The nuclear genomes of African and American trypanosomes are strikingly different

The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview

The recent availability of a number of fully sequenced genomes (including marine organisms) allowed to map very precisely the isochores, based on DNA sequences, confirming the results obtained before genome sequencing by the ultracentrifugation in CsCl. In fact, the analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong to a small number of families characterized by different GC levels. In this review, we will concentrate on some general genome features regarding the compositional organization from different organisms and their evolution, ranging from vertebrates to invertebrates until unicellular organisms. Since isochores are tightly linked to biological properties such as gene density, replication timing, and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function, and evolution. All the findings reported here confirm the idea that the isochores can be considered as a "fundamental level of genome structure and organization." We stress that we do not discuss in this review the origin of isochores, which is still a matter of controversy, but we focus on well established structural and physiological aspects.

Comparative codon and amino acid composition analysis of Tritryps-conspicuous features of Leishmania major

Comparative analyses of codon/amino acid usage in Leishmania major, Trypanosoma brucei and Trypanosoma cruzi reveal that gene expressivity and GC-bias play key roles in shaping the gene composition of all three parasites, and protein composition of L. major only. In T. brucei and T. cruzi, the major contributors to the variation in protein composition are hydropathy and/or aromaticity. Principle of Cost Minimization is followed by T. brucei, disregarded by T. cruzi and opposed by L. major. Slowly evolving highly expressed gene-products of L. major bear signatures of relatively AT-rich ancestor, while faster evolution under GC-bias has characterized the lowly expressed genes of the species by higher GC12-content.

The African trypanosome cyclophilin A homologue contains unusual conserved central and N-terminal domains and is developmentally regulated

We have cloned and characterized the homologue of cyclophilin A (CypA) from Trypanosoma brucei brucei, Trypanosoma congolense, Trypanosoma evansi and Trypanosoma vivax. The 1-kilobase African trypanosome CypA complementary DNA contains an open reading frame of 531 base pairs, corresponding to 177 amino acids with a calculated molecular weight of 18,700. The CypA gene is present at one copy/haploid genome in T. brucei, T. congolense and T. vivax and is located on large chromosomes (>3 Mb) in T. brucei. CypA is differentially transcribed in African trypanosomes and is localized in the cytosol as well as in the flagellum. It is also detected in the supernatant of in vitro cultivated parasites. The African trypanosome CypA is unique due to a ten amino acid residue N-terminus extension and a block that includes a three amino acid insertion around position 100 that might result in a differently structured surface. Wild-type recombinant CypA and several mutants were over-expressed in Escherichia coli and purified to >98% homogeneity. Antisera from cattle immunized with a trypanosome fraction containing immunosuppressive activity react strongly against CypA. These data indicate that trypanosome CypA might play an important role in the establishment and maintenance of infections in susceptible animals.

Genome research and evolution in trypanosomes

Trypanosoma brucei and Trypanosoma cruzi cause different human diseases. As strategies for immune evasion, T. brucei undergone antigenic variation whereas T. cruzi becomes an intracellular organism. This fundamental difference is reflected by major differences in their genome organizations. Recent comparisons of their gene sequences indicate that these two trypanosome species are highly divergent evolutionarily.

Compositional properties of nuclear genes from Plasmodium falciparum

We have analyzed the compositional distributions of coding sequences and their different codon positions, as well as the codon usage of the nuclear genes of Plasmodium falciparum, a parasite characterized by an extremely GC-poor genome. As expected, coding sequences are AT-rich, codon usage is strongly biased towards A or T in third codon positions, and some particular amino acids (aa) are especially abundant in the encoded proteins. Remarkably, however, no difference was detected between housekeeping (HK) and antigen (Ag) genes, in spite of differences in expression level and evolutionary constraints. Moreover, all the features found in P. falciparum are very similar to those found in a bacterium characterized by a very GC-poor genome, Staphylococcus aureus. These findings stress the importance of compositional constraints in determining codon usage and aa utilisation.

The compositional compartments of the nuclear genomes of Trypanosoma brucei and T. cruzi

Fractionation of DNA from Trypanosoma brucei and T. equiperdum by centrifugation in a Cs2SO4/BAMD density gradient indicated that these genomes are compositionally compartmentalized, a conclusion confirmed by the analysis of the compositional distribution of third codon positions from T. brucei and T. cruzi. In order to investigate whether this compartmentalization is accompanied by the often different properties of coding sequences, we have analyzed and compared the compositional compartments with respect to dinucleotide frequency and amino-acid usage of the encoded proteins of all gene sequences available in the GenBank database from T. brucei and T. cruzi. In all cases, the compartments displayed remarkable differences. These results are similar to findings obtained in highly compartmentalized genomes, like those of warm-blooded vertebrates.

Codon usage and genome evolution

The rates and patterns of evolution at silent sites in codons reveal much about the basic features of molecular evolution. Recent increases in the amount of sequence data available for various species and more precise knowledge of the chromosomal locations of those sequences, coming in particular from genome projects, reveal that some features of molecular evolution vary around the genome.