Genome Property Definition Page

NameDNA sulfur modification system dnd
DescriptionSeveral bacteria have an unusual DNA phenotype, Dnd (degradation during electrophoresis). This property results from a sulfur modification on a G residue, shown in one example to occur at a rate of about one sulfur per 6000 base pairs. Study of Streptomyces lividans 1326 showed a stringent requirement for a core motif GGCC within a longer recognition region represented as cGGCCgccg (see PMID: 17439960). Five characteristic genes, including a predicted cysteine sulfurtransferase related to IscS, appear responsible for the dnd phenotype. Through comparative genomic studies, we find that the, beyond a core set of the three genes dndC, dndD, and dndE, other proteins may be associated. That is, they show up specifically in genomes that carry dndCDE and occur nearby, but do not show up in all such genomes. Models TIGR03236, TIGR03237, and TIGR03238 are examples of such dnd-associated protein families.
JCVI RoleConserved
Parent PropertyGenProp0116: DNA metabolism
GenProp1067: Defense systems
Literature References
[ 1 ]Zhou X, He X, Liang J, Li A, Xu T, Kieser T, Helmann JD, Deng Z  A novel DNA modification by sulphur.  Mol Microbiol. 2005 Sep;57(5):1428-38.  PMID 16102010
[ 2 ] Liang J, Wang Z, He X, Li J, Zhou X, Deng Z   DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.   Nucleic Acids Res. 2007;35(9):2944-54.  PMID 17439960
[ 3 ]Xu T, Liang J, Chen S, Wang L, He X, You D, Wang Z, Li A, Xu Z, Zhou X, Deng Z  DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus.  BMC Microbiol. 2009 Feb 20;9:41.  PMID 19232083

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
dnd system cysteine sulfurtransferaseDndANOPF00266 (HMM-CLUST): aminotransferase, class V
TIGR03235 (HMM): cysteine desulfurase DndA
dnd operon putative ATPase DndBDndBNOTIGR03233 (HMM): DNA sulfur modification protein DndB
dnd operon putative sulfurtransferase DndCDndCYESTIGR03183 (HMM): putative sulfurtransferase DndC
dnd operon putative ATPase DndDDndDYESTIGR03185 (HMM): DNA sulfur modification protein DndD
dnd operon putative carboxylase DndEDndEYESTIGR03184 (HMM): DNA sulfur modification protein DndE
DNA phosphorothioation-dependent restriction protein DptFDptFNOTIGR03238 (HMM): DNA phosphorothioation-dependent restriction protein DptF
DNA phosphorothioation-dependent restriction protein DptGDptGNOTIGR03236 (HMM): DNA phosphorothioation-dependent restriction protein DptG
DNA phosphorothioation-dependent restriction protein DptHDptHNOTIGR03237 (HMM): DNA phosphorothioation-dependent restriction protein DptH
dnd system-associated protein 4assoc4NOTIGR04062 (HMM): dnd system-associated protein 4

Parent Properties
GenProp0116DNA metabolism
GenProp1067Defense systems

Sibling Properties
GenProp0115DNA repair
GenProp0198ruvABC Holliday junction complex
GenProp0263DNA polymerase III, bacterial
GenProp0455restriction enzyme system, type I
GenProp0487repABC-type alpha-proteobacterial replicon(s)
GenProp0650type II restriction system, Alw26I/Eco31I/Esp3I family
GenProp0806replication initiation, bacterial
GenProp0977DNA ligase/helicase system
GenProp1081replication restart, PriA/PriB primosome pathway
GenProp1095exodeoxyribonuclease VII
GenProp0021CRISPR region