1
|
Kim JS, Nanfara MT, Chodavarapu S, Jin KS, Babu VMP, Ghazy MA, Chung S, Kaguni JM, Sutton MD, Cho Y. Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing. Nucleic Acids Res 2017; 45:3888-3905. [PMID: 28168278 PMCID: PMC5397184 DOI: 10.1093/nar/gkx081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 02/03/2017] [Indexed: 11/13/2022] Open
Abstract
Regulatory inactivation of DnaA (RIDA) is one of the major regulatory mechanisms of prokaryotic replication licensing. In RIDA, the Hda–sliding clamp complex loaded onto DNA directly interacts with adenosine triphosphate (ATP)-bound DnaA and stimulates the hydrolysis of ATP to inactivate DnaA. A prediction is that the activity of Hda is tightly controlled to ensure that replication initiation occurs only once per cell cycle. Here, we determined the crystal structure of the Hda–β clamp complex. This complex contains two pairs of Hda dimers sandwiched between two β clamp rings to form an octamer that is stabilized by three discrete interfaces. Two separate surfaces of Hda make contact with the β clamp, which is essential for Hda function in RIDA. The third interface between Hda monomers occludes the active site arginine finger, blocking its access to DnaA. Taken together, our structural and mutational analyses of the Hda–β clamp complex indicate that the interaction of the β clamp with Hda controls the ability of Hda to interact with DnaA. In the octameric Hda–β clamp complex, the inability of Hda to interact with DnaA is a novel mechanism that may regulate Hda function.
Collapse
Affiliation(s)
- Jin S Kim
- Department of Life Science, Pohang University of Science and Technology, 35398 Pohang, South Korea
| | - Michael T Nanfara
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14228, USA
| | - Sundari Chodavarapu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Mi 48824-1319, USA
| | - Kyeong S Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, 35398 Pohang, South Korea
| | - Vignesh M P Babu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14228, USA
| | - Mohamed A Ghazy
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14228, USA
| | - Scisung Chung
- Department of Life Science, Pohang University of Science and Technology, 35398 Pohang, South Korea
| | - Jon M Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Mi 48824-1319, USA
| | - Mark D Sutton
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14228, USA
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, 35398 Pohang, South Korea
| |
Collapse
|
2
|
Likhoshvai VA, Khlebodarova TM. Mathematical modeling of bacterial cell cycle: the problem of coordinating genome replication with cell growth. J Bioinform Comput Biol 2014; 12:1450009. [PMID: 24969747 DOI: 10.1142/s0219720014500097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, we perform an analysis of bacterial cell-cycle models implementing different strategies to coordinately regulate genome replication and cell growth dynamics. It has been shown that the problem of coupling these processes does not depend directly on the dynamics of cell volume expansion, but does depend on the type of cell growth law. Our analysis has distinguished two types of cell growth laws, "exponential" and "linear", each of which may include both exponential and linear patterns of cell growth. If a cell grows following a law of the "exponential" type, including the exponential V(t) = V(0) exp (kt) and linear V(t) = V(0)(1 + kt) dynamic patterns, then the cell encounters the problem of coupling growth rates and replication. It has been demonstrated that to solve the problem, it is sufficient for a cell to have a repressor mechanism to regulate DNA replication initiation. For a cell expanding its volume by a law of the "linear" type, including exponential V(t) = V(0) + V(1) exp (kt) and linear V(t) = V(0) + kt dynamic patterns, the problem of coupling growth rates and replication does not exist. In other words, in the context of the coupling problem, a repressor mechanism to regulate DNA replication, and cell growth laws of the "linear" type displays the attributes of universality. The repressor-type mechanism allows a cell to follow any growth dynamic pattern, while the "linear" type growth law allows a cell to use any mechanism to regulate DNA replication.
