Archaea – How Are They Related to Other Prokaryotes :

The Archaea are presently recognized as one of the two main domains of prokaryotes [1;2]. The majority of genes that indicateArchaea to be different from Bacteria are for information transfer processes such as DNA replication, transcription and translation [3;4]. Of these, DNA replication machinery appears to be most different between the two domains [5]. In terms of transcription, the core subunits of the RNA polymerase (α, β and β’) are the same in Bacteria and Archaea, but archaea also contains several smaller subunits as well as certain transcription factors not found in bacteria. Most components of the translation machinery which includes different rRNAs, r-proteins, major elongation factors, various amino acid-charging enzymes and tRNAs, etc. are generally common to both Bacteria and Archaea [3;6]. Further, the r-proteins in Archaea are also arranged in operons similar to that seen in Bacteria. However, Archaea differ from Bacteria in some unique r-proteins as well as translation initiation factors. Archaea also differ from most bacteria in their cell membrane and cell wall composition [1;2;7]. (Fig. 1)

 
Fig. 1 Comparison of the membrane envelope between prokaryotes.

However, apart from these differences, Archaeaare extensively similar to Bacteria. Most of the metabolic pathways, which comprise the vast majority of any organism’s gene repertoire, are common between Archaea and Bacteria [8]. In terms of their cell structures, Archaea are indistinguishable from Gram-positive bacteria. Within prokaryotes, only these two groups of organisms are bounded by a single unit lipid membrane [9-11], and they generally contain a thick sacculus of varying chemical composition [12]. Some Archaea also show positive Gram staining and a few of them (viz. Thermoplasma), similar to certain Gram-positive bacteria (viz., mycoplasma), do not contain any cell wall [2].

The similarity between Archaea and Bacteria extends to numerous other characteristics including, their cellular size which is much smaller (< 100-1000 fold) than that of eukaryotic cells, absence of nucleus, cytoskeleton, histones, spliceosomal introns, circular organization of their genomes, organization of genes into operons, presence of 70S ribosomes, etc.[13] Koonin et al. [8] have shown that about 63% of the genes in M. janaschii are also found in other bacteria whereas only 5% of them are uniquely shared with Eukarya. Although about 1/3 rd of the total genes in this Archaea are unique (i.e. no similarity seen to other organisms), the same is true for most other prokaryotic genomes.

Fig. 2 Comparison of the protein sequence of Hsp70

In phylogenetic trees based on a number of different proteins archaeal species show polyphyletic branching within Gram-positive bacteria.[14-16] If one considers only prokaryotic homologs, then phylogenetic trees for the majority of proteins indicate that the Archaea are more closely related to Gram-positive bacteria (i.e., monoderm bacteria which include Thermotoga) than to Gram-negative bacteria (unpublished results).[9] Compelling evidence for a closer relationship between Archaea and Gram-positive bacteria, as compared to Gram-negative bacteria, is also provided by several prominent signature sequences (viz. 21-23 aa indel in Hsp70 (Fig. 2) and 26 aa indel in GS I) which are commonly and uniquely shared by these two groups of prokaryotes.[9;17]       

 
Fig. 3 Kandler's depiction of the universal ancestor

The question can now be asked how did these differences between Archaeaand Bacteria possibly arose and how are these two groups related to each other? Since the majority of the genes, which indicate Archaea to be distinct from Bacteria are for the information transfer processes, and these processes are of fundamental importance, it has been assumed that these differences arose in the universal ancestor before the separation of these two domains. Woese and Kandler [18;19] have suggested that these two domains as well as the eukaryotic cells, evolved from a pre-cellular community containing different types of genes by a process that led to fixation of specific subsets of genes in the ancestors of these domains. These pre-cellular entities are postulated to have no stable genealogy or chromosome and also lacking a typical cell membrane, allowing unrestricted lateral gene transfers [18;19]. According to these proposals all differences between Archaea and Bacteriaoriginated at a pre-cellular stage by non-Darwinian means, but they suggest no rationale as to how or why the observed differences between these two groups arose or evolved. Cavalier-Smith [20] has suggested the possibility of Archaea evolving from Gram-positive bacteria as an adaptation to hyperthermophily or hyperacidity, but it does not explain how various differences in the information transfer genes which distinguish Archaea from Bacteria arose.

