Gene Sequences Measure the Diversity of Prokaryotes (Genetics & Inherited Conditions)
Prokaryotic microorganisms have been on earth for as many as 3.5 billion years and have diverged tremendously in genetic and metabolic terms. Unfortunately, the magnitude of this divergence has made it difficult to measure the relatedness of prokaryotes to one another. In the 1970’s, Carl R. Woese addressed this problem using a method of reading short sequences of ribonucleotides from a highly conserved RNA molecule, the small subunit ribosomal RNA (ssu rRNA). Because this RNA is present in all organisms and has evolved very slowly, any two organisms have at least a few of these short nucleotide sequences in common. The proportion of shared sequences thus provided a quantitative index of similarity by which all cellular organisms could, in principle, be compared.
When the nucleotide sequence data were used to construct an evolutionary tree, eukaryotes (plants, animals, fungi, and protozoa) formed a cluster clearly separated from the common bacteria. Unexpectedly, however, a third cluster emerged that was equally distinct from both eukaryotes and common bacteria. This cluster consisted of prokaryotes that lacked biochemical features of most bacteria (such as a cell wall composed of peptidoglycan); possessed other features not found in any other organisms (such as membranes composed of isoprenoid ether lipids); and occurred in unusual, typically harsh, environments. Woese and his coworkers...
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Biology of the Domain Archaea (Genetics & Inherited Conditions)
Archaea tend to require unusual conditions for growth, which has made it challenging to determine their genetic properties. The methanogens, for example, live by converting hydrogen (H2) and carbon dioxide (CO2) or other simple carbon compounds into methane and are killed by even trace amounts of oxygen. The extreme halophiles, in contrast, normally live in brine lakes and utilize oxygen for growth. However, they require extremely high concentrations of salt to maintain their cellular structure. A third class of archaea, the extreme thermophiles, occur naturally in geothermal springs and grow best at temperatures ranging from 60-105 degrees Celsius (140-221 degrees Fahrenheit). Many derive energy from the oxidation or reduction of sulfur compounds. Sequencing of DNA fragments recovered from “moderate” environments, such as ocean water or soil, has revealed many additional archaeal species that presumably do not require unusual environmental conditions but have never been cultured in the laboratory.
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The Genetic Machinery of Archaea (Genetics & Inherited Conditions)
Because bacteria and eukaryotes differ greatly with respect to gene and chromosome structure and the details of gene expression, molecular biologists have examined the same properties in archaea and have found a mixture of “bacterial” and “eukaryotic” features. The organization of DNA within archaeal cells is bacterial, in the sense that archaeal chromosomes are circular DNAs of between 2 million and 4 million base pairs having single origins of replication, normally replicated bidirectionally. As in bacteria, the genes are densely packed and often grouped into clusters of related genes transcribed from a common promoter. The promoters themselves, however, resemble the TATA box/BRE element combination of eukaryotic DNA polymerase II (Pol II) promoters, and the RNA polymerases have the complex subunit composition of eukaryotes rather than the simple composition found in bacteria. Furthermore, archaea initiate transcription by a simplified version of the process seen in eukaryotic cells. Transcription factors (TATA-binding protein and a TFIIB) first bind to regions ahead of the promoter, then recruit RNA polymerase to attach and begin transcription. Introns are rare in archaea, however, and do not interrupt protein-encoding genes, but have been found to interrupt RNA-coding genes. Also, the regulation of transcription in archaea seems to depend heavily on the types of repressor and activator proteins found in...
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Genomes of Archaea (Genetics & Inherited Conditions)
The availability of complete DNA sequences now enables archaeal genomes to be compared to the genomes of bacteria and eukaryotes. One pattern that emerges from these comparisons is that most of the archaeal genes responsible for the processing of information (synthesis of DNA, RNA, and proteins) resemble their eukaryotic counterparts, whereas most of the archaeal genes for metabolic functions (biosynthetic pathways, for example) resemble their bacterial counterparts. The genomes of archaea also reveal probable cases of gene acquisition from distant relatives, a process called lateral gene transfer.
A third pattern to emerge from genome comparisons is that some archaea are missing genes thought to be important or essential. For example, the genomes of at least two methanogenic archaea do not encode an enzyme that charges transfer RNA (tRNA) with cysteine. These archaea instead use a novel strategy for making cysteinyl tRNA. Some of the seryl tRNA made by these cells is converted to cysteinyl tRNA by a specialized enzyme. A more severe example of gene deficiency is provided by Nanoarchaeum equitans, the first reported parasitic or symbiotic archaea that grows attached to an Ignicoccus, another hyperthermophile. N. equitans has been reported to have a volume approximating 1 percent of an Escherichia coli cell, the smallest nonviral cellular genome (0.49 Mbp), and numerous 16S rRNA...
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Unique Genetic Properties? (Genetics & Inherited Conditions)
This last observation raises an important question: Has an evolutionary history distinct from all conventional genetic systems, combined with the special demands of life in unusual environments, resulted in unique genetic properties in archaea? Although basic genetic assays can be performed in only a few species, the results help identify which genetic properties of cellular organisms are truly universal and which ones may have unusual features in archaea.
