1
|
Soultanas P, Janniere L. The metabolic control of DNA replication: mechanism and function. Open Biol 2023; 13:230220. [PMID: 37582405 PMCID: PMC10427196 DOI: 10.1098/rsob.230220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
Metabolism and DNA replication are the two most fundamental biological functions in life. The catabolic branch of metabolism breaks down nutrients to produce energy and precursors used by the anabolic branch of metabolism to synthesize macromolecules. DNA replication consumes energy and precursors for faithfully copying genomes, propagating the genetic material from generation to generation. We have exquisite understanding of the mechanisms that underpin and regulate these two biological functions. However, the molecular mechanism coordinating replication to metabolism and its biological function remains mostly unknown. Understanding how and why living organisms respond to fluctuating nutritional stimuli through cell-cycle dynamic changes and reproducibly and distinctly temporalize DNA synthesis in a wide-range of growth conditions is important, with wider implications across all domains of life. After summarizing the seminal studies that founded the concept of the metabolic control of replication, we review data linking metabolism to replication from bacteria to humans. Molecular insights underpinning these links are then presented to propose that the metabolic control of replication uses signalling systems gearing metabolome homeostasis to orchestrate replication temporalization. The remarkable replication phenotypes found in mutants of this control highlight its importance in replication regulation and potentially genetic stability and tumorigenesis.
Collapse
Affiliation(s)
- Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| |
Collapse
|
2
|
Vadlamani S, Karmakar R, Kumar A, Rajala MS. Non-metabolic role of alpha-enolase in virus replication. Mol Biol Rep 2023; 50:1677-1686. [PMID: 36402937 DOI: 10.1007/s11033-022-08067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/31/2022] [Indexed: 11/20/2022]
Abstract
Viruses are extremely complex and highly evolving microorganisms; thus, it is difficult to analyse them in detail. The virion is believed to contain all the essential components required from its entry to the establishment of a successful infection in a susceptible host cell. Hence, the virion composition is the principal source for its transmissibility and immunogenicity. A virus is completely dependent on a host cell for its replication and progeny production. Occasionally, they recruit and package host proteins into mature virion. These incorporated host proteins are believed to play crucial roles in the subsequent infection, although the significance and the molecular mechanism regulated are poorly understood. One such host protein which is hijacked by several viruses is the glycolytic enzyme, Enolase (Eno-1) and is also packaged into mature virion of several viruses. This enzyme exhibits a highly flexible nature of functions, ranging from metabolic to several non-metabolic activities. All the glycolytic enzymes are known to be moonlighting proteins including enolase. The non-metabolic functions of this moonlighting protein are also highly diverse with respect to its cellular localization. Although very little is known about the virological significance of this enzyme, several of its non-metabolic functions have been observed to influence the virus replication cycle in infected cells. In this review, we have attempted to provide a comprehensive picture of the non-metabolic role of Eno-1, its significance in the virus replication cycle and to stimulate interest around its scope as a therapeutic target for treating viral pathologies.
Collapse
Affiliation(s)
- Satya Vadlamani
- School of Biotechnology, Jawaharlal Nehru University, Delhi, India
| | - Ruma Karmakar
- School of Biotechnology, Jawaharlal Nehru University, Delhi, India
| | - Alok Kumar
- School of Biotechnology, Jawaharlal Nehru University, Delhi, India
| | | |
Collapse
|
3
|
Horemans S, Pitoulias M, Holland A, Pateau E, Lechaplais C, Ekaterina D, Perret A, Soultanas P, Janniere L. Pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication. BMC Biol 2022; 20:87. [PMID: 35418203 PMCID: PMC9009071 DOI: 10.1186/s12915-022-01278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
Background In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences for cell viability and human health, including cancer. To cope with these threats, cells tightly control replication initiation using well-known mechanisms. They also couple DNA synthesis to nutrient richness and growth rate through a poorly understood process thought to involve central carbon metabolism. One such process may involve the cross-species conserved pyruvate kinase (PykA) which catalyzes the last reaction of glycolysis. Here we have investigated the role of PykA in regulating DNA replication in the model system Bacillus subtilis. Results On analysing mutants of the catalytic (Cat) and C-terminal (PEPut) domains of B. subtilis PykA we found replication phenotypes in conditions where PykA is dispensable for growth. These phenotypes are independent from the effect of mutations on PykA catalytic activity and are not associated with significant changes in the metabolome. PEPut operates as a nutrient-dependent inhibitor of initiation while Cat acts as a stimulator of replication fork speed. Disruption of either PEPut or Cat replication function dramatically impacted the cell cycle and replication timing even in cells fully proficient in known replication control functions. In vitro, PykA modulates activities of enzymes essential for replication initiation and elongation via functional interactions. Additional experiments showed that PEPut regulates PykA activity and that Cat and PEPut determinants important for PykA catalytic activity regulation are also important for PykA-driven replication functions. Conclusions We infer from our findings that PykA typifies a new family of cross-species replication control regulators that drive the metabolic control of replication through a mechanism involving regulatory determinants of PykA catalytic activity. As disruption of PykA replication functions causes dramatic replication defects, we suggest that dysfunctions in this new family of universal replication regulators may pave the path to genetic instability and carcinogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01278-3.
