Trypanosomatidae codon usage and GC distribution

Alonso, Guilhermina; Guevara, Palmira; Ramirez, José L.

doi:10.1590/s0074-02761992000400009

Cited by 23 publications

(18 citation statements)

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“…2). The coding region is 53% GC, which is consistent with the average coding region GC content of 51.6% from 31 previously reported T. brucei genes (33).…”

Section: Genomic Analysis Of the Iagnh Locus In T B Brucei-supporting

confidence: 89%

Molecular Cloning and Expression of a Purine-specific N-Ribohydrolase from Trypanosoma brucei brucei

Pellé¹,

Schramm²,

Parkin³

1998

Journal of Biological Chemistry

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Protozoan parasites rely on preformed purine nucleosides or bases for the biosynthesis of purine ribonucleotides, since they do not contain de novo purine biosynthetic pathways (1-3). Parasites and host cells have several common steps in purine salvage pathways, but unique intermediate steps are determined by the response of the parasite to the purine composition of the host's cells or bloodstream. Protozoan parasites have evolved pathways to utilize any purine nucleoside or base in the environment (1). Intracellular hemoparasites, exemplified by the American trypanosomes, have different purine nucleosides or bases available than the extracellular hemoprotozoan parasites, such as the African trypanosomes. In addition, the various life-cycle stages of the African trypanosomes are exposed to diverse environments, which vary from the mouth and midgut of tsetse flies to the extracellular bloodstream of livestock, wildlife, and humans (4, 5).The purine salvage pathway can be divided into stages: 1) the biosynthesis of IMP from free nucleosides or bases, and 2) the conversion of IMP to adenylate and guanylate nucleotides (1). The biosynthetic enzymes of the purine salvage pathway are purine nucleoside kinases, hypoxanthine-guanine-xanthine phosphoribosyl-1-pyrophosphate transferases, and the purine N-ribohydrolases and/or phosphorylases.N-Ribohydrolases found in both African and American trypanosomes are potential chemotherapeutic targets, since no N-ribohydrolase activity or encoding genes have been identified in mammals (6). N-Ribohydrolases catalyze the hydrolysis of the N-ribosidic bond between N-9 of the purine base and C-1Ј of the (deoxy-) ribose, as shown by Reaction 1.These enzymes have been identified and characterized, to a greater or lesser extent, from Trypanosoma brucei brucei (7), Trypanosoma brucei gambiense (8), Trypanosoma cruzi (9), Leishmania donovani (10), Leishmania mexicana (11), and Crithidia fasciculata (12)(13)(14). In C. fasciculata, over 90% of nucleoside salvage occurs through the inosine-uridine-preferring (IU-) 1 nucleoside hydrolase and guanosine-inosine-preferring nucleoside hydrolases, establishing a role for these isozymes in the purine nucleoside salvage pathway (14).The IU-(13) and guanosine-inosine (14) nucleoside hydrolase from C. fasciculata and the inosine-adenosine-guanosine-preferring (IAG-) nucleoside hydrolase from T. b. brucei (7) have been extensively characterized. The IU-nucleoside hydrolase has been purified, the chemical and kinetic mechanisms determined (13), the transition state determined from kinetic isotope effects (15), the cDNA cloned and overexpressed in Escherichia coli (6), and the recombinant enzyme has been characterized by x-ray crystallography (16).Recent research has focused on the IAG-nucleoside hydro-* This work was supported by an African Regional Research Fulbright Award (to D. W. P. for 1994 -1995), by National Institutes of Health Research Grant GM41916 (to V. L. S.), and by the International Livestock Research Institute (ILRI), Nairobi, Kenya. Thi...

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“…2). The coding region is 53% GC, which is consistent with the average coding region GC content of 51.6% from 31 previously reported T. brucei genes (33).…”

Section: Genomic Analysis Of the Iagnh Locus In T B Brucei-supporting

confidence: 89%

Molecular Cloning and Expression of a Purine-specific N-Ribohydrolase from Trypanosoma brucei brucei

Pellé¹,

Schramm²,

Parkin³

1998

Journal of Biological Chemistry

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“…In order to investigate this aspect, variations in GC content were captured and analyzed among the Trypanosomatids. Previously, variations in GC content among Trypanosomatids were studied for a small set of genes in a limited number of species [27,28,30]. It was also predicted that there is a high GC mutational pressure for certain genes in certain Crithidia and Leishmania species in comparison to Trypanosoma species [27].…”

