Limits...
Identification of functional candidates amongst hypothetical proteins of Treponema pallidum ssp. pallidum.

Naqvi AA, Shahbaaz M, Ahmad F, Hassan MI - PLoS ONE (2015)

Bottom Line: However, functions of 237 HPs are predicted with less accuracy.We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen.Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.

ABSTRACT
Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, Treponema pallidum ssp. pallidum, a Gram-negative sphirochaete, is an obligate human parasite. Genome of T. pallidum ssp. pallidum SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of T. pallidum ssp. pallidum using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of T. pallidum ssp. pallidum and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.

No MeSH data available.


Related in: MedlinePlus

Classification of 207 HPs into various groups by utilizing the functional annotation results of various bioinformatics tools.The chart shows that there are 83 enzymes, 28 proteins involve in transportation, 58 binding proteins, 21 proteins involved in cellular processes like transcription, translation, replication etc. and 17 showing miscellaneous functions among 207 HPs from T. pallidum ssp. pallidum.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4403809&req=5

pone.0124177.g001: Classification of 207 HPs into various groups by utilizing the functional annotation results of various bioinformatics tools.The chart shows that there are 83 enzymes, 28 proteins involve in transportation, 58 binding proteins, 21 proteins involved in cellular processes like transcription, translation, replication etc. and 17 showing miscellaneous functions among 207 HPs from T. pallidum ssp. pallidum.

Mentions: The genome of the SS14 strain was sequenced to high accuracy by Matejková et al., [2] in 2008 using oligonucleotide array strategy. But errors in key features such as start codons (alternate or otherwise) and stop codons (due to sequencing errors) were observed. Recently, the complete genome sequence of the TPA Mexico, A strain was reported by Pětrošová et al., [28] using the Illumina sequencing technique. However, a recent report on resequencing of T. pallidum ssp. pallidum strains Nichols and SS14 has identified errors in 11.5% of all annotated genes and subsequently corrected [29]. Hence, we assume that the available genome sequence of T. pallidum ssp. pallidum in the database is free from experimental sequencing errors. Extensive sequence analysis of all 444 HPs based on the above mentioned tools helped us to precisely assign function to 207 HPs with high confidence (Table 1). We have also predicted functions for 237 HPs with low level of confidence (S9 Table). We annotated the function of these HPs using protein classification databases such as CATH, Superfamily, Pfam, PANTHER, SYSTERS. Recent studies pertaining to experimental analysis of T. pallidum ssp. pallidum genome (Nichols) have provided us with solid evidences that support most of the predictions of this work [30]. All of these studies are performed using Nichols strain which shows slight variations from SS14 strain of T. pallidum ssp. pallidum [2]. Besides slight variations in some regions, we have found substantive correlation with data provided by these studies with that of predicted function in the present work. We categorized all these 207 HPs in various functional classes that contain 83 enzymes, 58 binding proteins, 28 transporters, 31 proteins involved in various cellular processes like regulation mechanisms, and 17 proteins exhibiting miscellaneous functions (Fig 1). Various functional classes of these classified HPs are described below.


Identification of functional candidates amongst hypothetical proteins of Treponema pallidum ssp. pallidum.

Naqvi AA, Shahbaaz M, Ahmad F, Hassan MI - PLoS ONE (2015)

Classification of 207 HPs into various groups by utilizing the functional annotation results of various bioinformatics tools.The chart shows that there are 83 enzymes, 28 proteins involve in transportation, 58 binding proteins, 21 proteins involved in cellular processes like transcription, translation, replication etc. and 17 showing miscellaneous functions among 207 HPs from T. pallidum ssp. pallidum.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403809&req=5

pone.0124177.g001: Classification of 207 HPs into various groups by utilizing the functional annotation results of various bioinformatics tools.The chart shows that there are 83 enzymes, 28 proteins involve in transportation, 58 binding proteins, 21 proteins involved in cellular processes like transcription, translation, replication etc. and 17 showing miscellaneous functions among 207 HPs from T. pallidum ssp. pallidum.
Mentions: The genome of the SS14 strain was sequenced to high accuracy by Matejková et al., [2] in 2008 using oligonucleotide array strategy. But errors in key features such as start codons (alternate or otherwise) and stop codons (due to sequencing errors) were observed. Recently, the complete genome sequence of the TPA Mexico, A strain was reported by Pětrošová et al., [28] using the Illumina sequencing technique. However, a recent report on resequencing of T. pallidum ssp. pallidum strains Nichols and SS14 has identified errors in 11.5% of all annotated genes and subsequently corrected [29]. Hence, we assume that the available genome sequence of T. pallidum ssp. pallidum in the database is free from experimental sequencing errors. Extensive sequence analysis of all 444 HPs based on the above mentioned tools helped us to precisely assign function to 207 HPs with high confidence (Table 1). We have also predicted functions for 237 HPs with low level of confidence (S9 Table). We annotated the function of these HPs using protein classification databases such as CATH, Superfamily, Pfam, PANTHER, SYSTERS. Recent studies pertaining to experimental analysis of T. pallidum ssp. pallidum genome (Nichols) have provided us with solid evidences that support most of the predictions of this work [30]. All of these studies are performed using Nichols strain which shows slight variations from SS14 strain of T. pallidum ssp. pallidum [2]. Besides slight variations in some regions, we have found substantive correlation with data provided by these studies with that of predicted function in the present work. We categorized all these 207 HPs in various functional classes that contain 83 enzymes, 58 binding proteins, 28 transporters, 31 proteins involved in various cellular processes like regulation mechanisms, and 17 proteins exhibiting miscellaneous functions (Fig 1). Various functional classes of these classified HPs are described below.

Bottom Line: However, functions of 237 HPs are predicted with less accuracy.We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen.Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India.

ABSTRACT
Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, Treponema pallidum ssp. pallidum, a Gram-negative sphirochaete, is an obligate human parasite. Genome of T. pallidum ssp. pallidum SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of T. pallidum ssp. pallidum using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of T. pallidum ssp. pallidum and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.

No MeSH data available.


Related in: MedlinePlus