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Xu T, Mitra R, Tan D, Li Z, Zhou C, Chen T, Xie Z, Han J. Utilization of gene manipulation system for advancing the biotechnological potential of halophiles: A review. Biotechnol Adv 2024; 70:108302. [PMID: 38101552 DOI: 10.1016/j.biotechadv.2023.108302] [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: 10/09/2023] [Revised: 12/02/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023]
Abstract
Halophiles are salt-loving microorganisms known to have their natural resistance against media contamination even when cultivated in nonsterile and continuous bioprocess system, thus acting as promising cell factories for Next Generation of Industrial Biotechnology (NGIB). NGIB - a successor to the traditional industrial biotechnology, is a more sustainable and efficient bioprocess technology while saving energy and water in a more convenient way as well as reducing the investment cost and skilled workforce requirement. Numerous studies have achieved intriguing outcomes during synthesis of different metabolite using halophiles such as polyhydroxyalkanoates (PHA), ectoine, biosurfactants, and carotenoids. Present-day development in genetic maneuverings have shown optimistic effects on the industrial applications of halophiles. However, viable and competent genetic manipulation system and gene editing tools are critical to accelerate the process of halophile engineering. With the aid of such powerful gene manipulation systems, exclusive microbial chassis are being crafted with desirable features to breed another innovative area of research such as synthetic biology. This review provides an aerial perspective on how the expansion of adaptable gene manipulation toolkits in halophiles are contributing towards biotechnological advancement, and also focusses on their subsequent application for production improvement. This current methodical and comprehensive review will definitely help the scientific fraternity to bridge the gap between challenges and opportunities in halophile engineering.
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Affiliation(s)
- Tong Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Ruchira Mitra
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; International College, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Dan Tan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Zhengjun Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; College of Biochemical Engineering, Beijing Union University, Beijing 100023, People's Republic of China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing 100191, People's Republic of China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
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Lv J, Wang S, Zeng C, Huang Y, Chen X. Construction of a shuttle expression vector with a promoter functioning in both halophilic Archaea and Bacteria. FEMS Microbiol Lett 2013; 349:9-15. [PMID: 24106795 DOI: 10.1111/1574-6968.12278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/12/2013] [Indexed: 11/27/2022] Open
Abstract
A shuttle expression vector, designated as pAJ, was constructed based on the Haloferax volcanii-Escherichia coli shuttle vector pSY1. This new construct contains the amyH promoter from Haloarcula hispanica and was able to confer the promoter activity in both Hfx. volcanii and E. coli. pAJ successfully expressed proteins in Hfx. volcanii or E. coli, rendering it feasible to express target proteins in corresponding domains. In addition, pAJ contains a multiple cloning site with 11 restriction sites and a 6×His tag sequence, and the vector size was decreased to 8903 bp. To the best of our knowledge, pAJ is the first reported shuttle expression vector that can express proteins in both Bacteria and Archaea. Importantly, pAJ can even express the haloarchaeal heat shock protein DnaK in both domains. In conclusion, this novel vector only provides researchers with a new means to manipulate genes or express proteins in Haloarchaea but also serves as a convenient tool for the comparative study of the function of some highly conserved genes in Haloarchaea and in Bacteria.
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Affiliation(s)
- Jie Lv
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
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Zeng C, Zhao YZ, Cui CZ, Zhang H, Zhu JY, Tang XF, Shen P, Huang YP, Chen XD. Characterization of the Haloarcula hispanica amyH gene promoter, an archaeal promoter that confers promoter activity in Escherichia coli. Gene 2009; 442:1-7. [PMID: 19376209 DOI: 10.1016/j.gene.2009.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Revised: 04/03/2009] [Accepted: 04/09/2009] [Indexed: 11/28/2022]
Abstract
Archaea form a third domain of life that is distinct from Bacteria and Eukarya. According to the current knowledge, the basal transcription machinery of Archaea (including the core promoter architecture, the RNA polymerase, and the basal transcription factors) closely resembles that of Eukarya in structure and function, while differing considerably from the bacterial paradigm. In the present study, the promoter region of the halophilic archaeon Haloarcula hispanica's amyH gene was isolated and characterized, and it was surprisingly revealed that the amyH gene promoter could confer promoter activity (i.e., drive transcription) in haloarchaea (Archaea) as well as in Escherichia coli (Bacteria), where the transcriptions driven are initiated at the same adenine base. Further investigation revealed that the core structure of the amyH gene promoter possesses a combination of the typical structural characteristics of archaeal promoter, which are eukaryotic-like, and those of bacterial promoter. Our results indicate that the core promoter structures of some archaeal genes may possess a combination of eukaryotic- and bacterial-like features, and moreover, suggest a possible evolutionary relationship between basal transcription signals and transcription mechanisms of Archaea and the other two domains of life.
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Lu Q, Han J, Zhou L, Coker JA, DasSarma P, DasSarma S, Xiang H. Dissection of the regulatory mechanism of a heat-shock responsive promoter in Haloarchaea: a new paradigm for general transcription factor directed archaeal gene regulation. Nucleic Acids Res 2008; 36:3031-42. [PMID: 18390887 PMCID: PMC2396416 DOI: 10.1093/nar/gkn152] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Multiple general transcription factors (GTFs), TBP and TFB, are present in many haloarchaea, and are deemed to accomplish global gene regulation. However, details and the role of GTF-directed transcriptional regulation in stress response are still not clear. Here, we report a comprehensive investigation of the regulatory mechanism of a heat-induced gene (hsp5) from Halobacterium salinarum. We demonstrated by mutation analysis that the sequences 5′ and 3′ to the core elements (TATA box and BRE) of the hsp5 promoter (Phsp5) did not significantly affect the basal and heat-induced gene expression, as long as the transcription initiation site was not altered. Moreover, the BRE and TATA box of Phsp5 were sufficient to render a nonheat-responsive promoter heat-inducible, in both Haloferax volcanii and Halobacterium sp. NRC-1. DNA–protein interactions revealed that two heat-inducible GTFs, TFB2 from H. volcanii and TFBb from Halobacterium sp. NRC-1, could specifically bind to Phsp5 likely in a temperature-dependent manner. Taken together, the heat-responsiveness of Phsp5 was mainly ascribed to the core promoter elements that were efficiently recognized by specific heat-induced GTFs at elevated temperature, thus providing a new paradigm for GTF-directed gene regulation in the domain of Archaea.