Collapse
Affiliation(s)
- Steff Horemans
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Matthaios Pitoulias
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Alexandria Holland
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Emilie Pateau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Christophe Lechaplais
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dariy Ekaterina
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Panos Soultanas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Laurent Janniere
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France.
| |
Collapse
|
4
|
Ge Q, Cao W, Zhu F, Yuan Y, Chen L, Xu J, Li J, Chen H, Ma S, Sun L, Pan H, Taha RH, Yao Q, Chen K. Genomics and proteomics combined analysis revealed the toxicity response of silkworm Bombyx mori to the environmental pathogen Bacillus cereus ZJ-4. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 222:112467. [PMID: 34217115 DOI: 10.1016/j.ecoenv.2021.112467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Bacterial contamination has caused a major public health problem worldwide. Bacillus cereus is a conditional environmental pathogenic bacteria that can cause food poisoning. Whether environmental pathogens can cause widespread transmission in the insect kingdom is unclear. In this study, a Bacillus cereus ZJ-4 was isolated from the hospital environment of Zhenjiang City, Jiangsu Province, China. It was fatal by injection into the silkworm hemolymph. To investigated the potential toxic factors of ZJ-4 and clarified the toxicity response mechanism of silkworm by the ZJ-4 infection. Then, the whole genome of ZJ-4 was sequenced, and the immune mechanism of silkworm fat body to ZJ-4 pathogen was studied by HE pathological section and proteomics. Bacterial genome sequencing indicated that ZJ-4 had 352 drug resistance genes and 6 virulence genes. After 36 h of subcutaneous puncture with ZJ-4 suspension, the pathological changes were obviously found in HE pathological sections of fat body tissue. Comparative proteomic results indicated that differentially expressed proteins are mainly involved in stress reactions, biological regulation, and innate immunity. The qRT-PCR analysis showed that the expressions of β-GRP, Spaetzle, MyD88, Tube and Dorsal genes in Toll pathway were up-regulated, while Pell and Cactus genes were down-regulated; in the antimicrobial peptide pathway, Glv2, Lzm, Mor, and Leb3 genes were up-regulated, while attacin1 and defensin genes were down-regulated; Sod gene was up-regulated, while Cat gene was down-regulated in the antioxidant pathway; Ldh, Sdh, and Mdh genes were down-regulated in glucose metabolism pathway. These results indicated that ZJ-4 can damage the innate immune pathway of silkworm, and also affect the normal immune function of fat body cells.
Collapse
Affiliation(s)
- Qi Ge
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China; School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Weiping Cao
- The Fourth People's Hospital of Zhenjiang, Zhenjiang, Jiangsu 212001, PR China
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Yi Yuan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Liang Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Jia Xu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Jun Li
- Instrumental Analysis and Testing Center, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Han Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Lindan Sun
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Huiwen Pan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China; Zhenjiang First People's Hospital, Zhenjiang, Jiangsu 212002, PR China
| | - Rehab Hosny Taha
- Plant Protection Research Institute, Agricultural Research Center, Egypt
| | - Qin Yao
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China; School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China.
| |
Collapse
|
5
|
Quantitative proteomics reveals the mechanism of slightly acidic electrolyzed water-induced buckwheat sprouts growth and flavonoids enrichment. Food Res Int 2021; 148:110634. [PMID: 34507777 DOI: 10.1016/j.foodres.2021.110634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/21/2022]
Abstract
Previous work has demonstrated that slightly acidic electrolyzed water (SAEW) can promote growth and nutrient enrichment of buckwheat sprouts. In this study, iTRAQ-based quantitative proteomic analysis of SAEW-induced buckwheat sprouts was conducted to explore its mechanism of action. The results showed that 11, 10 and 14 differentially expressed proteins (DEPs) related to energy metabolism, oxidative stress and flavonoid biosynthesis accumulated upwards and downwards, respectively, in SAEW-treated buckwheat. Bioinformatics analysis revealed 118 GO categories were in relation to molecular function. In the SAEW group, a total of 9 DEPs (5 up-regulated) were mapped to 10 significantly enriched KEGG pathways. SAEW induced flavonoid enrichment by modulating zymoproteins (e.g. phenylalanine ammonialyase and flavonol synthase) in phenylpropanoid biosynthesis pathway. qRT-PCR results had consistency with abundance levels of their corresponding proteins. These findings are likely to reveal the molecular mechanisms underlying the biochemical enrichment of buckwheat sprouts by SAEW.
