Table 4 Replication proteins and their closest homologues

Initiation factors

hupB1

DNA-binding protein hu-beta

Beta chain of heterodimeric histone-like DNA-binding protein, wraps DNA to stabilize and prevent denaturation under extreme environmental conditions

LHK_02345

C. violaceum

hupB2

DNA-binding protein hu-beta

Beta chain of heterodimeric histone-like DNA-binding protein, wraps DNA to stabilize and prevent denaturation under extreme environmental conditions

LHK_02180

C. violaceum

ihfA/himA

Integration host factor subunit alpha

One of the two subunits of integration host factor, a specific DNA-binding protein

LHK_02751

L. nitroferrum

ihfB/himD

Integration host factor subunit beta

One of the two subunits of integration host factor, a specific DNA-binding protein

LHK_00870

L. nitroferrum

dnaA

Chromosomal replication initiator protein DnaA

Initiates and regulates chromosomal replication

LHK_03240

L. nitroferrum

dnaB

Replicative DNA helicase

Initiation and elongation, DNA-dependent ATPase

LHK_01738

C. violaceum

LHK_01506

N. gonorrhoeae

dnaG

DNA primase

Polymerase synthesizes small RNA primers for the Okazaki fragments on both template strands at replication forks

LHK_00463

C. violaceum

ssb

Single-stranded DNA binding protein, Ssb

Forms homotetramer and binds single-stranded DNA to protect susceptible ssDNA from nucleolytic digestion and prevents secondary-structure formation

LHK_01479

M. flagellatus

ssb2

Single-stranded DNA binding protein

Forms a homotetramer and binds single-stranded DNA to protect susceptible ssDNA from nucleolytic digestion and prevents secondary-structure formation

LHK_01496

L. hongkongensis HLHK9 (Ssb protein)

fis

DNA-binding protein Fis

Nucleoid-associated protein

LHK_03207

C. violaceum

hvrA

H-NS like protein

Binds tightly to dsDNA, increases thermal stability and inhibits transcription

LHK_00853

C. violaceum

LHK_00959

C. violaceum

iciA

Chromosome initiation inhibitor

In vitro inhibitor of chromosomal replication initiation

LHK_00797

Acinetobacter baumannii

Elongation factors

dnaE

DNA polymerase III subunit alpha

Subunit of DNA polymerase

LHK_01389

L. nitroferrum

dnaN

DNA polymerase III subunit beta

Subunit of DNA polymerase, initiates replication

LHK_03241

L. nitroferrum

holC

DNA polymerase III subunit chi

Subunit of DNA polymerase

LHK_01415

C. violaceum

holA

DNA polymerase III subunit delta

Subunit of DNA polymerase, interacts with gamma subunit to transfer beta subunit on DNA

LHK_00117

C. violaceum

holB

DNA polymerase III subunit delta'

Subunit of DNA polymerase

LHK_02696

L. nitroferrum

dnaQ

DNA polymerse III subunit epsilon

Subunit of DNA polymerase, a 3'-5' exonuclease possesses proofreading function

LHK_00881

C. violaceum

LHK_01009

C. violaceum

LHK_02526

C. violaceum

dnaX

DNA polymerse III subunits gamma and tau

Subunits of DNA polymerase, tau subunit serves as scaffold in dimerization of the core complex while gamma subunit interacts with delta subunit to transfer beta subunit on DNA

LHK_00963

C. violaceum

rnhA

Ribonuclease HI

Endonuclease degrades RNA of RNA-DNA hybrids, specifies the origin of replication by suppressing initiation at origins other than the oriC locus, removes RNA primers from the Okazaki fragments of lagging strands

LHK_00880

L. nitroferrum

rnhB

Ribonuclease HII

Endonuclease degrades RNA of RNA-DNA hybrids

LHK_00722

L. nitroferrum

polA

DNA polymerase I

DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity

LHK_02983

C. violaceum

ligA

DNA ligase

Catalyzes phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA, essential for DNA replication and repair

LHK_02877

C. taiwanensis

Termination factors

dam

DNA adenine methylase

Methylates DNA within the sequence GATC and protects the DNA from cleavage by restriction endonuclease

LHK_01749

C. violaceum

LHK_02602

C. violaceum

LHK_00398

C. violaceum

hda

DnaA-homolog protein hda

Mediates interactions of DnaA with beta subunit sliding clamp, controls initiation of DNA replication by inhibiting reinitiation of replication

LHK_00510

C. violaceum

Topoisomerases

gyrA

DNA gyrase subunit A

Negatively supercoils closed circular double-stranded DNA, catalyzes interconversion of topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Consists of subunit A and B. Responsible for DNA breakage and rejoining, forms A2B2 tetramer

LHK_01836

L. nitroferrum

gyrB

DNA gyrase subunit B

Negatively supercoils closed circular double-stranded DNA, catalyzes interconversion of topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Consists of subunit A and B. Catalyzes ATP hydrolysis, forms A2B2 tetramer

LHK_03242

L. nitroferrum

parC

DNA topoisomerse 4 subunit A

Essential for chromosome segregation, relaxation of supercoiled DNA. Performs decatenation during replication of circular DNA molecule. Composed of subunits ParC and ParE

LHK_00093

L. nitroferrum

parE

DNA topoisomerase 4 subunit B

Essential for chromosome segregation, relaxation of supercoiled DNA. Performs decatenation during replication of circular DNA molecule. Composed of subunits ParC and ParE

LHK_00606

L. nitroferrum

topA

DNA topoisomerase 1

Conversion of one DNA topological isomer to another

LHK_03143

C. violaceum