Genome compartmentalization

Indeed, genome compartmentalization was not only found in warm-blooded, and to a smaller extent, in cold-blooded vertebrates, but also in other eukaryotes, ranging from trypanosomes to Drosophila. At least in some cases, this compartmentalization seemed also to be linked to the thermodynamic stability of DNA. 

Medrano L., Bernard G., Couturier J., Dutrillaux B., Bernard G. (1988). Chromosome banding and genome compartmentalization in fishes. Chromosoma 96 178-183. 

Bacteria, being procaryotic, do not show compartmentation of the biosynthetic processes. The genome of a bacterium relates directly to the cytoplasm of the cell. Transcription into mRNA can lead directly to translation, and the processes of transcription and translation are not carried out in separate organelles. Animal cells, being eucaryotic, show compartmentation of the transcription and translation processes. Transcription of the genome into mRNA occurs in the nucleus, whereas translation occurs in the cytoplasm. The messenger RNA in the eucaryote is usually modified by adding to it... 

Abstract The DNA in eukaryotic genome is compartmentalized into various domains by a... 

When considered in this way, the chimeric organism would be a fermenting aerotolerant prokaryote, surrounded by a single bacterial membrane and endowed with compartmentalized methanogenesis and a mosaic genome dominated by archaeal genes. Such an eccentric prokaryote is further suggested to have once become a host for a mitochondrial symbiont (Sect. 9.4.2). 

In conclusion, the compositional patterns of the Trypanosome genomes indicate that compartmentalization is a phylogenetically very widespread situation in eukaryotes, as already predicted (Bernardi et al., 1985b). 

Isacchi A., Bemardi G., Bernard G. (1993). Compositional compartmentalization of the nuclear genomes of Trypanosoma hrucei and Trypanosoma equiperdum. FEBS Letters 335 181-183. 

Mouchiroud D., Fichant G., Bernard G. (1987). Compositional compartmentalization and gene composition in the genome of vertebrates. J. Mol. Evol. 26 198-204... 

The interaction of small molecules with cells should also be investigated at the protein (proteome) level since the concentration (abundance), transcriptional alteration, posttranslational modification, formation of complexes with other proteins or cellular components, modulation of the activity with small molecule effectors, and compartmentation cannot be revealed at the genome level. 

Genomic and transcriptomic technologies have been used to rapidly identify biosynthetic steps. There are currently over 40,000 expressed enzyme tags (ESTs) generated fi om alkaloid-producing plants that have been used to isolate genes involved in the alkaloid pathway [7]. Some alkaloid biosynthetic steps occur as spontaneous chemical reactions without the use of enzymes, for example, conversion of the intermediate neopine into codeinone in the morphine biosynthetic pathway. Also, some enzymes may catalyze two or more separate reactions in the pathway, for example, hyoscyamine 6-hydroxylase, which carries out two consecutive steps in the scopolamine biosynthetic pathway. Alkaloid biosynthesis also involves compartmentalization. Tissue-specific localization studies have shown that sequential biosynthetic enzymes can occur in distinct cell types [8, 9]. During the biosynthesis of the indole alkaloids vinblastine and vincristine in Catharanthus roseus, different enzymatic steps are carried out in different cellular compartments (Fig. 8.5) [10]. Various steps in the pathway are carried out in different types of cell. This requires the intercellular transport of metabolic intermediates. Similarly, scopolamine biosynthesis also involves two different cell types. 

Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14 1298-1309... 

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