Section: Comparing Gc Mutational Bias Between Leishmania and Other Trmentioning

confidence: 99%

“…Previously, variations in GC content among Trypanosomatids were studied for a small set of genes in a limited number of species [27,28,30]. It was also predicted that there is a high GC mutational pressure for certain genes in certain Crithidia and Leishmania species in comparison to Trypanosoma species [27]. In order to examine this GC bias universally across genes between different known Leishmania genomes and to compare its behavior with other Trypanosomatids, a two tier analysis of the GC content variation was performed.…”

Section: Comparing Gc Mutational Bias Between Leishmania and Other Trmentioning

confidence: 99%

“…Previous studies on codon usage patterns in Leishmania have primarily attempted to uncover the evolutionary events that shape CUB [27][28][29][30][31][32]. Since these have been limited either by the low number of genes available or by the fewer number of species considered for comparison, a strong basis for CUB across Genus Leishmania cannot be established.…”

Section: Introductionmentioning

confidence: 99%

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Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions

Subramanian

Sarkar

2015

Genomics

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Understanding the variations in gene organization and its effect on the phenotype across different Leishmania species, and to study differential clinical manifestations of parasite within the host, we performed large scale analysis of codon usage patterns between Leishmania and other known Trypanosomatid species. We present the causes and consequences of codon usage bias in Leishmania genomes with respect to mutational pressure, translational selection and amino acid composition bias. We establish GC bias at wobble position that governs codon usage bias across Leishmania species, rather than amino acid composition bias. We found that, within Leishmania, homogenous codon context coding for less frequent amino acid pairs and codons avoiding formation of folding structures in mRNA are essentially chosen. We predicted putative differences in global expression between genes belonging to specific pathways across Leishmania. This explains the role of evolution in shaping the otherwise conserved genome to demonstrate species-specific function-level differences for efficient survival.

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“…Except for the fact that these three insect parasites have a higher-biased codon usage, they show preferences very similar to those in L. mexicana and Phytomonas sp. We do not present here a detailed analysis of the codon usage of L. mexicana and both Trypanosoma species, since a number of such studies, all including the GAPDH data, have already been published (Michels 1986;Parsons et al 1991;Alonso et al 1992;Alvarez et al 1994). Concerning the partial sequences, L. major shows the same codon usage as L. mexicana, whereas the preferences of the three Trypanosoma species are very close to that of T. brucei (data not shown).…”

Section: Nucleotide Composition and Codon Usage Of The Gapdh Genesmentioning

confidence: 99%

Comparison and Evolutionary Analysis of the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Different Kinetoplastida

Hannaert¹,

Opperdoes

Michels

1998

J Mol Evol

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In this work, we present the sequences and a comparison of the glycosomal GAPDHs from a number of Kinetoplastida. The complete gene sequences have been determined for some species (Crithidia fasciculata, Herpetomonas samuelpessoai, Leptomonas seymouri, and Phytomonas sp), whereas for other species (Trypanosoma brucei gambiense, Trypanosoma congolense, Trypanosoma vivax, and Leishmania major), only partial sequences have been obtained by PCR amplification. The structure of all available glycosomal GAPDH genes was analyzed in detail. Considerable variations were observed in both their nucleotide composition and their codon usage. The GC content varies between 64.4% in L. seymouri and 49.5% in the previously sequenced GAPDH gene from Trypanoplasma borreli. A highly biased codon usage was found in C. fasciculata, with only 34 triplets used, whereas in T. borreli 57 codons were employed. No obvious correlation could be observed between the codon usage and either the nucleotide composition or the level of gene expression. The glycosomal GAPDH is a very well-conserved enzyme. The maximal overall difference observed in the amino acid sequences is only 25%. Specific insertions and extensions are retained in all sequences. The residues involved in catalysis, substrate, and inorganic phosphate binding are fully conserved, whereas some variability is observed in the cofactor-binding pocket. The implications of these data for the design of new trypanocidal drugs targeted against GAPDH are discussed. All available gene and amino acid sequences of glycosomal GAPDHs were used for a phylogenetic analysis. The division of the Kinetoplastida into two suborders, Bodonina and Trypanosomatina, was well supported. Within the letter group, the Trypanosoma species appeared to be monophyletic, whereas the other trypanosomatids form a second clade.

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Trypanosomatidae codon usage and GC distribution

Cited by 23 publications

References 0 publications

Molecular Cloning and Expression of a Purine-specific N-Ribohydrolase from Trypanosoma brucei brucei

Molecular Cloning and Expression of a Purine-specific N-Ribohydrolase from Trypanosoma brucei brucei

Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions

Comparison and Evolutionary Analysis of the Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Different Kinetoplastida

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