Collapse
Affiliation(s)
- Vitaly A Likhoshvai
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentieva 10, Novosibirsk 630090, Russia , Novosibirsk State University, av. Pirogova 2, Novosibirsk 630090, Russia
| | | |
Collapse
|
3
|
Baxter JC, Sutton MD. Evidence for roles of the Escherichia coli Hda protein beyond regulatory inactivation of DnaA. Mol Microbiol 2012; 85:648-68. [PMID: 22716942 DOI: 10.1111/j.1365-2958.2012.08129.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The ATP-bound form of the Escherichia coli DnaA protein binds 'DnaA boxes' present in the origin of replication (oriC) and operator sites of several genes, including dnaA, to co-ordinate their transcription with initiation of replication. The Hda protein, together with the β sliding clamp, stimulates the ATPase activity of DnaA via a process termed regulatory inactivation of DnaA (RIDA), to regulate the activity of DnaA in DNA replication. Here, we used the mutant dnaN159 strain, which expresses the β159 clamp protein, to gain insight into how the actions of Hda are co-ordinated with replication. Elevated expression of Hda impeded growth of the dnaN159 strain in a Pol II- and Pol IV-dependent manner, suggesting a role for Hda managing the actions of these Pols. In a wild-type strain, elevated levels of Hda conferred sensitivity to nitrofurazone, and suppressed the frequency of -1 frameshift mutations characteristic of Pol IV, while loss of hda conferred cold sensitivity. Using the dnaN159 strain, we identified 24 novel hda alleles, four of which supported E. coli viability despite their RIDA defect. Taken together, these findings suggest that although one or more Hda functions are essential for cell viability, RIDA may be dispensable.
Collapse
Affiliation(s)
- Jamie C Baxter
- Department of Biochemistry, The School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | | |
Collapse
|
4
|
Ghosh C, Gupta R, Mukherjee KJ. An inverse metabolic engineering approach for the design of an improved host platform for over-expression of recombinant proteins in Escherichia coli. Microb Cell Fact 2012; 11:93. [PMID: 22759404 PMCID: PMC3537655 DOI: 10.1186/1475-2859-11-93] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 06/11/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A useful goal for metabolic engineering would be to generate non-growing but metabolically active quiescent cells which would divert the metabolic fluxes towards product formation rather than growth. However, for products like recombinant proteins, which are intricately coupled to the growth process it is difficult to identify the genes that need to be knocked-out/knocked-in to get this desired phenotype. To circumvent this we adopted an inverse metabolic engineering strategy which would screen for the desired phenotype and thus help in the identification of genetic targets which need to be modified to get overproducers of recombinant protein. Such quiescent cells would obviate the need for high cell density cultures and increase the operational life span of bioprocesses. RESULTS A novel strategy for generating a library, consisting of randomly down regulated metabolic pathways in E. coli was designed by cloning small genomic DNA fragments in expression vectors. Some of these DNA fragments got inserted in the reverse orientation thereby generating anti-sense RNA upon induction. These anti-sense fragments would hybridize to the sense mRNA of specific genes leading to gene 'silencing'. This library was first screened for slow growth phenotype and subsequently for enhanced over-expression ability. Using Green Fluorescent Protein (GFP) as a reporter protein on second plasmid, we were able to identify metabolic blocks which led to significant increase in expression levels. Thus down-regulating the ribB gene (3, 4 dihydroxy-2-butanone-4-phosphate synthase) led to a 7 fold increase in specific product yields while down regulating the gene kdpD (histidine kinase) led to 3.2 fold increase in specific yields. CONCLUSION We have designed a high throughput screening approach which is a useful tool in the repertoire of reverse metabolic engineering strategies for the generation of improved hosts for recombinant protein expression.
