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The Natural Evolutionary Relationships Among Prokaryotes
Abstract
Two contrasting and very different proposals have been put forward to account for the evolutionary relationships among prokaryotes. The currently widely accepted three domain proposal by Woese et al. (Proc. Natl. Acad. Sci. USA (1990) 87: 4576-4579) calls for the division of prokaryotes into two primary groups or domains, termed archaebacteria (Archaea) and eubacteria (Bacteria), both of which are suggested to have originated independently from a universal ancestor. However, this proposal, which is based primarily on genes involved in the information transfer processes, is inconsistent with the ultrastructural characteristics of prokaryotes as well as with many gene phylogenies and provides no explanation as to how the structural and molecular differences seen between these groups arose and how other prokaryotic taxa are related or evolved from the common ancestor. It also postulates that the last common ancestor of all organisms was a hypothetical entity lacking a cell membrane, which is contrary to the basic requirement of a cell membrane to define and separate all forms of life from the surrounding environment. A second alternate proposal for the evolutionary relationships among prokaryotes has emerged from extensive analyses of numerous conserved inserts and deletions found in various proteins (Gupta, R. S., Microbiol. Mol. Biol. Rev. (1998)62: 1435-1491; FEMS Microbiol. Rev. (2000) 24: in press. This proposal points to a specific relationship between archaebacteria and gram-positive bacteria, both of which are prokaryotes bounded by a single cell membrane (monoderm prokaryotes). Gram-negative bacteria, which are bounded by two different membranes (diderm prokaryotes), are indicated to comprise a structurally and phylogenetically distinct taxa originating from gram-positive bacteria. This proposal postulates that the earliest prokaryote was a gram-positive bacteria from which both archaebacteria and diderm prokaryotes evolved by normal evolutionary mechanisms in response to the strong selection pressure exerted by antibiotics produced by certain groups of gram-positive bacteria. This proposal accounts for both the molecular as well structural differences seen among the main groups of prokaryotes by known evolutionary mechanisms without invoking any hypothetical process or entity and thus is a closer representation of the natural relationships among prokaryotes than the proposal for two distinct domains. Based on this new proposal, it is now possible to logically deduce the branching order of different prokaryotic taxa from the common ancestor, which is as follows: Gram-positive bacteria (Low G + C) (<=> Archaebacteria) => Gram-positive bacteria (High G + C) (<=> Archaebacteria)=> Deinococcus-Thermus => Green nonsulfur bacteria => Cyanobacteria => Spirochetes => Chlamydia- Cytophaga-Green sulfur bacteria => Proteobacteria-1 (epsilon, delta)=> Proteobacteria-2 (alpha) => Proteobacteria-3 (beta) => Proteobacteria-4 (gamma). A surprising but very important aspect of the relationship deduced here is that the main eubacterial phyla are related to each other linearly rather than in a tree-like manner, suggesting that the major evolutionary changes within prokaryotes (bacteria) have occurred in a directional manner.
... Conversely, all the products did not reveal any Gram-negative bacteria growth inhibition in the employed concentration range. That is in accordance with earlier studies which indicated that Gram-positive bacteria are more receptive to small or macromolecular products than Gramnegative bacteria due to their mesh-like peptidoglycan layer, located outside the plasma membrane, which can be easily traversed by different biocides [21,22]. Instead, in the case of Gram-negative bacteria, the peptidoglycan layer is sandwiched between an inner cell membrane and an outer membrane which make extremely difficult the passive diffusion of the compounds [21,22]. ...
... That is in accordance with earlier studies which indicated that Gram-positive bacteria are more receptive to small or macromolecular products than Gramnegative bacteria due to their mesh-like peptidoglycan layer, located outside the plasma membrane, which can be easily traversed by different biocides [21,22]. Instead, in the case of Gram-negative bacteria, the peptidoglycan layer is sandwiched between an inner cell membrane and an outer membrane which make extremely difficult the passive diffusion of the compounds [21,22]. This behaviour is similar to other antimicrobial small molecules or polymers which contained 1,2,3triazole moieties in their chemical structure [16,63]. ...
