1
|
Glasscock C, Lucks J, DeLisa M. Engineered Protein Machines: Emergent Tools for Synthetic Biology. Cell Chem Biol 2016; 23:45-56. [DOI: 10.1016/j.chembiol.2015.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022]
|
2
|
Bertonha FB, Barros Filho MDC, Kuasne H, Dos Reis PP, da Costa Prando E, Muñoz JJAM, Roffé M, Hajj GNM, Kowalski LP, Rainho CA, Rogatto SR. PHF21B as a candidate tumor suppressor gene in head and neck squamous cell carcinomas. Mol Oncol 2015; 9:450-62. [PMID: 25454821 PMCID: PMC5528662 DOI: 10.1016/j.molonc.2014.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/22/2014] [Accepted: 09/23/2014] [Indexed: 01/12/2023] Open
Abstract
A significant association between DNA losses on 22q13.31 and head and neck squamous cell carcinomas (HNSCC) was previously reported by our group. Our data indicated that PHF21B gene, mapped on 22q13.31 and encoding a protein with function of chromatin-mediated transcriptional regulation, might be a putative tumor suppressor gene. To test this hypothesis, gene copy number was assessed in 75 HNSCC and 49 matched peripheral blood samples. PHF21B losses were detected in 43 tumors and were significantly associated with patients with familial history of cancer (P < 0.0001); i.e., 36/43 cases showed a positive family history of cancer and 22/36 had first-degree relatives with cancer (P = 0.049). In attempt to investigate other mechanisms for PHF21B loss of function, DNA sequencing was performed and no mutations were detected. We next evaluated the gene expression levels after inhibition of DNA methylation in nine HNSCC and breast carcinoma cell lines. Additionally, PHF21B expression levels were evaluated in colon cancer HCT116 cells as well as in its counterpart DKO (double knockout of DNMT1 and DNMT3B). The higher expression levels of PHF21B gene detected in DKO cells were inversely correlated with the DNA methylation. Further, DNA methylation in the specific promoter-associated CpG Island was investigated. Interestingly, gene hypermethylation was detected in 13/37 tumors: 5/13 HNSCC cases had family history of cancer in first-degree relatives and 8/13 showed both, DNA methylation and PHF21B losses in the tumor sample. One patient had PHF21B loss in the peripheral blood cells and PHF21B methylation in the tumor sample. Additionally, overexpression of PHF21B in cell lines drastically reduces clonogenic and migratory abilities. These data suggest that PHF21B is a novel tumor suppressor gene that can be inactivated by genetic and epigenetic mechanisms in the human cancer.
Collapse
MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 22/metabolism
- DNA Methylation
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Epigenesis, Genetic
- Female
- Gene Expression Regulation
- Gene Knockdown Techniques
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/metabolism
- Head and Neck Neoplasms/pathology
- Humans
- Male
- Middle Aged
- Retrospective Studies
- Tumor Suppressor Proteins/biosynthesis
- Tumor Suppressor Proteins/genetics
Collapse
Affiliation(s)
- Fernanda Bernardi Bertonha
- International Center of Research and Training (CIPE), A. C. Camargo Cancer Center, Sao Paulo, SP 01.508-010, Brazil.
| | | | - Hellen Kuasne
- International Center of Research and Training (CIPE), A. C. Camargo Cancer Center, Sao Paulo, SP 01.508-010, Brazil.
| | - Patricia Pintor Dos Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, UNESP - Sao Paulo State University, Botucatu, SP 18.618-970, Brazil.
| | - Erika da Costa Prando
- Department of Genetics, Institute of Biosciences, UNESP - Sao Paulo State University, Botucatu, SP 18.618-970, Brazil.
| | | | - Martín Roffé
- International Center of Research and Training (CIPE), A. C. Camargo Cancer Center, Sao Paulo, SP 01.508-010, Brazil.
| | - Glaucia Noeli Maroso Hajj
- International Center of Research and Training (CIPE), A. C. Camargo Cancer Center, Sao Paulo, SP 01.508-010, Brazil.
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A. C. Camargo Cancer Center, Sao Paulo, SP 01.508-010, Brazil; National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo, SP 01.509-010, Brazil.
| | - Claudia Aparecida Rainho
- Department of Genetics, Institute of Biosciences, UNESP - Sao Paulo State University, Botucatu, SP 18.618-970, Brazil.
| | - Silvia Regina Rogatto
- International Center of Research and Training (CIPE), A. C. Camargo Cancer Center, Sao Paulo, SP 01.508-010, Brazil; Department of Head and Neck Surgery and Otorhinolaryngology, A. C. Camargo Cancer Center, Sao Paulo, SP 01.508-010, Brazil; Department of Urology, Faculty of Medicine, UNESP - Sao Paulo State University, Botucatu, SP 18.618-970, Brazil.
| |
Collapse
|
3
|
Tay Y, Ho C, Droge P, Ghadessy FJ. Selection of bacteriophage lambda integrases with altered recombination specificity by in vitro compartmentalization. Nucleic Acids Res 2009; 38:e25. [PMID: 19966270 PMCID: PMC2831311 DOI: 10.1093/nar/gkp1089] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In vitro compartmentalization (IVC) was employed for the first time to select for novel bacteriophage λ integrase variants displaying significantly enhanced recombination activity on a non-cognate target DNA sequence. These variants displayed up to 9-fold increased recombination activity over the parental enzyme, and one mutant recombined the chosen non-cognate substrate more efficiently than the parental enzyme recombined the wild-type DNA substrate. The in vitro specificity phenotype extended to the intracellular recombination of episomal vectors in HEK293 cells. Surprisingly, mutations conferring the strongest phenotype do not occur in the λ integrase core-binding domain, which is known to interact directly with cognate target sequences. Instead, they locate to the N-terminal domain which allosterically modulates integrase activity, highlighting a previously unknown role for this domain in directing integrase specificity. The method we describe provides a robust, completely in vitro platform for the development of novel integrase reagent tools for in vitro DNA manipulation and other biotechnological applications.