Collapse
Affiliation(s)
- Chaitali Ghosh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | | | | |
Collapse
|
5
|
Essential biological processes of an emerging pathogen: DNA replication, transcription, and cell division in Acinetobacter spp. Microbiol Mol Biol Rev 2010; 74:273-97. [PMID: 20508250 DOI: 10.1128/mmbr.00048-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Within the last 15 years, members of the bacterial genus Acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. The driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. There is an urgent need for new antibacterial compounds to combat the threat imposed by Acinetobacter spp. and other intractable bacterial pathogens. The essential processes of chromosomal DNA replication, transcription, and cell division are attractive targets for the rational design of antimicrobial drugs. The goal of this review is to examine the wealth of genome sequence and gene knockout data now available for Acinetobacter spp., highlighting those aspects of essential systems that are most suitable as drug targets. Acinetobacter spp. show several key differences from other pathogenic gammaproteobacteria, particularly in global stress response pathways. The involvement of these pathways in short- and long-term antibiotic survival suggests that Acinetobacter spp. cope with antibiotic-induced stress differently from other microorganisms.
Collapse
|
6
|
Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol 2009; 191:5706-16. [PMID: 19633089 DOI: 10.1128/jb.00525-09] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromosome replication in Caulobacter crescentus is tightly regulated to ensure that initiation occurs at the right time and only once during the cell cycle. The timing of replication initiation is controlled by both CtrA and DnaA. CtrA binds to and silences the origin. Upon the clearance of CtrA from the cell, the DnaA protein accumulates and allows loading of the replisome at the origin. Here, we identify an additional layer of replication initiation control that is mediated by the HdaA protein. In Escherichia coli, the Hda protein inactivates DnaA after replication initiation. We show that the Caulobacter HdaA homologue is necessary to restrict the initiation of DNA replication to only once per cell cycle and that it dynamically colocalizes with the replisome throughout the cell cycle. Moreover, the transcription of hdaA is directly activated by DnaA, providing a robust feedback regulatory mechanism that adjusts the levels of HdaA to inactivate DnaA.
Collapse
|
7
|
Hegde SR, Manimaran P, Mande SC. Dynamic changes in protein functional linkage networks revealed by integration with gene expression data. PLoS Comput Biol 2008; 4:e1000237. [PMID: 19043542 PMCID: PMC2580820 DOI: 10.1371/journal.pcbi.1000237] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 10/20/2008] [Indexed: 12/12/2022] Open
Abstract
Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein:protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data.
Collapse
Affiliation(s)
- Shubhada R. Hegde
- Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
| | | | - Shekhar C. Mande
- Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
| |
Collapse
|
8
|
Su'etsugu M, Nakamura K, Keyamura K, Kudo Y, Katayama T. Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis. J Biol Chem 2008; 283:36118-31. [PMID: 18977760 DOI: 10.1074/jbc.m803158200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP-DnaA is the initiator of chromosomal replication in Escherichia coli, and the activity of DnaA is regulated by the regulatory inactivation of the DnaA (RIDA) system. In this system, the Hda protein promotes DnaA-ATP hydrolysis to produce inactive ADP-DnaA in a mechanism that is mediated by the DNA-loaded form of the replicase sliding clamp. In this study, we first revealed that hda translation uses an unusual initiation codon, CUG, located downstream of the annotated initiation codon. The CUG initiation codon could be used for restricting the Hda level, as this initiation codon has a low translation efficiency, and the cellular Hda level is only approximately 100 molecules per cell. Hda translated using the correct reading frame was purified and found to have a high RIDA activity in vitro. Moreover, we found that Hda has a high affinity for ADP but not for other nucleotides, including ATP. ADP-Hda was active in the RIDA system in vitro and stable in a monomeric state, whereas apo-Hda formed inactive homomultimers. Both ADP-Hda and apo-Hda could form complexes with the DNA-loaded clamp; however, only ADP-Hda-DNA-clamp complexes were highly functional in the following interaction with DnaA. Formation of ADP-Hda was also observed in vivo, and mutant analysis suggested that ADP binding is crucial for cellular Hda activity. Thus, we propose that ADP is a crucial Hda ligand that promotes the activated conformation of the protein. ADP-dependent monomerization might enable the arginine finger of the Hda AAA+ domain to be accessible to ATP bound to the DnaA AAA+ domain.
