Genome Property Definition Page

Accession

GenProp0701

Name

DNA sulfur modification system dnd

Type

SYSTEM

Description

Several 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 Role

Conserved

Parent Property

GenProp0116: 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

Components

Step Name	Step Num	Required	Evidence (Method)
dnd system cysteine sulfurtransferase	DndA	NO	PF00266 (HMM-CLUST): aminotransferase, class V TIGR03235 (HMM): cysteine desulfurase DndA
dnd operon putative ATPase DndB	DndB	NO	TIGR03233 (HMM): DNA sulfur modification protein DndB
dnd operon putative sulfurtransferase DndC	DndC	YES	TIGR03183 (HMM): putative sulfurtransferase DndC
dnd operon putative ATPase DndD	DndD	YES	TIGR03185 (HMM): DNA sulfur modification protein DndD
dnd operon putative carboxylase DndE	DndE	YES	TIGR03184 (HMM): DNA sulfur modification protein DndE
DNA phosphorothioation-dependent restriction protein DptF	DptF	NO	TIGR03238 (HMM): DNA phosphorothioation-dependent restriction protein DptF
DNA phosphorothioation-dependent restriction protein DptG	DptG	NO	TIGR03236 (HMM): DNA phosphorothioation-dependent restriction protein DptG
DNA phosphorothioation-dependent restriction protein DptH	DptH	NO	TIGR03237 (HMM): DNA phosphorothioation-dependent restriction protein DptH
dnd system-associated protein 4	assoc4	NO	TIGR04062 (HMM): dnd system-associated protein 4

Parent Properties

Accession	Name
GenProp0116	DNA metabolism
GenProp1067	Defense systems

Sibling Properties

Accession	Name
GenProp0115	DNA repair
GenProp0198	ruvABC Holliday junction complex
GenProp0263	DNA polymerase III, bacterial
GenProp0455	restriction enzyme system, type I
GenProp0487	repABC-type alpha-proteobacterial replicon(s)
GenProp0650	type II restriction system, Alw26I/Eco31I/Esp3I family
GenProp0806	replication initiation, bacterial
GenProp0977	DNA ligase/helicase system
GenProp1081	replication restart, PriA/PriB primosome pathway
GenProp1095	exodeoxyribonuclease VII
GenProp0021	CRISPR region