Collapse
|
6
|
The Role of Metabolites in the Link between DNA Replication and Central Carbon Metabolism in Escherichia coli. Genes (Basel) 2020; 11:genes11040447. [PMID: 32325866 PMCID: PMC7231150 DOI: 10.3390/genes11040447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 02/01/2023] Open
Abstract
A direct link between DNA replication regulation and central carbon metabolism (CCM) has been previously demonstrated in Bacillus subtilis and Escherichia coli, as effects of certain mutations in genes coding for replication proteins could be specifically suppressed by particular mutations in genes encoding CCM enzymes. However, specific molecular mechanism(s) of this link remained unknown. In this report, we demonstrate that various CCM metabolites can suppress the effects of mutations in different replication genes of E. coli on bacterial growth, cell morphology, and nucleoid localization. This provides evidence that the CCM-replication link is mediated by metabolites rather than direct protein-protein interactions. On the other hand, action of metabolites on DNA replication appears indirect rather than based on direct influence on the replication machinery, as rate of DNA synthesis could not be corrected by metabolites in short-term experiments. This corroborates the recent discovery that in B. subtilis, there are multiple links connecting CCM to DNA replication initiation and elongation. Therefore, one may suggest that although different in detail, the molecular mechanisms of CCM-dependent regulation of DNA replication are similar in E. coli and B. subtilis, making this regulation an important and common constituent of the control of cell physiology in bacteria.
Collapse
|
7
|
Li G, Shi M, Zhao S, Long Y, Zhu Y. Toxicity response of silkworm intestine to Bacillus cereus SW7-1 pathogen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:1282-1290. [PMID: 31539960 DOI: 10.1016/j.scitotenv.2019.07.349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/20/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
Bacillus cereus is a foodborne pathogen that causes gastrointestinal disease in hosts. The interactions between pathogenic bacteria and silkworms (Bombyx mori L.) involve complex processes. This study aimed to investigate the potential genetic traits of B. cereus SW7-1 and profile the toxicity response of silkworm intestine upon infection by the SW7-1 pathogen. Bacterial genome sequencing and polymerase chain reaction (PCR) detection indicated that B. cereus SW7-1 possesses multiple antibiotic-resistant genes and nine virulence factor genes. Then, silkworm larvae were infected with SW7-1. Comparative transcriptomic analysis revealed that 273 differentially expressed genes (DEGs) with known functions were successfully annotated to the silkworm reference genome. Specifically, 18 DEGs were up-regulated, and 255 DEGs were down-regulated. Compared with the control group, the treated group revealed down-regulated DEGs that are related to stress reactions, immunity, autophagy and apoptosis, DNA replication, ribosomal stress, and carbohydrate metabolism. Quantitative real time PCR analysis showed that many key genes in the Toll pathway, immune deficiency pathway, Janus kinase/signal transducers and activators of transcription pathway, and melanization reaction were up-regulated. Thus, B. cereus SW7-1 pathogen could damage the silkworm intestine, as confirmed by the histological section assay. In addition, SW7-1 can affect the normal physiological functions of intestinal cells. This study contributes toward an improved understanding of the toxicity response of silkworm to the B. cereus pathogen and provides new insights into the molecular mechanisms of the complex interactions between pathogenic microbes and silkworms.
Collapse
Affiliation(s)
- Guannan Li
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.
| | - Min Shi
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Shan Zhao
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China
| | - Yaohang Long
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China
| | - Yong Zhu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing 400715, China.