The methanogen Methanococcus voltae transfers short pieces of chromosome from one cell to another, using particles that resemble bacterial viruses (bacteriophages). This means of gene transfer has been seen in only a few bacteria. In other methanogens, researchers have used more conventional genetic phenomena, such as antibiotic-resistance genes, plasmids, and transposable elements, to develop tools for cloning or inactivating genes. As a result, new details about the regulation of gene expression in archaea and the genetics of methane formation are now coming to light.
The extreme halophile Halobacterium salinarum exhibits extremely high rates of spontaneous mutation of the genes for its photosynthetic pigments and gas vacuoles. This genetic instability reflects the fact that insertion sequences transpose very frequently into these and other genes. A distantly related species, Haloferax volcanii, has the ability to transfer...
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Impact (Genetics & Inherited Conditions)
Woese’s monumental discovery that two very different prokaryotic groups (bacteria and archaea) exist based on DNA sequencing of a conserved macromolecule (rRNA) led to a complete reevaluation of the evolution of not only bacteria (previously including archaea) but also eukaryotes. Before, it was thought that eukaryotes evolved from prokaryotes. His data definitively showed that all three were derived from a common ancestor. Even more surprising was the fact the all eukaryotes were found to be more closely related to each other and distantly related to both bacteria and archaea. Finally, his data showed that archaea were more closely related to eukaryotes than bacteria and were the most ancient organisms derived first from the common ancestor.
Since then, the DNA sequences of numerous archaeal isolates of different groups have been compared to each other and also to those of both bacteria and eukaryotes, further delineating the evolution of different diverse archaeal groups. These data suggest that a hyperthermophile was probably the common ancestor of Archaea. Also, the properties of numerous types of archaea have been studied. Many are found in extremely harsh environments that normal bacteria and eukaryotes cannot tolerate. This has led to molecular and genetic studies of the macromolecules including proteins and lipids that allow survival of these organisms, so that their mechanisms can be elucidated. Finally, various...
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Further Reading (Genetics & Inherited Conditions)
Cavicchioii, Richard, ed. Archaea: Molecular and Cellular Biology. New York: ASM Press, 2007. This book contains a series of review articles written by experts in the field highlighting all aspects of molecular and cellular biology of this group of organisms that allow them to survive under extreme conditions.
Garrett, Roger A., and Hans-Peter Klenk, eds. Archaea: Evolution, Physiology, and Molecular Biology. New York: Wiley-Blackwell, 2007. This book contains a series of broad review articles exploring all aspects of archaea and specialist articles concentrating on the molecular biological aspects of the organism.
Madigan, Michael T., and John M. Martinko. Brock Biology of Micro-organisms. 11th ed. Upper Saddle River, N.J.: Prentice Hall, 2006. Chapter 13 of this popular microbiology text provides an accurate and well-illustrated overview of the biological diversity of the archaea.
Olsen, Gary, and Carl R. Woese. “Archaeal Genomics: An Overview.” Cell 89 (1997): 991-994. This mini-review article, along with several accompanying articles, summarizes for specialists numerous molecular differences and similarities between archaea and bacteria or eukaryotes, based on the first archaeal genomes to be sequenced.
Woese, Carl R. “Archaebacteria.” Scientific American 244 (1981): 98-122. A clear, though somewhat dated, description of the archaea and the various...
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Archaea (World of Microbiology and Immunology)
Genes that code for vital cellular functions are highly conserved through evolutionary time, and because even these genes experience random changes over time, the comparison of such genes allows the relatedness of different organisms to be assessed. American microbiologist Carl Woese and his colleagues obtained sequences of the genes coding for RNA in the subunit of the ribosome from different organisms to argue that life on Earth is comprised of three primary groups, or domains. These domains are the Eukarya (which include humans), Bacteria, and Archaea.
While Archae are microorganisms, they are no more related to bacteria than to eukaryotes. They share some traits with bacteria, such as having a single, circular molecule of DNA, the presence of more mobile pieces of genetic material called plasmids, similar enzymes for producing copies of DNA. However, their method of protein production and organization of their genetic material bears more similarity to eukaryotic cells.
The three domains are thought to have diverged from one another from an extinct or as yet undiscovered ancestral line. The archae and eukarya may have branched off from a common ancestral line more recently than the divergence of these two groups from bacteria. However, this view remains controversial and provisional.
The domain Archae includes a relatively small number of microoganisms. They inhabit environments which are too harsh for other microbes. Such environments include hot, molten vents at the bottom of the ocean, the highly salt water of the Great Salt Lake and the Dead Sea, and in the hot sulfurous springs of Yellowstone National Park. Very recently, it has been shown that two specific archael groups, pelagic euryarchaeota and pelagic crenarchaeota are one of the ocean's dominant cell types. Their dominance suggests that they have a fundamentally important function in that ecosystem.
See also Bacterial kingdoms; Evolution and evolutionary mechanisms; Evolutionary origin of bacteria and viruses