Amphiphilic dextran-based esters were synthesized by coupling several disubstituted 1,2,3-triazole derivatives on the poly-saccharide. The polymers were characterized by elemental analysis and spectroscopy measurements: X-ray photoelectron (XPS), Fourier transform infrared (FTIR), carbon-13 nuclear magnetic resonance (13 C NMR). Triazole derivatives and their corresponding dextran esters showed a moderate to good antimicrobial activity, the antifungal activity being stronger than the antibacterial one. Halogenated polymers proved to be potential external biocides due to their both bactericidal and fungicidal activity. Rezumat Esterii amfifili bazați pe dextrani au fost sintetizați prin cuplarea pe polizaharida a mai multor derivați disubstituiți ai 1,2,3-triazolului. Polimerii au fost caracterizați prin analiza elementală și măsurători spectroscopice (de fotoelectroni cu raze X-XPS, în infraroșu cu transformată Fourier-FTIR, rezonanță magnetică nucleară carbon-13-13 C RMN). Derivații de triazol și esterii dextranului corespunzători au prezentat o activitate antimicrobiană moderată spre bună, activitatea antifungică fiind mai puternică decât cea antibacteriană. Polimerii halogenați s-au dovedit a fi produse potențiale biocide externe datorită activității lor bactericide și fungicide.
... Interactions between species in marine ecosystems are one of the fundamental mechanisms that ensure the sustainability of ecosystems. In addition, from an evolutionary perspective, they are also important in terms of the emergence of mitochondria from the association of bacteria and archaea as the strength of a symbiotic relationship in the existence of eukaryotes (Gupta, 2000). Therefore, the diversity of eukaryotes, that is, plants and animals, has been shaped by the symbiotic relationships between beneficial microorganisms (McFall-Ngai et al., 2013;Garcia and Gerardo, 2014). ...
... On the basis of genome sequence coverage/identity and RSTs, we hypothesized the evolution of O serogroups. The O antigens of simpler structures and components may appear earlier than more complex O antigens and much simpler O serogroups may appear in earlier RSTs [35]. The major O serogroup of RST2-1 is O26, which is composed of linearly linked trisaccharides without side branches [→3)-L-Rha-(α1→4)-L-FucNAc-(α1→3)-DGlcNAc-(β1→] [3]. ...
Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk.
... Bacteria are single-celled, prokaryotic organisms with many different forms and can be found in the air, water, soil and other living things. They reproduce in a non-sexual manner, mainly by binary division, which, under favorable conditions, explains their rapid proliferation in infections [28]. A widely employed alternative in water analysis concerning fecal contamination is scanning the samples for one or more microorganisms. ...
Water is considered a natural resource of high importance to the society whose availability and quality are in great demand. The water that reaches homes may contain different species, among them microorganisms like bacteria, protozoa and viruses that can contaminate and compromise the health and safety of the population. Thus, frequent water analysis would allow the monitoring of potentially harmful and/or toxic species that can be found in water resources. The application of point-of-care devices (POCs) for monitoring water ensures faster on-site analysis. The use of electrochemistry as a detection technique for a specific analyte presents itself as a promising way, being able to serve different targets reporting fast, selective and reproducible responses. After the COVID-19 outbreak in the world, the necessity of the development of such devices that may monitor species quickly, even at low concentrations was evidenced. The conventional methods of water analysis are still the most widely employed, despite the existence of already well-established modes of detection of target species by electrochemical techniques allowing on-site detection with point-of-care devices (POCs). In the quest to elucidate such issues, this review aims to show some biosensors devices developed for the detection of bacteria, protozoa, and viruses, attempting to understand what would still be needed for the large-scale application of these devices in water monitoring, identifying the innovative features and shortcomings of POCs.
... These selective pressures repeatedly create the same adaptive syndrome -a set of characteristics which come together to allow a specific lifestyle or perform a certain task (Reich et al., 2003). In many instances in the past, convergent evolutionary syndromes have confounded taxonomists, who (for example) mistakenly grouped New-World and Old-World vultures (Seibold & Helbig, 1995), all marine mammals (Foote et al., 2015), and many disparate lineages of microscopic organisms (Scamardella, 1999;Palenik & Haselkorn, 1992;Gupta, 2000), into clades which ultimately proved to be paraphyletic. ...
Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines the convergence of functional overrepresentation of genes previously implicated in plant carnivory. Gene Ontology (GO) coding was used to quantitatively score functional representation in these taxa, in terms of proportion of carnivory-associated functions relative to all functional sequence. Statistical analysis revealed that, in carnivorous plants as a group, only two of the 24 functions tested showed a signal of substantial overrepresentation. However, when the four carnivorous taxa were analyzed individually, 11 functions were found to be significant in at least one taxon. Though carnivorous plants collectively may show overrepresentation in functions from the predicted set, the specific functions that are overrepresented vary substantially from taxon to taxon. While it is possible that some functions serve a similar practical purpose such that one taxon does not need to utilize both to achieve the same result, it appears that there are multiple approaches for the evolution of carnivorous function in plant genomes. Our approach could be applied to tests of functional convergence in other systems provided on the availability of genomes and annotation data for a group.
Schiff’s base compound (1E)-4-methyl-1-((4-oxo-4H -chromen-3-yl)methylene)-4-phenylthiosemicarbazide (HL) was synthesized. Elemental analyses and spectral studies were used for structural elucidation. As DNA gyrase plays a vital role in bacterial cell survival, it is used as a target for the development of new antimicrobial agents. A molecular docking study was performed for this compound to evaluate its affinity towards bacterial protein, DNA gyrase B (PDB ID: 3TTZ) of Staphylococcus aureus using the Glide dock program, further authenticated by in vitro studies. Moreover, HL and its metal complexes were screened for its antimicrobial property.
Water quality monitoring has become crucial due to the increasing exposure of water bodies to pollutants from the growing global population and industrialization. Detection strategies such as electrochemical and optical analysis techniques have gained popularity in environmental monitoring owing to their sensitivity, selectivity, rapidity, low cost, and easy operation that are not obtainable in the conventional methods. However, most sensors derived from these techniques are confined to laboratory significance and need experts for signals and results analysis. In recent times, many researchers have proposed the exploitation of the robustness of these optical and electrochemical techniques for point-of-care applications in water quality monitoring. In this review, different species of water contaminants, such as biological, physical, and chemical components, were quantified and successfully detected using POCs based on these techniques. The POCs sensors demonstrated high sensitivity, reliability, and relevance at the point of need. However, the designs and implementation of these portable POC systems to support high sensitivity, selectivity, low cost, less analysis time, and robustness when deployed in complex matrices remain a challenge. Comprehending and overcoming these setbacks and limitations demand more investigations and research resources, which could delay, at the least, the development, implementation, and commercialization of POCs, even when the need is very pressing and application and merits well lauded.
Polyphosphate [poly(P)] is described as a homopolymer of inorganic phosphates. Nicotinamide adenine dinucleotide kinase (NAD kinase) catalyzes the phosphorylation of NAD+ to NADP+ in the presence of ATP (ATP-NAD kinase). Novel NAD kinase that explicitly phosphorylates NAD+ to NADP+ using poly(P), besides ATP [ATP/poly(P)-NAD kinase], was found in bacteria, in particular, Gram-positive bacteria, and the gene encoding ATP/poly(P)-NAD kinase was also newly identified in Mycobacterium tuberculosis H37Rv. Both NAD kinases required multi-homopolymeric structures for activity expression. The enzymatic and genetic results, combined with their primary and tertiary structures, have led to the discovery of a long-awaited human mitochondrial NAD kinase. This discovery showed that the NAD kinase is a bacterial type of ATP/poly(P)-NAD kinase. These pioneering findings, i.e., ATP/poly(P)-NAD kinase, NAD kinase gene, and human mitochondrial NAD kinase, have significantly enhanced research on the biochemistry, molecular biology, and evolutionary biology of NAD kinase, mitochondria, and poly(P), including some biotechnological knowledge applicable to NADP+ production.