Collapse
Affiliation(s)
- Masayuki Su'etsugu
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | | | | | | |
Collapse
|
9
|
Kivistik PA, Putrins M, Püvi K, Ilves H, Kivisaar M, Hõrak R. The ColRS two-component system regulates membrane functions and protects Pseudomonas putida against phenol. J Bacteriol 2006; 188:8109-17. [PMID: 17012397 PMCID: PMC1698186 DOI: 10.1128/jb.01262-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As reported, the two-component system ColRS is involved in two completely different processes. It facilitates the root colonization ability of Pseudomonas fluorescens and is necessary for the Tn4652 transposition-dependent accumulation of phenol-utilizing mutants in Pseudomonas putida. To determine the role of the ColRS system in P. putida, we searched for target genes of response regulator ColR by use of a promoter library. Promoter screening was performed on phenol plates to mimic the conditions under which the effect of ColR on transposition was detected. The library screen revealed the porin-encoding gene oprQ and the alginate biosynthesis gene algD occurring under negative control of ColR. Binding of ColR to the promoter regions of oprQ and algD in vitro confirmed its direct involvement in regulation of these genes. Additionally, the porin-encoding gene ompA(PP0773) and the type I pilus gene csuB were also identified in the promoter screen. However, it turned out that ompA(PP0773) and csuB were actually affected by phenol and that the influence of ColR on these promoters was indirect. Namely, our results show that ColR is involved in phenol tolerance of P. putida. Phenol MIC measurement demonstrated that a colR mutant strain did not tolerate elevated phenol concentrations. Our data suggest that increased phenol susceptibility is also the reason for inhibition of transposition of Tn4652 in phenol-starving colR mutant bacteria. Thus, the current study revealed the role of the ColRS two-component system in regulation of membrane functionality, particularly in phenol tolerance of P. putida.
Collapse
Affiliation(s)
- Paula Ann Kivistik
- Estonian Biocentre and Institute of Molecular and Cell Biology, Tartu University, 51010 Tartu, Estonia
| | | | | | | | | | | |
Collapse
|
10
|
Kongsuwan K, Josh P, Picault MJ, Wijffels G, Dalrymple B. The plasmid RK2 replication initiator protein (TrfA) binds to the sliding clamp beta subunit of DNA polymerase III: implication for the toxicity of a peptide derived from the amino-terminal portion of 33-kilodalton TrfA. J Bacteriol 2006; 188:5501-9. [PMID: 16855240 PMCID: PMC1540049 DOI: 10.1128/jb.00231-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The broad-host-range plasmid RK2 is capable of replication and stable maintenance within a wide range of gram-negative bacterial hosts. It encodes the essential replication initiation protein TrfA, which binds to the host initiation protein, DnaA, at the plasmid origin of replication (oriV). There are two versions of the TrfA protein, 44 and 33 kDa, resulting from alternate in-frame translational starts. We have shown that the smaller protein, TrfA-33, and its 64-residue amino-terminal peptide (designated T1) physically interact with the Escherichia coli beta sliding clamp (beta(2)). This interaction appears to be mediated through a QLSLF peptide motif located near the amino-terminal end of TrfA-33 and T1, which is identical to the previously described eubacterial clamp-binding consensus motif. T1 forms a stable complex with beta(2) and was found to inhibit plasmid RK2 replication in vitro. This specific interaction between T1 and beta(2) and the ability of T1 to block DNA replication have implications for the previously reported cell lethality caused by overproduction of T1. The toxicity of T1 was suppressed when wild-type T1 was replaced with mutant T1, carrying an LF deletion in the beta-binding motif. Previously, T1 toxicity has been shown to be suppressed by Hda, an intermediate regulatory protein which helps prevent over-initiation in E. coli through its interaction with the initiator protein, DnaA, and beta(2). Our results support a model in which T1 toxicity is caused by T1 binding to beta(2), especially when T1 is overexpressed, preventing beta(2) from interacting with host replication proteins such as Hda during the early events of chromosome replication.
Collapse
Affiliation(s)
- Kritaya Kongsuwan
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia QLD 4067, Australia.
| | | | | | | | | |
Collapse
|