Trends of Amino Acid Usage in the Proteins from the Unicellular Parasite Giardia lamblia

Garat, Beatríz; Musto, Héctor

doi:10.1006/bbrc.2000.4051

Cited by 28 publications

(18 citation statements)

References 39 publications

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“…In other words, the smaller and energetically less expensive amino acids are preferred by leading strand gene products than that of the lagging strand. Since the highly expressed genes are mostly located on the leading strand of replication, this observation indicates that proteins encoded by highly expressed genes are preferentially constructed with smaller residues because these residues are energetically less expensive, as were also reported for the proteins in Giardia lamblia 30 and Thermotoga maritime. 29 This indicates that B. henselae and B. quintana, both in spite of their intracellular lifestyle, follow the cost-minimization hypothesis.…”

Section: Major Sources Of Variation In Protein Composition 341 Infsupporting

confidence: 66%

Codon and Amino Acid Usage in Two Major Human Pathogens of Genus Bartonella -- Optimization Between Replicational-Transcriptional Selection, Translational Control and Cost Minimization

et al. 2005

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Intra-genomic variation in synonymous codon and amino acid usage in two human pathogens Bartonella henselae and B. quintana has been carried out through multivariate analysis. Asymmetric mutational bias, coupled with replicational-transcriptional selection, has been identified as the prime selection force behind synonymous codon selection -a characteristic of the genus Bartonella, not exhibited by any other alphaproteobacterial genome. Distinct codon usage patterns and low synonymous divergence values between orthologous sequences of highly expressed genes from the two Bartonella species indicate that there exists a residual intra-strand synonymous codon bias in the highly expressed genes, possibly operating at the level of translation. In the case of amino acid usage, the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact, while strand-specific mutational pressure and gene expressivity strongly influence the inter-strand variations. In both species under study, the highly expressed gene products tend not to contain heavy and/or aromatic residues, following the costminimization hypothesis in spite of their intracellular lifestyle. The codon and amino acid usage in these two human pathogens are, therefore, consequences of a complex balance between replicational-transcriptional selection, translational control, protein hydropathy and cost minimization.

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Section: Major Sources Of Variation In Protein Composition 341 Infsupporting

confidence: 66%

Codon and Amino Acid Usage in Two Major Human Pathogens of Genus Bartonella -- Optimization Between Replicational-Transcriptional Selection, Translational Control and Cost Minimization

et al. 2005

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“…3 the sequences displaying negative values on the second axis are the ones with the lowest MMWs. For G. lamblia, we have recently reported that the most highly expressed sequences are preferentially constructed with smaller residues, and we postulated that the rationale of this finding might be that smaller amino acids are energetically cheaper than big ones (Garat and Musto 2000). Three correlations suggest that this is the case in T. maritima too.…”

Section: Amino Acid Frequenciesmentioning

confidence: 87%

“…In Escherichia coli (Lobry and Gautier 1994) it was found that the three most important sources of variation were the hydrophobicity, expressivity, and aromaticity of the proteins. In the anaerobic unicellular eukaryote Giardia lamblia it was recently shown (Garat and Musto 2000) that the most relevant factors are related to the particular mechanism of defenses against reactive oxygen species, namely, the increment of sulfur-containing and aromatic residues. In addition, since the most abundant proteins tend to use smaller amino acids, the cell economy seems to be another prominent feature reducing energetic costs.…”

Section: Amino Acid Frequenciesmentioning

confidence: 99%

“…In E. coli the axis related to this feature was the third (Lobry and Gautier 1994), while in G. lamblia it was the second (Garat and Musto 2000). In trying to understand the biological causes of this correlation it should be taken into account, as noted by Lobry and Gautier (1994), that (a) aromatic residues (Phe, Tyr, and Trp) are variable among proteins (although usually rare), and (b) their biosynthesis is energetically expensive.…”

Section: Amino Acid Frequenciesmentioning

confidence: 99%

“…These six residues have in common the property of being the preferential targets of reactive oxygen species and can act as sinks for radical fluxes through electron transfer between amino acids on the protein (Dean et al 1993;Berlett and Stadtman 1997). It has been suggested that these residues could confer some resistance to reactive oxygen species in the anaerobic unicellular eukaryote G. lamblia (Garat and Musto 2000). It is not easy to understand this result in T. maritima since its exposure to reactive oxygen species in its natural habitat is rather improbable.…”

Section: Amino Acid Frequenciesmentioning

confidence: 99%

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Trends in Codon and Amino Acid Usage in Thermotoga maritima

Zavala

Naya

Romero

et al. 2002

Journal of Molecular Evolution

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Abstract. The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino acid in this species) was detected as the second most prominent source of variation. However, this result is probably an artifact due to the very low frequency of Cys together with the nonbiased composition of this genome. The third trend was related to the preferential usage of a subset of codons among highly expressed genes, and these triplets are presumed to be translationally optimal. Concerning the amino acid usage, the hydropathy level of each protein (and therefore the frequency of charged residues) was the main trend, while the second factor was related to the frequency of usage of the smaller residues, suggesting that the cell economy strongly influences the architecture of the proteins. The third axis of the analysis discriminated the usage of Phe, Tyr, Trp (aromatic residues) plus Cys, Met, and His. These six residues have in common the property of being the preferential targets of reactive oxygen species, and therefore the anaerobic condition of T. maritima is an important factor for the amino acid frequencies. Finally, the Cys content of each protein was the fourth trend.

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Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich Nonsynonymous Codons in Highly Expressed Genes

2005

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The parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, is one of the extremely AT-rich genomes sequenced so far and known to possess many atypical characteristics. Using multivariate statistical approaches, the present study analyzes the amino acid usage pattern in 5038 annotated protein-coding sequences in P. falciparum clone 3D7. The amino acid composition of individual proteins, though dominated by the directional mutational pressure, exhibits wide variation across the proteome. The Asn content, expression level, mean molecular weight, hydropathy, and aromaticity are found to be the major sources of variation in amino acid usage. At all stages of development, frequencies of residues encoded by GC-rich codons such as Gly, Ala, Arg, and Pro increase significantly in the products of the highly expressed genes. Investigation of nucleotide substitution patterns in P. falciparum and other Plasmodium species reveals that the nonsynonymous sites of highly expressed genes are more conserved than those of the lowly expressed ones, though for synonymous sites, the reverse is true. The highly expressed genes are, therefore, expected to be closer to their putative ancestral state in amino acid composition, and a plausible reason for their sequences being GC-rich at nonsynonymous codon positions could be that their ancestral state was less AT-biased. Negative correlation of the expression level of proteins with respective molecular weights supports the notion that P. falciparum, in spite of its intracellular parasitic lifestyle, follows the principle of cost minimization.

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Trends of Amino Acid Usage in the Proteins from the Unicellular Parasite Giardia lamblia

Cited by 28 publications

References 39 publications

Codon and Amino Acid Usage in Two Major Human Pathogens of Genus Bartonella -- Optimization Between Replicational-Transcriptional Selection, Translational Control and Cost Minimization

Codon and Amino Acid Usage in Two Major Human Pathogens of Genus Bartonella -- Optimization Between Replicational-Transcriptional Selection, Translational Control and Cost Minimization

Trends in Codon and Amino Acid Usage in Thermotoga maritima

Proteome Composition in Plasmodium falciparum: Higher Usage of GC-Rich Nonsynonymous Codons in Highly Expressed Genes

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