Limits...
Comparative Analysis of Apicoplast-Targeted Protein Extension Lengths in Apicomplexan Parasites.

Seliverstov AV, Zverkov OA, Istomina SN, Pirogov SA, Kitsis PS - Biomed Res Int (2015)

Bottom Line: We focus on results obtained for the model species T. gondii, Neospora caninum, and Plasmodium falciparum.With our method, cross species comparisons demonstrate that, in average, apicoplast-targeted protein extensions in T. gondii are 1.5-fold longer than in N. caninum and 2-fold longer than in P. falciparum.Extensions in P. falciparum less than 87 residues in size are longer than the corresponding extensions in N. caninum and, reversely, are shorter if they exceed 88 residues.

View Article: PubMed Central - PubMed

Affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.

ABSTRACT
In general, the mechanism of protein translocation through the apicoplast membrane requires a specific extension of a functionally important region of the apicoplast-targeted proteins. The corresponding signal peptides were detected in many apicomplexans but not in the majority of apicoplast-targeted proteins in Toxoplasma gondii. In T. gondii signal peptides are either much diverged or their extension region is processed, which in either case makes the situation different from other studied apicomplexans. We propose a statistic method to compare extensions of the functionally important regions of apicoplast-targeted proteins. More specifically, we provide a comparison of extension lengths of orthologous apicoplast-targeted proteins in apicomplexan parasites. We focus on results obtained for the model species T. gondii, Neospora caninum, and Plasmodium falciparum. With our method, cross species comparisons demonstrate that, in average, apicoplast-targeted protein extensions in T. gondii are 1.5-fold longer than in N. caninum and 2-fold longer than in P. falciparum. Extensions in P. falciparum less than 87 residues in size are longer than the corresponding extensions in N. caninum and, reversely, are shorter if they exceed 88 residues.

No MeSH data available.


Plot of protein length extensions in N. caninum Liverpool versus P. falciparum 3D7 relative to their orthologs in Synechocystis sp. PCC 6803. Differences in lengths between sporozoan and cyanobacterial orthologous proteins are plotted as follows: N-S on the x-axis, P-S on the y-axis.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4465681&req=5

fig3: Plot of protein length extensions in N. caninum Liverpool versus P. falciparum 3D7 relative to their orthologs in Synechocystis sp. PCC 6803. Differences in lengths between sporozoan and cyanobacterial orthologous proteins are plotted as follows: N-S on the x-axis, P-S on the y-axis.

Mentions: In Figures 1–3, the cases of N. caninum-T. gondii (N-T), P. falciparum-T. gondii (P-T), and P. falciparum-N. caninum (P-N) are analyzed using three sets of points. Each coordinate is the difference in lengths between the sporozoan and cyanobacterial orthologs: T. gondii versus Synechocystis (T-S), N. caninum versus Synechocystis (N-S), and P. falciparum versus Synechocystis (P-S). The sets of points are then statistically analyzed. The following statistic was used to test the hypotheses that “a constant is better compatible with the set of points {(xi, yi)∣1 ≤ i ≤ n} than the nontrivial affine function y = kx + b, k ≠ 0” and “the linear function y = kx is better compatible with this set of points than the affine function y = kx + b, b ≠ 0”: , where in the numerator is a constant (mean over all y) or linear regression y = kx and in the denominator is affine regression y = kx + b. This statistic can be explained more clearly: it determines whether there is a correlation between the difference and xi. This statistic is standard and substantiated in [31, 32]. The value of F was compared against a threshold defined as the Student random variable at significance level α, t(n − 2, α). Under the number of degrees of freedom n − 2 > 30, the Student and standard Gaussian distributions approximate each other, and the threshold t(266,0.05) equals 1.96. An analogous statistic was used to test the hypothesis “affine function versus general polynomial of second degree.” The confidence interval radius and the radius of the intercept (further referred to as radius) for the affine regression slope as well as the slope coefficient radius for linear regression were calculated in a standard fashion [32]. The Student test statistic S was used as well [32]. Deming regression and screening singular points were tested as well.


