Related Research Articles
A protein kinase is a kinase which selectively modifies other proteins by covalently adding phosphates to them (phosphorylation) as opposed to kinases which modify lipids, carbohydrates, or other molecules. Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes. There are two main types of protein kinase. The great majority are serine/threonine kinases, which phosphorylate the hydroxyl groups of serines and threonines in their targets and the other are tyrosine kinases, although additional types exist. Protein kinases are also found in bacteria and plants. Up to 30% of all human proteins may be modified by kinase activity, and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction.
The three-domain system is a biological classification introduced by Carl Woese et al. in 1990 that divides cellular life forms into archaea, bacteria, and eukaryote domains. The key difference from earlier classifications is the splitting of archaea from bacteria.
The myxobacteria are a group of bacteria that predominantly live in the soil and feed on insoluble organic substances. The myxobacteria have very large genomes relative to other bacteria, e.g. 9–10 million nucleotides except for Anaeromyxobacter and Vulgatibacter. One species of myxobacteria, Minicystis rosea, has the largest known bacterial genome with over 16 million nucleotides. The second largest is another myxobacteria Sorangium cellulosum. Myxobacteria are included among the delta group of proteobacteria, a large taxon of Gram-negative forms.
The Planctomycetes are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammonium oxidation, also known as anammox. Many planctomycetes occur in relatively high abundance as biofilms, often associating with other organisms such as macroalgae and marine sponges.
Mollicutes is a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis, and cutis. Individuals are very small, typically only 0.2–0.3 μm in size and have a very small genome size. They vary in form, although most have sterols that make the cell membrane somewhat more rigid. Many are able to move about through gliding, but members of the genus Spiroplasma are helical and move by twisting. The best-known genus in the Mollicutes is Mycoplasma.
The bacterium, despite its simplicity, contains a well-developed cell structure which is responsible for some of its unique biological structures and pathogenicity. Many structural features are unique to bacteria and are not found among archaea or eukaryotes. Because of the simplicity of bacteria relative to larger organisms and the ease with which they can be manipulated experimentally, the cell structure of bacteria has been well studied, revealing many biochemical principles that have been subsequently applied to other organisms.
In molecular biology, biochemistry and cell signaling the kinome of an organism is the complete set of protein kinases encoded in its genome. Kinases are usually enzymes that catalyze phosphorylation reactions and fall into several groups and families, e.g., those that phosphorylate the amino acids serine and threonine, those that phosphorylate tyrosine and some that can phosphorylate both, such as the MAP2K and GSK families. The term was first used in 2002 by Gerard Manning and colleagues in twin papers analyzing the 518 human protein kinases, and refers to both protein kinases and protein pseudokinases and their evolution of protein kinases throughout the eukaryotes. Other kinomes have been determined for rice, several fungi, nematodes, and insects, sea urchins, Dictyostelium discoideum, and the process of infection by Mycobacterium tuberculosis. Although the primary sequence of protein kinases shows substantial divergence between unrelated eukaryotes, and amino acid differences in catalytic motifs have permitted their separation of kinomes into canonical and pseudokinase subtypes, the variation found in the amino acid motifs adjacent to the site of actual phosphorylation of substrates by eukaryotic kinases is much smaller.
Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.
Protein phosphorylation is a reversible post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or modifying its function. Approximately 13000 human proteins have sites that are phosphorylated.
A prokaryote is a typically unicellular organism that lacks a nuclear membrane-enclosed nucleus. The word prokaryote comes from the Greek πρό and κάρυον. In the two-empire system arising from the work of Édouard Chatton, prokaryotes were classified within the empire Prokaryota. But 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. In the study of the origins of life, prokaryotes are thought to have arisen before eukaryotes.
Archaea constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
Red algae, or Rhodophyta, are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority of species (6,793) are found in the Florideophyceae (class), and mostly consist of multicellular, marine algae, including many notable seaweeds. Red algae are abundant in marine habitats but are relatively rare in freshwaters. Approximately 5% of the red algae occur in freshwater environments with greater concentrations found in warmer areas. Except for two coastal cave dwelling species in the asexual class Cyanidiophyceae, there are no terrestrial species, which may be due to an evolutionary bottleneck where the last common ancestor lost about 25% of its core genes and much of its evolutionary plasticity.
Jakobids are an order of free-living, heterotrophic, flagellar eukaryotes in the supergroup Excavata. They are small, and can be found in aerobic and anaerobic environments. The order Jakobida, believed to be monophyletic, consists of only twenty species at present, and was classified as a group in 1993. There is ongoing research into the mitochondrial genomes of jakobids, which are unusually large and bacteria-like, evidence that jakobids may be important to the evolutionary history of eukaryotes.