| |
Collapse
|
8
|
Wieczorek A, Fornalewicz K, Mocarski Ł, Łyżeń R, Węgrzyn G. Double silencing of relevant genes suggests the existence of the direct link between DNA replication/repair and central carbon metabolism in human fibroblasts. Gene 2018; 650:1-6. [PMID: 29407228 DOI: 10.1016/j.gene.2018.01.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 01/15/2023]
Abstract
Genetic evidence for a link between DNA replication and glycolysis has been demonstrated a decade ago in Bacillus subtilis, where temperature-sensitive mutations in genes coding for replication proteins could be suppressed by mutations in genes of glycolytic enzymes. Then, a strong influence of dysfunctions of particular enzymes from the central carbon metabolism (CCM) on DNA replication and repair in Escherichia coli was reported. Therefore, we asked if such a link occurs only in bacteria or it is a more general phenomenon. Here, we demonstrate that effects of silencing (provoked by siRNA) of expression of genes coding for proteins involved in DNA replication and repair (primase, DNA polymerase ι, ligase IV, and topoisomerase IIIβ) on these processes (less efficient entry into the S phase of the cell cycle and decreased level of DNA synthesis) could be suppressed by silencing of specific genes of enzymes from CMM. Silencing of other pairs of replication/repair and CMM genes resulted in enhancement of the negative effects of lower expression levels of replication/repair genes. We suggest that these results may be proposed as a genetic evidence for the link between DNA replication/repair and CMM in human cells, indicating that it is a common biological phenomenon, occurring from bacteria to humans.
Collapse
Affiliation(s)
- Aneta Wieczorek
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Karolina Fornalewicz
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Łukasz Mocarski
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Robert Łyżeń
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| |
Collapse
|
9
|
Fornalewicz K, Wieczorek A, Węgrzyn G, Łyżeń R. Silencing of the pentose phosphate pathway genes influences DNA replication in human fibroblasts. Gene 2017; 635:33-38. [PMID: 28887160 DOI: 10.1016/j.gene.2017.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 08/01/2017] [Accepted: 09/04/2017] [Indexed: 12/21/2022]
Abstract
Previous reports and our recently published data indicated that some enzymes of glycolysis and the tricarboxylic acid cycle can affect the genome replication process by changing either the efficiency or timing of DNA synthesis in human normal cells. Both these pathways are connected with the pentose phosphate pathway (PPP pathway). The PPP pathway supports cell growth by generating energy and precursors for nucleotides and amino acids. Therefore, we asked if silencing of genes coding for enzymes involved in the pentose phosphate pathway may also affect the control of DNA replication in human fibroblasts. Particular genes coding for PPP pathway enzymes were partially silenced with specific siRNAs. Such cells remained viable. We found that silencing of the H6PD, PRPS1, RPE genes caused less efficient enterance to the S phase and decrease in efficiency of DNA synthesis. On the other hand, in cells treated with siRNA against G6PD, RBKS and TALDO genes, the fraction of cells entering the S phase was increased. However, only in the case of G6PD and TALDO, the ratio of BrdU incorporation to DNA was significantly changed. The presented results together with our previously published studies illustrate the complexity of the influence of genes coding for central carbon metabolism on the control of DNA replication in human fibroblasts, and indicate which of them are especially important in this process.
Collapse
Affiliation(s)
- Karolina Fornalewicz
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Aneta Wieczorek
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Robert Łyżeń
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland.
| |
Collapse
|
10
|
Nicolas E, Golemis EA, Arora S. POLD1: Central mediator of DNA replication and repair, and implication in cancer and other pathologies. Gene 2016; 590:128-41. [PMID: 27320729 PMCID: PMC4969162 DOI: 10.1016/j.gene.2016.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/10/2016] [Accepted: 06/14/2016] [Indexed: 02/06/2023]
Abstract
The evolutionarily conserved human polymerase delta (POLD1) gene encodes the large p125 subunit which provides the essential catalytic activities of polymerase δ (Polδ), mediated by 5′–3′ DNA polymerase and 3′–5′ exonuclease moieties. POLD1 associates with three smaller subunits (POLD2, POLD3, POLD4), which together with Replication Factor C and Proliferating Nuclear Cell Antigen constitute the polymerase holoenzyme. Polδ function is essential for replication, with a primary role as the replicase for the lagging strand. Polδ also has an important proofreading ability conferred by the exonuclease activity, which is critical for ensuring replicative fidelity, but also serves to repair DNA lesions arising as a result of exposure to mutagens. Polδ has been shown to be important for multiple forms of DNA repair, including nucleotide excision repair, double strand break repair, base excision repair, and mismatch repair. A growing number of studies in the past decade have linked germline and sporadic mutations in POLD1 and the other subunits of Polδ with human pathologies. Mutations in Polδ in mice and humans lead to genomic instability, mutator phenotype and tumorigenesis. The advent of genome sequencing techniques has identified damaging mutations in the proofreading domain of POLD1 as the underlying cause of some inherited cancers, and suggested that mutations in POLD1 may influence therapeutic management. In addition, mutations in POLD1 have been identified in the developmental disorders of mandibular hypoplasia, deafness, progeroid features and lipodystrophy and atypical Werner syndrome, while changes in expression or activity of POLD1 have been linked to senescence and aging. Intriguingly, some recent evidence suggests that POLD1 function may also be altered in diabetes. We provide an overview of critical Polδ activities in the context of these pathologic conditions.
