Discriminative features of type I and type III secreted proteins from Gram-negative bacteria

Abstract

Abstract:The amino acid composition of sequences and structural attributes (α-helices, β-sheets) of C-and N-terminal fragments (50 amino acids) were compared to annotated (SWISS-PROT/ TrEMBL) type I (20 sequences) and type III (22 sequences) secreted proteins of Gramnegative bacteria. The discriminant analysis together with the stepwise forward and backward selection of variables revealed the frequencies of the residues Arg, Glu, Gly, Ile, Met, Pro, Ser, Tyr, Val as a set of strong (1-P< 0.001) predictor variables to discriminate between the sequences of type I and type III secreted proteins with a cross-validated accuracy of 98.6-100 % . The internal and external validity of discriminant analysis was confirmed by multiple (15 repeats) test-retest procedures using a randomly split original set of proteins; this validation method demonstrated an accuracy of 100 % for 191 non-selected (retest) sequences. The discriminant analysis was also applied using selected variables from the propensities for β-sheets and polarity of C-terminal fragments. This approach produced the next highest and comparable cross-validated classification accuracy for randomly selected and retest proteins (85.4-86.0 % and 82.4-84.5 %, respectively). The proposed sets of predictor variables could be used to assess the compatibility between secretion substrates and secretion pathways of Gram-negative bacteria by means of discriminant analysis.

Distinctive amino acid residue periodicities in terminal sequences of type III and type I secreted proteins from proteobacteria

“…The patterns of average intensities for corresponding periodicity profiles (Figure 3) support this view, however, only a minor part of intensities as selected variables were found to differ significantly by the Mann -Wittney U test (FT orders of n = 14 for aromatic amino acids and n = 5; 7; 18 for aliphatic ones, i.e., periodicities of 6 and 12.8; 9.14; 3.55 residues, respectively). Similar to previously reported frequencies of occurrence for amino acid residues [7], certain variables on the basis of C-terminal periodicities can therefore achieve necessary levels of statistical tolerance [16,18] and discrimination power ( Table 3, Table 4), with slight differences between the groups. These differences are possibly due to intrinsic links between the definite location of aromatic and aliphatic residues and structural determinants of differently secreted proteins [7].…”

“…Similar to previously reported frequencies of occurrence for amino acid residues [7], certain variables on the basis of C-terminal periodicities can therefore achieve necessary levels of statistical tolerance [16,18] and discrimination power ( Table 3, Table 4), with slight differences between the groups. These differences are possibly due to intrinsic links between the definite location of aromatic and aliphatic residues and structural determinants of differently secreted proteins [7].…”

“…Nevertheless, the currently approved (Table 4) classification function (Table 3) demonstrates an acceptable prediction success, being almost equivalent to that previously reported for discriminative amino acid frequencies (9 variables) in type III and type I secreted proteins [7].…”

“…For example, extracellular flagellin and two flagellar hook-associated proteins from Bacillus subtilis (FLA BACSU, FLGK BACSU and FLID BACSU) have been proposed as possibly secreted by the type III secretion system [3]. Estimates of periodicity profiles for these proteins by proposed predictor variables of classification function (Table 3) as well as discriminative frequencies of occurrence for amino acid residues [7] were found to be perfectly concordant with this view. Moreover, the secretion of recombinant interleukin-1 (O43645 HUMAN) from B. subtilis [24,25] may proceeds via the type III pathway since this protein sequence demonstrates exactly the same discriminative features as other type III proteins.…”

“…Our recent studies [7] revealed definite amino acid (R, E, G, I, M, P, S, Y, V) frequencies of occurrence as the strong predictor variables to discriminate between the full sequences of annotated type III and type I secreted proteins of proteobacteria with an accuracy up to 100% in leave-one-out and test-retest procedures.…”