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In this article we will discuss about the evolution of genomes in microorganisms.
The prokaryotes contain a large single, circular dsDNA molecule, usually less than 5 Mb long. In addition, they may also contain plasmids. The genome is arranged into operons. A typical prokaryotic genome contains a small amount of non-coding DNA distributed throughout the sequence. For example, E.coli contains only -11% the non-coding DNA. On the other hand, the eukaryotic cells contain chromosomes present in the nucleus.
Each chromosome contains a single dsDNA molecule. A small amount of DNA appears in two organelles i.e. mitochondria and chloroplasts. The genetic code of nuclear and organellar genes are translated differently. The difference in genome size of different organisms is due to different amounts of simple repetitive sequences often called as junk DNA.
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The genomic sequences have been found useful in the study of evolution of genomes. The comparative genomics gives the information about the gene arrangement in the genome of microorganisms belonging to different classes, varying nature of proteins and its expression patterns.
The function of the protein present in one class of microbe has a homology in the other. If so, the homologus proteins carry out the same function in microorganisms belonging to two different classes.
Andrade and co-workers compared the protein functions of three major domains of life. Their classification contained as major processes involving energy, information, and communication and regulation.
In case of energy a number of processes such as biosynthesis of co-factors, amino acids, metabolisms, fatty acids including lipid analysis, nucleotide biosynthesis and transport have been included, whereas replication, transcription and translation processes comprised of information.
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The communication and regulation deal with regulatory functions, cell envelop into cell wall and cellular processes. They determine number of genes in three genera of different phyla i.e. Haemophilus influenzae (bacteria), Methanococcus jannashii (archaea) and Saccharomyces cerevisiae (eukarya) which contain 1680, 1735 and 6278 genes, respectively. Some of the proteins are shared but some are unique to each domain. M. jannaschii shares some proteins with H. influenzae and some with S. cerevisiae.
Mushegian and Konin (1996) compared the genomes of Mycoplasma genitalium and H. influenzae. From 1703 protein-coding genes of H. influenzae, 240 are homologues of proteins of M. genitalium. They concluded that these proteins must be essential, but might not be sufficient for autonomous life. Some essential functions might be carried out by unrelated proteins in the two genomes.
For example, the common set of 240 proteins left gaps in essential pathways, which could be filled by adding 22 enzymes from M. genitalicum. A number of 250 genes proposed necessary and sufficient minimal set finally after removing functional redundancy and parasite-specific genes.
According to them, the proposed minimal genome functional class includes protein synthesis, DNA replication, recombination and repair, transcription apparatus, chaperon-like proteins, glycolytic pathway, no nucleotide biosynthesis, amino acid or fatty acid biosynthesis, protein export machinery and limited functions of metabolic transport proteins.
The identification of the gene complement of the common ancestor of M. genitalium and H. influenzae remained unanswered. The 71% proteins of 256 genes have been found to have recognizable homologues among eukaryotic or archaeal proteins.
Genome analysis has revealed families of proteins with homologues in archaea, bacteria and eukarya. It is assumed that these got evolved from an individual ancestral gene through a series of evolution and duplication events. This may be due to effects of horizontal gene transfer.
In case of Aquiflex aeolicus, 83% of the proteins have archaeal and eukaryotic homologues to Borrelia burgdorferi in which 52% of the proteins have archaeal and eukaryotic homologues. Archaeal genomes have 62-71% proteins higher with bacterial and eukaryotic homologues but only 35% of the proteins of yeast have bacterial and archaeal homologues.
It is further necessary to know whether the common set of proteins present in different phyla have common functions. The minimal set of proteins of M. genitalium has around 30% homologues in all genomes. Other essential functions must be carried out by unrelated proteins. The common protein families appearing in archaea, bacteria and eukarya involved in translation process are given in Table 27.13.