Gupta [9;10] has suggested an alternate proposal to explain the striking similarities seen between Archaea and Gram-positive bacteria in their cell structures, in many different gene phylogenies and a number of other important observations. An important characteristic of Archaea is that they are resistant to wide variety of antibiotics that are primarily produced by Gram-positive bacteria [9]. These antibiotics act on the genes (viz. information transfer processes and or synthesis of cell wall and membrane components), which primarily distinguish Archaea from Bacteria. These observations are of central importance for understanding the origin of Archaea. If the differences that characterize Archaea from Bacteria evolved at a pre-cellular stage,then it is difficult to understand how Archaea developed resistance to various antibiotics that are produced by Gram-positive bacteria [21;22]. It also seems too much of a coincidence that most of the genes, which distinguish Archaea from Bacteriaprovide the main targets for these antibiotics.

Protein Synthesis 30S Ribosome	Protein Synthesis 50S Ribosome	Inhibitors of Cell wall Synthesis	Inhibition of Nucleic Acid Biosynthesis	Inhibition/Damage to Cell Membrane
Streptomycin  Neomycin  Tetracyclines  Spectinomycin  Pactamycin  Kanamycin	Erythromycin  Chloramphenicol  Lincomycin  Streptogramins  Spiromycin  Fusidic acid	Penicillins  Cephalosporins  Bacitracin  Vancomycin  Cycloserine	Rifampicin  Novobiocin  Bleomycin  Chromomycin  Actinomycin D  Daunomycin  Adriamycin  Mithramycin  Mitomycin Streptonigrin  Streptozotocin	Polymyxin  Tyrothricin  Gramicidin S  Caperomycin

The table above describes the sites of action of antibiotics. Most of the known antibiotics are produced by Gram-positive bacteria

Stategies taken to counter antibiotics

To account for these observations, Gupta has proposed that the earliest groups of prokaryotes that evolved were related to the Gram-positive bacteria [9;10;21;22]. The characteristics that distinguish Archaea from Bacteria, rather than evolving independently at a precellular stage, evolved from Gram-positive bacteria in response to antibiotic selection pressure. In one plausible scenario, after certain group of Gram-positive bacteria developed the ability to produce different types of antibiotics, to survive in this strongly selective environment some bacteria underwent extensive changes in genes that are the targets of these antibiotics. The changes leading to resistance were of different kinds including mutations, insertions/deletions, non-homologous recombination as well as replacement of the target genes with non-orthologous genes. Prolonged and successive selections in different antibiotics-containing environment led to the eventual development of a resistant strain that had undergone extensive changes in many genes that were the targets of these antibiotics and this strain represented the common ancestor of present day Archaea [9;10;21;22]. The evolution of Archaea in response to antibiotic selection also provides a plausible explanation for their adaptation to harsher environments such as high temperature, high salts or high temperature and acidity, etc. It is suggested that these adaptations constituted defensive strategies to find niches which are ‘hostile’ to antibiotic producing organisms [9;10;21;22]. Thus, unlike other proposals, this proposal can logically account for the evolution of most of the distinguishing characteristics of Archaea from known groups of bacteria by normal evolutionary mechanisms, without attributing such differences to the unusual properties of the universal ancestor. Because these differences between Archaea and Bacteria evolved at a very early stage in prokaryotic history (Fig. 4), the Archaea appear distinct from Bacteria in phylogenetic trees based on such characteristics. It is of interest in this regard that the analyses of genomic sequences by Lake and coworkers provide evidence that the root of the tree of life does not lie in either Archaea [23] or Gram-negative (diderm) bacteria [24].