Comparative Analysis of Apicoplast-Targeted Protein Extension Lengths in Apicomplexan Parasites.

Seliverstov AV, Zverkov OA, Istomina SN, Pirogov SA, Kitsis PS - Biomed Res Int (2015)

Plot of protein length extensions in N. caninum Liverpool versus P. falciparum 3D7 relative to their orthologs in Synechocystis sp. PCC 6803. Differences in lengths between sporozoan and cyanobacterial orthologous proteins are plotted as follows: N-S on the x-axis, P-S on the y-axis.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4465681&req=5

fig3: Plot of protein length extensions in N. caninum Liverpool versus P. falciparum 3D7 relative to their orthologs in Synechocystis sp. PCC 6803. Differences in lengths between sporozoan and cyanobacterial orthologous proteins are plotted as follows: N-S on the x-axis, P-S on the y-axis.
Mentions: In Figures 1–3, the cases of N. caninum-T. gondii (N-T), P. falciparum-T. gondii (P-T), and P. falciparum-N. caninum (P-N) are analyzed using three sets of points. Each coordinate is the difference in lengths between the sporozoan and cyanobacterial orthologs: T. gondii versus Synechocystis (T-S), N. caninum versus Synechocystis (N-S), and P. falciparum versus Synechocystis (P-S). The sets of points are then statistically analyzed. The following statistic was used to test the hypotheses that “a constant is better compatible with the set of points {(xi, yi)∣1 ≤ i ≤ n} than the nontrivial affine function y = kx + b, k ≠ 0” and “the linear function y = kx is better compatible with this set of points than the affine function y = kx + b, b ≠ 0”: , where in the numerator is a constant (mean over all y) or linear regression y = kx and in the denominator is affine regression y = kx + b. This statistic can be explained more clearly: it determines whether there is a correlation between the difference and xi. This statistic is standard and substantiated in [31, 32]. The value of F was compared against a threshold defined as the Student random variable at significance level α, t(n − 2, α). Under the number of degrees of freedom n − 2 > 30, the Student and standard Gaussian distributions approximate each other, and the threshold t(266,0.05) equals 1.96. An analogous statistic was used to test the hypothesis “affine function versus general polynomial of second degree.” The confidence interval radius and the radius of the intercept (further referred to as radius) for the affine regression slope as well as the slope coefficient radius for linear regression were calculated in a standard fashion [32]. The Student test statistic S was used as well [32]. Deming regression and screening singular points were tested as well.

Bottom Line: We focus on results obtained for the model species T. gondii, Neospora caninum, and Plasmodium falciparum.With our method, cross species comparisons demonstrate that, in average, apicoplast-targeted protein extensions in T. gondii are 1.5-fold longer than in N. caninum and 2-fold longer than in P. falciparum.Extensions in P. falciparum less than 87 residues in size are longer than the corresponding extensions in N. caninum and, reversely, are shorter if they exceed 88 residues.

View Article: PubMed Central - PubMed

Affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.

ABSTRACT
In general, the mechanism of protein translocation through the apicoplast membrane requires a specific extension of a functionally important region of the apicoplast-targeted proteins. The corresponding signal peptides were detected in many apicomplexans but not in the majority of apicoplast-targeted proteins in Toxoplasma gondii. In T. gondii signal peptides are either much diverged or their extension region is processed, which in either case makes the situation different from other studied apicomplexans. We propose a statistic method to compare extensions of the functionally important regions of apicoplast-targeted proteins. More specifically, we provide a comparison of extension lengths of orthologous apicoplast-targeted proteins in apicomplexan parasites. We focus on results obtained for the model species T. gondii, Neospora caninum, and Plasmodium falciparum. With our method, cross species comparisons demonstrate that, in average, apicoplast-targeted protein extensions in T. gondii are 1.5-fold longer than in N. caninum and 2-fold longer than in P. falciparum. Extensions in P. falciparum less than 87 residues in size are longer than the corresponding extensions in N. caninum and, reversely, are shorter if they exceed 88 residues.

No MeSH data available.