Limits...
A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case.

Yu GX, Snyder EE, Boyle SM, Crasta OR, Czar M, Mane SP, Purkayastha A, Sobral B, Setubal JC - Nucleic Acids Res. (2007)

Bottom Line: GenVar also helps identify gene disruptions probably caused by sequencing errors.We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes.Brucella is an important human pathogen and zoonotic agent.

View Article: PubMed Central - PubMed

Affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.

ABSTRACT
We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes. Brucella is an important human pathogen and zoonotic agent. The analysis revealed hundreds of missed gene calls, new split genes and indels, several of which are species specific and hence provide valuable clues to the understanding of the genome basis of Brucella pathogenicity and host specificity.

Show MeSH

Related in: MedlinePlus

Pairwise alignments of the Type IV secretion system protein VirB10 gene sequence. Panel I shows the alignment between the B. abortus 9-941 gene (gi/62317019) against that of B. melitensis 16M (gi/17988378), and panel II shows the alignment between the B. suis 1330 gene (gi/23499827) also against that of B. melitensis 16M. The two alignments show that B. melintensis 16M has an 8-residue deletion with respect to its orthologs in B. abortus 9-941 and B. suis 1330 (blue sections in panels I and II). B. suis 1330 has a 3-residue insertion (yellow part of panel II).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1919506&req=5

Figure 4: Pairwise alignments of the Type IV secretion system protein VirB10 gene sequence. Panel I shows the alignment between the B. abortus 9-941 gene (gi/62317019) against that of B. melitensis 16M (gi/17988378), and panel II shows the alignment between the B. suis 1330 gene (gi/23499827) also against that of B. melitensis 16M. The two alignments show that B. melintensis 16M has an 8-residue deletion with respect to its orthologs in B. abortus 9-941 and B. suis 1330 (blue sections in panels I and II). B. suis 1330 has a 3-residue insertion (yellow part of panel II).

Mentions: An 8-residue deletion was found in the gene coding for type IV secretion system protein VirB10 when compared to B. abortus 9-941, B. abortus 2308 and B. suis 1330; the same gene in B. suis 1330 has a 3-residue insertion unique to this species, among those compared (Figure 4). VirB10, as an energy-sensing bridge between the inner and outer membranes, is essential for the transfer of substrates from the inner to the outer membrane (17). While almost all type IV genes are highly conserved among the four Brucella genomes, virB10 is the only one that has indel polymorphisms. The first is a three-proline insertion specific to B. suis 1330 (Figure 4), part of a proline-rich region, which is a predicted extended structure in the periplasm (18). The second is an 8-residue insertion specific to both B. abortus and to B. suis 1330. Although the biological significance of such indels has yet to be investigated, their importance could not be over-emphasized considering the nature of this gene and its associated protein complex. The type IV secretion system is used by many Gram-negative bacteria to translocate virulence factors into eukaryotic cells, to mediate conjugative transfer of broad-host-range plasmids, and to facilitate host–pathogen interactions that enable bacterial survival in widely different habitats (19). Thus, experiments based on the results of this analysis may provide experimental data that would help determine the role these variants play in host specificity and other pathogenesis-related functions.Figure 4.


A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case.

Yu GX, Snyder EE, Boyle SM, Crasta OR, Czar M, Mane SP, Purkayastha A, Sobral B, Setubal JC - Nucleic Acids Res. (2007)

Pairwise alignments of the Type IV secretion system protein VirB10 gene sequence. Panel I shows the alignment between the B. abortus 9-941 gene (gi/62317019) against that of B. melitensis 16M (gi/17988378), and panel II shows the alignment between the B. suis 1330 gene (gi/23499827) also against that of B. melitensis 16M. The two alignments show that B. melintensis 16M has an 8-residue deletion with respect to its orthologs in B. abortus 9-941 and B. suis 1330 (blue sections in panels I and II). B. suis 1330 has a 3-residue insertion (yellow part of panel II).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1919506&req=5

Figure 4: Pairwise alignments of the Type IV secretion system protein VirB10 gene sequence. Panel I shows the alignment between the B. abortus 9-941 gene (gi/62317019) against that of B. melitensis 16M (gi/17988378), and panel II shows the alignment between the B. suis 1330 gene (gi/23499827) also against that of B. melitensis 16M. The two alignments show that B. melintensis 16M has an 8-residue deletion with respect to its orthologs in B. abortus 9-941 and B. suis 1330 (blue sections in panels I and II). B. suis 1330 has a 3-residue insertion (yellow part of panel II).
Mentions: An 8-residue deletion was found in the gene coding for type IV secretion system protein VirB10 when compared to B. abortus 9-941, B. abortus 2308 and B. suis 1330; the same gene in B. suis 1330 has a 3-residue insertion unique to this species, among those compared (Figure 4). VirB10, as an energy-sensing bridge between the inner and outer membranes, is essential for the transfer of substrates from the inner to the outer membrane (17). While almost all type IV genes are highly conserved among the four Brucella genomes, virB10 is the only one that has indel polymorphisms. The first is a three-proline insertion specific to B. suis 1330 (Figure 4), part of a proline-rich region, which is a predicted extended structure in the periplasm (18). The second is an 8-residue insertion specific to both B. abortus and to B. suis 1330. Although the biological significance of such indels has yet to be investigated, their importance could not be over-emphasized considering the nature of this gene and its associated protein complex. The type IV secretion system is used by many Gram-negative bacteria to translocate virulence factors into eukaryotic cells, to mediate conjugative transfer of broad-host-range plasmids, and to facilitate host–pathogen interactions that enable bacterial survival in widely different habitats (19). Thus, experiments based on the results of this analysis may provide experimental data that would help determine the role these variants play in host specificity and other pathogenesis-related functions.Figure 4.

Bottom Line: GenVar also helps identify gene disruptions probably caused by sequencing errors.We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes.Brucella is an important human pathogen and zoonotic agent.

View Article: PubMed Central - PubMed

Affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA.

ABSTRACT
We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes. Brucella is an important human pathogen and zoonotic agent. The analysis revealed hundreds of missed gene calls, new split genes and indels, several of which are species specific and hence provide valuable clues to the understanding of the genome basis of Brucella pathogenicity and host specificity.

Show MeSH
Related in: MedlinePlus