We provide data and analysis to support the hypothesis that the ancestor of animal mitochondria (Mt) and many primitive amitochondrial
(a-Mt) eukaryotes was a fusion microbe composed of a Clostridium-like eubacterium and a Sulfolobus-like archaebacterium. The analysis is based on several observations: (i) The genome signatures (dinucleotide relative abundance values) of Clostridium and Sulfolobus are compatible (sufficiently similar) and each has significantly more similarity in genome signatures with animal Mt sequences
than do all other available prokaryotes. That stable fusions may require compatibility in genome signatures is suggested by
the compatibility of plasmids and hosts. (ii) The expanded energy metabolism of the fusion organism was strongly selective for cementing such a fusion. (iii) The molecular apparatus of endospore formation in Clostridium serves as raw material for the development of the nucleus and cytoplasm of the eukaryotic cell.
While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.
The three-domain proposal of Woeseet al.(Proc. Natl. Acad. Sci. USA87, 4576 (1990)) divides all living organisms into three primary groups or domains namedArchaea(or archaebacteria),Bacteria(or eubacteria), andEucarya(or eukaryotes), withEucaryabeing relatives (or descendants) of Archaea. Although this proposal is currently widely accepted, sequence features and phylogenies derived from many highly conserved proteins are inconsistent with it and point to a close and specific relationship between archaebacteria and gram-positive bacteria, whereas gram-negative bacteria are indicated to be phylogenetically distinct. A closer relationship of archaebacteria to gram-positive bacteria in comparison to gram-negative bacteria is generally seen for the majority of the available gene/protein sequences. To account for these results, and the fact that both archaebacteria and gram-positive bacteria are prokaryotes surrounded by a single cell membrane, I propose that the primary division within prokaryotes is between Monoderm prokaryotes (surrounded by a single membrane) and Diderm prokaryotes (i.e., all true gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). This proposal is consistent with both cell morphology and signature sequences in different proteins. Protein phylogenies and signature sequences also show thatall eukaryotic cellshave received significant gene contributions from both an archaebacterium and a gram- negative eubacterium. Thus, the hypothesis that archaebacteria and eukaryotes shared a common ancestor exclusive of eubacteria, or that the ancestral eukaryotic cell directly descended from an archaea, is erroneous. These results call into question the validity of the currently popular three-domain proposal and the assignment of a domain status to archaebacteria. A new classifica- tion of organisms consistent with phenotype and macromolecular sequence data is proposed.
Evolutionary relations are better represented by new classifications than by the traditional two kingdoms.
MICROBES, IMMUNITY, AND DISEASEWhen full DNA sequences opened the way to comparing many different genes in different organisms, the comparisons proved confounding. Rather than clarifying the tree that seeks to show how life evolved, they often produced new trees that differ from the traditional tree and conflict with each other as well. Now some microbiologists, pointing to evidence that microbes have swapped genes wantonly over evolutionary history, say that many of these genes are an unreliable guide to evolutionary history and the old tree is still basically sound. But others think it's time to uproot the old tree and are proposing candidates for new trees based on specific features of the genome and cell structure. And still others worry that gene swapping has turned the tree of life into a tangled briar whose lineages will be next to impossible to discern.
EVOLUTIONThe new wealth of microbial genome sequences is threatening to overturn evolutionists' "tree of life." In the current tree, a universal common ancestor gave rise to the two microbial branches, the archaea and bacteria (which lack cell nuclei), and the archaea then gave rise to the eukarya (all organisms that have cell nuclei). But the new sequences show that genes don't evolve at the same rate or in the same way, so the evolutionary history inferred from one gene may be different from what another gene appears to show. Even more perplexing, some genomes have been found to contain a mix of DNAs from both the archaea and the bacteria. Many evolutionary biologists are coming to believe that these mosaics arose because genes hopped from branch to branch as early organisms either stole genes from their food or swapped DNA with their neighbors. If this gene swapping was extensive enough, the tree's "base" may turn out to be indecipherable: a network of branches that merge and split and merge again before sprouting the modern kingdoms.