SEA-PHAGES | GTP cyclohydrolase I

Link to this post \| posted 20 Dec, 2017 14:13
best	I've been QC'ing annotations for three Cluster B2 genomes, and I decided to look a little deeper into the GTP Cyclohydrolase I protein (gp6 in all B2's to date). There are several annotations assigned to this gene in non-draft genomes: GTP cyclohydrolase GTP cyclohydrolase I FolE-like FolE Putative T-Fold protein The gene sits at the end of a run of genes associated with queuosine biosynthesis, so it is possible that it could be associated with queuosine. HHpred results indicate very good hits with GTP cyclohydrolase I (FolE) structures and to QueF structures. These are very similar proteins and folds, but they perform distinct transformations in the queuosine pathway, with QueF being specific to the pathway and GTP cyclohydrolase I producing a precursor to the pathway (i.e., the precursor can be shuttled to different pathways other than for queuosine). This paper is highly relevant to making the correct call: http://www.pnas.org/content/102/12/4264.full When looking at the alignments on HHpred, the motifs absent from QueF homologs and present in GTP cyclohydrolase homologs are present in the phage proteins. So that is a strike against the QueF-like designation. However, the fact that it is in an operon with QueCDE-like genes argues for a contextual basis for the QueF-like designation. See Figure 5 from the linked paper. The green QueF unique region is clearly like the cyclohydrolase group in the phage protein. The blue and yellow highlighted catalytic residues for HH and HxC are also in the phage protein. For now, the annotation should be "GTP cyclohydrolase I", which is a specific annotation, still associated with a precursor to the queuosine pathway, and avoids a simple gene name (FolE) derived from model bacteria. A "QueF-like" designation should not be added to the annotation, for instance, like the form of the annotations for the previous genes in the genome as found on the approved function list, "Queosine biosynthesis protein, QueE-like". This would be tempting given the hit probabilities in HHpred, but it would be inaccurate. Finally, it could be interesting to clone this gene at some point and do some old fashioned biochemistry. In this more recent paper, http://www.pnas.org/content/113/11/E1452.full, it is noted that queF-like genes have been identified in other phage. Novel cross reactivity? Who knows. The function "GTP cyclohydrolase I" should be added to the approved function list. Edited 20 Dec, 2017 14:14

Link to this post | posted 20 Dec, 2017 14:13

I've been QC'ing annotations for three Cluster B2 genomes, and I decided to look a little deeper into the GTP Cyclohydrolase I protein (gp6 in all B2's to date). There are several annotations assigned to this gene in non-draft genomes:

GTP cyclohydrolase
GTP cyclohydrolase I
FolE-like
FolE
Putative T-Fold protein

The gene sits at the end of a run of genes associated with queuosine biosynthesis, so it is possible that it could be associated with queuosine.

HHpred results indicate very good hits with GTP cyclohydrolase I (FolE) structures and to QueF structures. These are very similar proteins and folds, but they perform distinct transformations in the queuosine pathway, with QueF being specific to the pathway and GTP cyclohydrolase I producing a precursor to the pathway (i.e., the precursor can be shuttled to different pathways other than for queuosine). This paper is highly relevant to making the correct call: http://www.pnas.org/content/102/12/4264.full

When looking at the alignments on HHpred, the motifs absent from QueF homologs and present in GTP cyclohydrolase homologs are present in the phage proteins. So that is a strike against the QueF-like designation. However, the fact that it is in an operon with QueCDE-like genes argues for a contextual basis for the QueF-like designation. See Figure 5 from the linked paper. The green QueF unique region is clearly like the cyclohydrolase group in the phage protein. The blue and yellow highlighted catalytic residues for HH and HxC are also in the phage protein.

For now, the annotation should be "GTP cyclohydrolase I", which is a specific annotation, still associated with a precursor to the queuosine pathway, and avoids a simple gene name (FolE) derived from model bacteria. A "QueF-like" designation should not be added to the annotation, for instance, like the form of the annotations for the previous genes in the genome as found on the approved function list, "Queosine biosynthesis protein, QueE-like". This would be tempting given the hit probabilities in HHpred, but it would be inaccurate.

Finally, it could be interesting to clone this gene at some point and do some old fashioned biochemistry. In this more recent paper, http://www.pnas.org/content/113/11/E1452.full, it is noted that queF-like genes have been identified in other phage. Novel cross reactivity? Who knows.

The function "GTP cyclohydrolase I" should be added to the approved function list.

Edited 20 Dec, 2017 14:14

Link to this post \| posted 20 Dec, 2017 15:42
welkin	Done!

Link to this post \| posted 20 Dec, 2017 16:03
best

Link to this post \| posted 06 Aug, 2020 15:25
debbie	This has been revised a bit, please check the approved Function Assignment list (Google doc) and the Pre Qo pathway Case Study in the Bioinformatics Guide. August 6, 2020.

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GTP cyclohydrolase I