Different DNA-binding proteins along with their structures and functions including dps, cbpA, cbpB, many other proteins including future aspects

1. Role of DNA-binding proteins in
bacterial metabolism
PRESENTED BY:
Jaspreet Kaur
L-2013-BS-10-IM

2. Introduction

8. Dps (DNA-binding protein from starved cell) Google image

9. The DNA-binding ability of Dps was initially
discovered when purified Dps was added
separately to supercoiled plasmid DNA and
linear DNA.
From this simple yet elegant binding assay,
several critical DNA-binding properties of
Dps were revealed;

10. 1
• Intense stability of DNA-Dps complex: Dps bound to DNA
prior to heating is able to withstand intense acute heat shock
in excess of 100⁰C and continues to be a highly stable
complex, even after prolonged heating at 65⁰C.
2
• Dps-bound DNA reveals no clear footprint after
digestion with DNAse I: a binding characteristic very similar
to that observed with other histone-like proteins.
3
• Self-aggregation of Dps: This property of E. coli Dps
demonstrates its ability to bind DNA without any apparent
sequence specificity. Immediately upon the addition of DNA,
Dps dodecamers undergo extensive aggregation and quickly
form multilayered plate-like crystals thereafter.

11. DNA is not thought to bind directly to the
surface of the protein; as the surface of Dps
dodecamers does not display DNA-binding
motifs and is dominated by negative charges
that would likely repel negatively charged
DNA molecules. Frenkiel-Krispin et al (2001)
proposed that Dps is unable to directly bind
DNA and that DNA-Dps complex formation
relies on ion bridges formed by Mg2+.

12. Calhoun and Kwon 2010

14. (Calhoun and Kwon

15. PROTEIN IDENTIFIED FUNCTION
CbpA Curved DNA-binding protein A
CbpB Curved DNA-binding protein B
DnaA DNA-binding protein A
Dps DNA-binding protein from starved cells
Fis Factor for inversion stimulation
Hfq Host factor for phage Q beta
H-NS Histone-like nucleoid structuring protein
HU Heat-unstable nucleoid protein
Ici A Inhibitor of chromosome initiation A
IHF Integration host factor
Lrp Leucine-responsive regulatory protein
StpA Suppressor of td mutant phenotype A
H1 Unknown

18. Science Direct image

20. CbpB protein structure (Wikipedia)

22. * Initiation of replication is
regulated through the DnaA
protein.
* Many molecules of DnaA protein
may be needed to assemble on
the origin to allow initiation.

28. (i) RNA Polymerase at promoter is surrounded by curved DNA.
(ii) This curved ADNA wraps around the polymerase.
(iii) H-NS binds to the curved DNA to lock the RNA polymerase at the promoter and
prevents transcription from occurring.
(iv) Environmental signals and transcription factors release the DNA bacterial binding
protein and allows transcription to proceed. Dorman et al 2003

30. HU protein structure
Bahloul et al 2001

37. With manipulation of bacterial genetics, physiology,
multiplexed genome editing and programmable gene
regulation desired results can be obtained.
Researchers have used bacterial DNA-binding proteins to research
Salmonella typhimurium, in which the T6SS genes are activated
from a macrophage or mouse infection. Assays are created that
combine reporter fusions, electrophoretic mobility shift
assay, Dnase footprinting and fluorescence microscopy to
silence the T6SS gene by histone like nucleoid binding
protein (H-NS).