Phylogenetic Classification Systems †Free Samples for Students

Question: Discuss About the Phylogenetic Classification Systems? Answer: Introducation The earlier taxonomic and phylogenetic classification systems were based on morphology. As the science of microscopy developed and it became possible to study the cellular structure, classification of organisms was based on the differences in cell structure. With the advent of ability to sequence DNA and RNA, it became possible to compare the sequences. This led to the ability to distinguish between organisms on the basis of dissimilarities between the sequences. The three tax domains as per the current system of classification are eubacteria and archaeabacteria, both prokaryotic and the eukaryotes. Prokaryotes and eukaryotes were earlier differentiated on the basis of cellular morphology. The absence or presence of nucleus was the main structure that differentiated them. Carl Woese suggested that the classification should be based on the 16S rRNA or 18S rRNA sequences rather than on morphological differences (Woese, Kandler, Wheelis, 1990). The basis for earlier methods for classification was organism based, it was later based on cellular Management and is now based on differences at the molecular level. As a result phylogeny is now understood on a molecular basis rather than a phenotypic basis. The basis for description of eukaryotes appeared to be based on the shared complexity of cellular organisation. But the same was not true for prokaryotes, the differences amongst the organisms could not be phylogenetically described just because these cells did not contain a nucleus. This was revealed when it was discovered that the archaeabacteria are as different from bacteria as the y are different from the eukaryotes and thus three domains were proposed, namely, eubacteria, archaeabacteria and the eukaryotes. The archaeabacteria that were studied later are methanogenic, thermophilic and tolerant to high salt concentrations, conditions that were prevalent on earth in ancient times. All organisms have DNA and the genes are expressed through protein synthesis. Ribosomes are the sites for protein synthesis and rRNA molecules are components of ribosomes. The rRNA molecules are also encoded by DNA. Mutations have occurred in the rRNA genes during evolution. The reason why rRNA was suited to be the molecule of choice for molecular phylogeny was because it was present in all organisms and the mutations that occurred in the molecule were such that they allowed the formation of ribosomes. Any mutation that could have disrupted the formation of ribosomes was eliminated through natural selection. rRNA can be easily isolated in the laboratory and comparison of rRNA sequences from two organisms can help determine how closely (or distantly) they are related on an evolutionary time scale. The rRNA molecules fold into secondary and tertiary structures due to complementary base sequences. The tertiary structure of rRNA exhibits differences between eubacteria, archaebacteria and eukaryotes. The small subunit rRNA in the eubacteria is different from the archaebacteria and eukaryotes between bases 500 to 545 that form the bulge that protrudes from the stalk in the tertiary structure. It is 6 nucleotides long in the former while the bulge is made up of seven nucleotides in the latter, the compositions of the nucleotide stretches are also different in eubacteria. The region of small subunit rRNA in eukaryotes has a sequence between nucleotides 585 and 655 which is peculiar to the domain (Gutell, Weiser, Woese, Noller, 1985). The prokaryotes have a different but common structure in the corresponding region. The archaebacteria have a unique domain in their 16S rRNA between 180-197 positions and between 405 and 498 positions (Woese, Gutell, Gupta, Noller, 1983). A comparison of the three domains yields similarities between the eubacteria and the archaeabacteria but more similarities occur between the archaeans and the eukaryotes. The nuclear membrane and unit-membrane enclosed organelles are present in the eukaryotes but re absent among the two prokaryotic domains. The eubacteria have a peptidoglycan cell wall that is absent in the other two domains. Eubacteria have only one kind of RNA polymerase while archaebacteria and eukaryotes have several kinds of RNA polymerases that share structural homology (Huet, Schnabel, Sentenac, Zillig, 1983). During protein synthesis the initiator amino acid among the eubacteria is formyl-methionine, but methionine is the initiator amino acid in the other two domains. Both archaebacteria and eukaryotes have genes with introns but eubacteria have genes without introns. Antibiotics like streptomycin and chloramphenicol can only inhibit the eubacteria. DNA is packaged with the help of histone proteins in the eu karyotes, some archaeabacterial species but none of the eubacteria. The prokaryotes have circular chromosomes. Some species of archaeabacteria are thermophilic and can grow beyond the temperature of 100oC. Thus there are several similarities between the archaebacteria and eukaryotes (Reece, et al., 2014). In conclusion, the new system of taxonomic classification is based the differences between the rRNA and some gene sequences. The position of the archaeabacteria as a separate domain has been established based on their similarities with eukaryotes and the eubacteria. The similarities and mutations in the small subunit of rRNA have been extensively studied to establish the domains and form the basis for molecular phylog References Gutell, R. R., Weiser, B., Woese, C. R., Noller, H. F. (1985). Comparative anatomy of 16-S-like ribosomal RNA. Progress in Nucleic Acid Research and Molecular Biology, 32, 155-216. Huet, J., Schnabel, R., Sentenac, A., Zillig, W. (1983). Archaebacteria Accounting eukaryotes possess DNA-dependent RNA polymerases of a common type. EMBO, 2(8): 12911294. Reece, J., Urry, L., Cain, M., Wasserman, S., Minorsky, P., Jackson, R. (2014). Campbell Biology. Pearson. Woese, C., Gutell, R., Gupta, R., Noller, H. (1983). Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiological Reviews, 47(4): 621669. Woese, C., Kandler, O., Wheelis, M. (1990). Towards a natural system of organisms: Proposal for the domains. PNAS, USA, 87: 4576-4579, .