Eukaryotes are organisms whose cells have a nucleus enclosed within a nuclear envelope. Eukaryotes belong to the domain Eukaryota or Eukarya; their name comes from the Greek εὖ and κάρυον. The domain Eukaryota makes up one of the three domains of life; bacteria and archaea make up the other two domains. The eukaryotes are usually now regarded as having emerged in the Archaea or as a sister of the now cultivated Asgard archaea. Eukaryotes represent a tiny minority of the number of organisms; however, due to their generally much larger size, their collective global biomass is estimated to be about equal to that of prokaryotes. Eukaryotes emerged approximately 2.1–1.6 billion years ago, during the Proterozoic eon, likely as flagellated phagotrophs.
The Eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota, a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major phylum of archaea, the Euryarchaeota.
Poribacteria are a candidate phylum of bacteria originally discovered in the microbiome of marine sponges (Porifera). Poribacteria are Gram-negative primarily aerobic mixotrophs with the ability for oxidative phosphorylation, glycolysis, and autotrophic carbon fixation via the Wood – Ljungdahl pathway. Poribacterial heterotrophy is characterised by an enriched set of glycoside hydrolases, uronic acid degradation, as well as several specific sulfatases. This heterotrophic repertoire of poribacteria was suggested to be involved in the degradation of the extracellular sponge host matrix.
Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group (DSAG), also known as Marine Benthic Group B (MBG-B). 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.
Gemmata obscuriglobus is a species of Gram-negative, aerobic, heterotrophic bacteria of the phylum Planctomycetes. G. obscuriglobus occur in freshwater habitats and was first described in 1984, and is the only described species in its genus.
Plesiocystis is a genus of myxobacteria. It is a monotypic taxon containing only its type species, Plesiocystis pacifica. Both the genus and the species were first described in 2003, based on two strains isolated from samples collected from the Pacific coast of Japan.
Enhygromyxa salina is a species of marine myxobacteria. Like other members of this order, E. salina is a rod-shaped Gram-negative bacterium that can move by gliding and can form aggregates of cells called fruiting bodies. E. salina is slightly halophilic (salt-tolerant) and can grow at lower temperatures than other marine myxobacteria. Several novel secondary metabolites have been identified in the species, including unusual sterols. The species was first described in 2003, based on six strains isolated from samples collected from the coastlines of Japan.
References
- 1 2 3 4 5 6 7 8 Iizuka, T. (1 January 2003). "Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan". International Journal of Systematic and Evolutionary Microbiology. 53 (1): 189–195. doi: 10.1099/ijs.0.02418-0 . PMID 12656172.
- ↑ "Plesiocystis". List of Prokaryotic Names with Standing in Nomenclature.
- 1 2 Schäberle, Till F.; Galinski, Erwin A.; Boehringer, Nils; Moghaddam, Jamshid Amiri; Kunte, Hans-Jörg; Burdziak, Amal (1 April 2016). "Different strategies of osmoadaptation in the closely related marine myxobacteria Enhygromyxa salina SWB007 and Plesiocystis pacifica SIR-1". Microbiology. 162 (4): 651–661. doi: 10.1099/mic.0.000250 . PMID 26842314.
- ↑ Garcia, R.; Pistorius, D.; Stadler, M.; Muller, R. (11 February 2011). "Fatty Acid-Related Phylogeny of Myxobacteria as an Approach to Discover Polyunsaturated Omega-3/6 Fatty Acids". Journal of Bacteriology. 193 (8): 1930–1942. doi:10.1128/JB.01091-10. PMC 3133044 . PMID 21317327.
- ↑ Garcia, Ronald; Müller, Rolf (2014). "The Family Nannocystaceae". The Prokaryotes: Deltaproteobacteria and Epsilonproteobacteria. pp. 213–229.
- ↑ Perez, J.; Castaneda-Garcia, A.; Jenke-Kodama, H.; Muller, R.; Munoz-Dorado, J. (3 October 2008). "Eukaryotic-like protein kinases in the prokaryotes and the myxobacterial kinome". Proceedings of the National Academy of Sciences. 105 (41): 15950–15955. Bibcode:2008PNAS..10515950P. doi: 10.1073/pnas.0806851105 . PMC 2572974 . PMID 18836084.
- ↑ Desmond, E.; Gribaldo, S. (10 September 2009). "Phylogenomics of Sterol Synthesis: Insights into the Origin, Evolution, and Diversity of a Key Eukaryotic Feature". Genome Biology and Evolution. 1: 364–381. doi:10.1093/gbe/evp036. PMC 2817430 . PMID 20333205.