Collapse
Affiliation(s)
- Yvonne Tay
- p53 Laboratory, 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
| | | | | | | |
Collapse
|
5
|
Desai TA, Rodionov DA, Gelfand MS, Alm EJ, Rao CV. Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res 2009; 37:2493-503. [PMID: 19264798 PMCID: PMC2677863 DOI: 10.1093/nar/gkp079] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The transcriptional program for a gene consists of the promoter necessary for recruiting RNA polymerase along with neighboring operator sites that bind different activators and repressors. From a synthetic biology perspective, if the DNA-binding specificity of these proteins can be changed, then they can be used to reprogram gene expression in cells. While many experimental methods exist for generating such specificity-altering mutations, few computational approaches are available, particularly in the case of bacterial transcription factors. In a previously published computational study of nitrogen oxide metabolism in bacteria, a small number of amino-acid residues were found to determine the specificity within the CRP (cAMP receptor protein)/FNR (fumarate and nitrate reductase regulatory protein) family of transcription factors. By analyzing how these amino acids vary in different regulators, a simple relationship between the identity of these residues and their target DNA-binding sequence was constructed. In this article, we experimentally tested whether this relationship could be used to engineer novel DNA–protein interactions. Using Escherichia coli CRP as a template, we tested eight designs based on this relationship and found that four worked as predicted. Collectively, these results in this work demonstrate that comparative genomics can inform the design of bacterial transcription factors.
Collapse
Affiliation(s)
- Tasha A Desai
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | | | | |
Collapse
|
6
|
Increasing cloning possibilities using artificial zinc finger nucleases. Proc Natl Acad Sci U S A 2008; 105:12785-90. [PMID: 18725642 DOI: 10.1073/pnas.0803618105] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to accurately digest and ligate DNA molecules of different origins is fundamental to modern recombinant DNA research. Only a handful of enzymes are capable of recognizing and cleaving novel and long DNA sequences, however. The slow evolution and engineering of new restriction enzymes calls for alternative strategies to design novel and unique restriction enzymes capable of binding and digesting specific long DNA sequences. Here we report on the use of zinc finger nucleases (ZFNs)-hybrid synthetic restriction enzymes that can be specifically designed to bind and cleave long DNA sequences-for the purpose of DNA recombination. We show that novel ZFNs can be designed for the digestion of specific sequences and can be expressed and used for cloning purposes. We also demonstrate the power of ZFNs in DNA cloning by custom-cloning a target DNA sequence and assembling dual-expression cassettes on a single target plasmid, a task that rarely can be achieved using type-II restriction enzymes. We demonstrate the flexibility of ZFN design and the ability to shuffle monomers of different ZFNs for the digestion of compatible recognition sites through ligation of compatible ends and their cleavage by heterodimer ZFNs. Of no less importance, we show that ZFNs can be designed to recognize and cleave existing DNA sequences for the custom-cloning of native target DNA molecules.
Collapse
|
7
|
Voigt K, Izsvák Z, Ivics Z. Targeted gene insertion for molecular medicine. J Mol Med (Berl) 2008; 86:1205-19. [PMID: 18607557 DOI: 10.1007/s00109-008-0381-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 05/22/2008] [Accepted: 05/27/2008] [Indexed: 11/24/2022]
Abstract
Genomic insertion of a functional gene together with suitable transcriptional regulatory elements is often required for long-term therapeutical benefit in gene therapy for several genetic diseases. A variety of integrating vectors for gene delivery exist. Some of them exhibit random genomic integration, whereas others have integration preferences based on attributes of the targeted site, such as primary DNA sequence and physical structure of the DNA, or through tethering to certain DNA sequences by host-encoded cellular factors. Uncontrolled genomic insertion bears the risk of the transgene being silenced due to chromosomal position effects, and can lead to genotoxic effects due to mutagenesis of cellular genes. None of the vector systems currently used in either preclinical experiments or clinical trials displays sufficient preferences for target DNA sequences that would ensure appropriate and reliable expression of the transgene and simultaneously prevent hazardous side effects. We review in this paper the advantages and disadvantages of both viral and non-viral gene delivery technologies, discuss mechanisms of target site selection of integrating genetic elements (viruses and transposons), and suggest distinct molecular strategies for targeted gene delivery.
Collapse
Affiliation(s)
- Katrin Voigt
- Max Delbrück Center for Molecular Medicine, Robert-Rössle Strasse 10, 13092, Berlin, Germany
| | | | | |
Collapse
|
9
|
Abstract
Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.
Collapse
Affiliation(s)
- Ling Yuan
- Department of Plant and Soil Sciences, and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.
| | | | | | | |
Collapse
|