as a two-phase, colloidal system comprising vectorially structured cytogel and dilute cytosol. From a geochemical perspective, Earth's rotation kept prebiotic molecules in continuous cyclic disequilibria in Usiglio-type intertidal pools, rich in potassium and magnesium ions, the last cations to precipitate from evaporatig seawater. These ions impart biochemical functionality to extant proteins and RNAs. The prebiotic molecules were repeatedly purified by phase separation in response to tidal drying and rewetting; they were chemically evolving as briny, carbonaceous inclusions in tidal sediments until the crowding transition allowed chemical evolution to proceeed toward Woesian progenotes, the Last Universal Common Ancestors (LUCAs) and the first prokaryotes. These cellular and geochemical processes are summarized as a jigsaw puzzle of the emerging and evolving prokaryotes. Their unavoidable cyclic fusions and rehydrations along Archaean coastlines initiated the emergence of complex Precambrian eukaryotes.
Topics: Prokaryotic Cells; Animals; Eukaryotic Cells; Biological Evolution; Origin of Life
PubMed: 37226840
DOI: 10.1113/JP284428 -
Current Biology : CB Oct 2020Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most... (Review)
Review
Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most commonly relies on the endonuclease-mediated cleavage of any incoming DNA that lacks a specific epigenetic modification, through a system known as restriction-modification. CRISPR-Cas-mediated adaptive immunity relies on the insertion of short DNA sequences from parasite genomes into CRISPR arrays on the host genome to provide sequence-specific protection. The discovery of each of these systems has revolutionised our ability to carry out genetic manipulations, and, as a consequence, the enzymes involved have been characterised in exquisite detail. In comparison, much less is known about the importance of these two arms of the defence for the ecology and evolution of prokaryotes and their parasites. Here, we review our current ecological and evolutionary understanding of these systems in isolation, and discuss the need to study how innate and adaptive immune responses are integrated when they coexist in the same cell.
Topics: Adaptive Immunity; Archaea; Bacteria; Biological Evolution; Ecology; Evolution, Molecular; Immune System; Immunity, Innate; Prokaryotic Cells
PubMed: 33022264
DOI: 10.1016/j.cub.2020.08.028 -
Philosophical Transactions of the Royal... Oct 2009Phototaxis in the broadest sense means positive or negative displacement along a light gradient or vector. Prokaryotes most often use a biased random walk strategy,... (Review)
Review
Phototaxis in the broadest sense means positive or negative displacement along a light gradient or vector. Prokaryotes most often use a biased random walk strategy, employing type I sensory rhodopsin photoreceptors and two-component signalling to regulate flagellar reversal. This strategy only allows phototaxis along steep light gradients, as found in microbial mats or sediments. Some filamentous cyanobacteria evolved the ability to steer towards a light vector. Even these cyanobacteria, however, can only navigate in two dimensions, gliding on a surface. In contrast, eukaryotes evolved the capacity to follow a light vector in three dimensions in open water. This strategy requires a polarized organism with a stable form, helical swimming with cilia and a shading or focusing body adjacent to a light sensor to allow for discrimination of light direction. Such arrangement and the ability of three-dimensional phototactic navigation evolved at least eight times independently in eukaryotes. The origin of three-dimensional phototaxis often followed a transition from a benthic to a pelagic lifestyle and the acquisition of chloroplasts either via primary or secondary endosymbiosis. Based on our understanding of the mechanism of phototaxis in single-celled eukaryotes and animal larvae, it is possible to define a series of elementary evolutionary steps, each of potential selective advantage, which can lead to pelagic phototactic navigation. We can conclude that it is relatively easy to evolve phototaxis once cell polarity, ciliary swimming and a stable cell shape are present.
Topics: Animals; Biological Evolution; Eukaryota; Light Signal Transduction; Prokaryotic Cells
PubMed: 19720645
DOI: 10.1098/rstb.2009.0072