# HISTORY
24 Mar 2016: Updated by: TOUCHUP-v1.15
14 Mar 2016: Updated by: TOUCHUP-v1.12

# molecular_function
20110125: Eukaryota_PTN000033230 has function DNA topoisomerase type I activity (GO:0003917) 

# cellular_component
20120402: Eukaryota_PTN000033230 is found in nucleolus (GO:0005730) 
20120402: Eukaryota_PTN000033230 is found in replication fork protection complex (GO:0031298) 
20110125: Amniota_PTN000033239 is found in mitochondrial nucleoid (GO:0042645) 
20120402: Amniota_PTN000033239 is NOT found in nucleolus (GO:0005730) 
20120402: Amniota_PTN000033239 is NOT found in replication fork protection complex (GO:0031298) 

# biological_process
20120402: Eukaryota_PTN000033230 participates in chromatin remodeling (GO:0006338) 
20120402: Eukaryota_PTN000033230 participates in chromosome segregation (GO:0007059) 
20120402: Eukaryota_PTN000033230 participates in DNA replication (GO:0006260) 
20110125: Eukaryota_PTN000033230 participates in DNA topological change (GO:0006265) 
20120402: Amniota_PTN000033239 does NOT participate in chromatin remodeling (GO:0006338) 
20120402: Amniota_PTN000033239 does NOT participate in chromosome segregation (GO:0007059) 

# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED

# NOTES
Description of phylogeny
Family is DNA topoisomerase IB.  Duplication at the base of the amniotes, with duplicates encoding nuclear vs mitochondrial proteins.  Duplications also in the teleosts and plants, but not clear if functions differ.  Propagate topoisomerase activity and nuclear location to root, and a change in location for top1 vs top1mt clades in amniotes.
MF
1) The core MF of this protein family is DNA topoisomerase type I activity (GO:0003917).  This function has been well characterized in a number of species across the family.  GO:0003917 is propagated to AN0 with the exception of the following gene based on long branch distance and the fact that only a single (C-terminal) domain is included, that is also found outside topoisomerases:
ARATH xx458
CC
DNA topoisomerase can be found in the nucleus or mitochondria or chloroplast (plants), therefore caution is required for CC annotation. The most parsimonious scenario for this tree is nucleus at the root, with mitochondria for the top1mt clade.
1) AN9 is a clade with clear evidence to be located in the mitochondria based on existing GO annotations and protein descriptions. Term 'mitochondrial nucleoid' is propagated to AN9
BP
The term 'DNA topological change' related to the core function of this protein family was propagated to AN0, as well as DNA replication.  Other processes for the predicted nuclear genes were: meiotic chromosome segregation and chromatin remodeling
Submitted 2011-01-25 DHL
Revised 2011-02-22 DHL
Revised 2012-04-01 PDT

# REFERENCE
Annotation inferences using phylogenetic trees
The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).