Collapse
Affiliation(s)
- Emmanuelle Nicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sanjeevani Arora
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
| |
Collapse
|
11
|
Konieczna A, Szczepańska A, Sawiuk K, Węgrzyn G, Łyżeń R. Effects of partial silencing of genes coding for enzymes involved in glycolysis and tricarboxylic acid cycle on the enterance of human fibroblasts to the S phase. BMC Cell Biol 2015; 16:16. [PMID: 26017754 PMCID: PMC4446904 DOI: 10.1186/s12860-015-0062-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/15/2015] [Indexed: 11/16/2022] Open
Abstract
Background Previously published reports indicated that some enzymes of the central carbon metabolism (CCM), particularly those involved in glycolysis and the tricarboxylic acid cycle, may contribute to regulation of DNA replication. However, vast majority of such works was performed with the use of cancer cells, in the light of carcinogenesis. On the other hand, recent experiments conducted on bacterial models provided evidence for the direct genetic link between CCM and DNA replication. Therefore, we asked if silencing of genes coding for glycolytic and/or Krebs cycle enzymes may affect the control of DNA replication in normal human fibroblasts. Results Particular genes coding for these enzymes were partially silenced with specific siRNAs. Such cells remained viable. We found that silencing of certain genes resulted in either less efficient or delayed enterance to the S phase. This concerned following genes: HK2, PFKM, TPI, GAPDH, ENO1, LDHA, CS1, ACO2, SUCLG2, SDHA, FH and MDH2. Decreased levels of expression of HK2, GADPH, CS1, ACO2, FH and MDH2 caused also a substantial impairment in DNA synthesis efficiency. Conclusions The presented results illustrate the complexity of the influence of genes coding for enzymes of glycolysis and the tricarboxylic acid cycle on the control of DNA replication in human fibroblasts, and indicate which of them are especially important in this process. Electronic supplementary material The online version of this article (doi:10.1186/s12860-015-0062-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aleksandra Konieczna
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Aneta Szczepańska
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Karolina Sawiuk
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| | - Robert Łyżeń
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland.
| |
Collapse
|
12
|
Homocysteine thiolactone and N-homocysteinylated protein induce pro-atherogenic changes in gene expression in human vascular endothelial cells. Amino Acids 2015; 47:1319-39. [PMID: 25802182 PMCID: PMC4458266 DOI: 10.1007/s00726-015-1956-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/04/2015] [Indexed: 12/11/2022]
Abstract
Genetic or nutritional deficiencies in homocysteine (Hcy) metabolism lead to hyperhomocysteinemia (HHcy) and cause endothelial dysfunction, a hallmark of atherosclerosis. In addition to Hcy, related metabolites accumulate in HHcy but their role in endothelial dysfunction is unknown. Here, we examine how Hcy-thiolactone, N-Hcy-protein, and Hcy affect gene expression and molecular pathways in human umbilical vein endothelial cells. We used microarray technology, real-time quantitative polymerase chain reaction, and bioinformatic analysis with PANTHER, DAVID, and Ingenuity Pathway Analysis (IPA) resources. We identified 47, 113, and 30 mRNAs regulated by N-Hcy-protein, Hcy-thiolactone, and Hcy, respectively, and found that each metabolite induced a unique pattern of gene expression. Top molecular pathways affected by Hcy-thiolactone were chromatin organization, one-carbon metabolism, and lipid-related processes [−log(P value) = 20–31]. Top pathways affected by N-Hcy-protein and Hcy were blood coagulation, sulfur amino acid metabolism, and lipid metabolism [−log(P value)] = 4–11; also affected by Hcy-thiolactone, [−log(P value) = 8–14]. Top disease related to Hcy-thiolactone, N-Hcy-protein, and Hcy was ‘atherosclerosis, coronary heart disease’ [−log(P value) = 9–16]. Top-scored biological networks affected by Hcy-thiolactone (score = 34–40) were cardiovascular disease and function; those affected by N-Hcy-protein (score = 24–35) were ‘small molecule biochemistry, neurological disease,’ and ‘cardiovascular system development and function’; and those affected by Hcy (score = 25–37) were ‘amino acid metabolism, lipid metabolism,’ ‘cellular movement, and cardiovascular and nervous system development and function.’ These results indicate that each Hcy metabolite uniquely modulates gene expression in pathways important for vascular homeostasis and identify new genes and pathways that are linked to HHcy-induced endothelial dysfunction and vascular disease.
Collapse
|