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Affiliation(s)
- Qiuhe Lu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
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Coker JA, DasSarma S. Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA. BMC Genet 2007; 8:61. [PMID: 17892563 PMCID: PMC2121645 DOI: 10.1186/1471-2156-8-61] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 09/24/2007] [Indexed: 11/10/2022] Open
Abstract
Background Archaea are prokaryotic organisms with simplified versions of eukaryotic transcription systems. Genes coding for the general transcription factors TBP and TFB are present in multiple copies in several Archaea, including Halobacterium sp. NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters. Results We attempted to knock out all six TBP and seven TFB genes in Halobacterium sp. NRC-1 using the ura3-based gene deletion system. Knockouts were obtained for six out of thirteen genes, tbpCDF and tfbACG, indicating that they are not essential for cell viability under standard conditions. Screening of a population of 1,000 candidate mutants showed that genes which did not yield mutants contained less that 0.1% knockouts, strongly suggesting that they are essential. The transcriptomes of two mutants, ΔtbpD and ΔtfbA, were compared to the parental strain and showed coordinate down regulation of many genes. Over 500 out of 2,677 total genes were regulated in the ΔtbpD and ΔtfbA mutants with 363 regulated in both, indicating that over 10% of genes in both strains require the action of both TbpD and TfbA for normal transcription. Culturing studies on the ΔtbpD and ΔtfbA mutant strains showed them to grow more slowly than the wild-type at an elevated temperature, 49°C, and they showed reduced viability at 56°C, suggesting TbpD and TfbA are involved in the heat shock response. Alignment of TBP and TFB protein sequences suggested the expansion of the TBP gene family, especially in Halobacterium sp. NRC-1, and TFB gene family in representatives of five different genera of haloarchaea in which genome sequences are available. Conclusion Six of thirteen TBP and TFB genes of Halobacterium sp. NRC-1 are non-essential under standard growth conditions. TbpD and TfbA coordinate the expression of over 10% of the genes in the NRC-1 genome. The ΔtbpD and ΔtfbA mutant strains are temperature sensitive, possibly as a result of down regulation of heat shock genes. Sequence alignments suggest the existence of several families of TBP and TFB transcription factors in Halobacterium which may function in transcription of different classes of genes.
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Affiliation(s)
- James A Coker
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Shiladitya DasSarma
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 East Pratt Street, Baltimore, MD 21202, USA
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Reiss DJ, Baliga NS, Bonneau R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics 2006; 7:280. [PMID: 16749936 PMCID: PMC1502140 DOI: 10.1186/1471-2105-7-280] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Accepted: 06/02/2006] [Indexed: 12/23/2022] Open
Abstract
Background The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided by reducing the dimensionality of the search space by means of clustering genes into putatively co-regulated groups, as opposed to those that are simply co-expressed. Be cause genes may be co-regulated only across a subset of all observed experimental conditions, biclustering (clustering of genes and conditions) is more appropriate than standard clustering. Co-regulated genes are also often functionally (physically, spatially, genetically, and/or evolutionarily) associated, and such a priori known or pre-computed associations can provide support for appropriately grouping genes. One important association is the presence of one or more common cis-regulatory motifs. In organisms where these motifs are not known, their de novo detection, integrated into the clustering algorithm, can help to guide the process towards more biologically parsimonious solutions. Results We have developed an algorithm, cMonkey, that detects putative co-regulated gene groupings by integrating the biclustering of gene expression data and various functional associations with the de novo detection of sequence motifs. Conclusion We have applied this procedure to the archaeon Halobacterium NRC-1, as part of our efforts to decipher its regulatory network. In addition, we used cMonkey on public data for three organisms in the other two domains of life: Helicobacter pylori, Saccharomyces cerevisiae, and Escherichia coli. The biclusters detected by cMonkey both recapitulated known biology and enabled novel predictions (some for Halobacterium were subsequently confirmed in the laboratory). For example, it identified the bacteriorhodopsin regulon, assigned additional genes to this regulon with apparently unrelated function, and detected its known promoter motif. We have performed a thorough comparison of cMonkey results against other clustering methods, and find that cMonkey biclusters are more parsimonious with all available evidence for co-regulation.
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Affiliation(s)
- David J Reiss
- Institute for Systems Biology, 1441 N. 34th St. Seattle, WA 98103-8904, USA
| | - Nitin S Baliga
- Institute for Systems Biology, 1441 N. 34th St. Seattle, WA 98103-8904, USA
| | - Richard Bonneau
- New York University Dept. of Biology, Dept. of Computer Science, New York, USA
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DasSarma S, Berquist BR, Coker JA, DasSarma P, Müller JA. Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1. SALINE SYSTEMS 2006; 2:3. [PMID: 16542428 PMCID: PMC1447603 DOI: 10.1186/1746-1448-2-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 03/16/2006] [Indexed: 11/21/2022]
Abstract
Halobacteriumsp. NRC-1 is an extremely halophilic archaeon that is easily cultured and genetically tractable. Since its genome sequence was completed in 2000, a combination of genetic, transcriptomic, proteomic, and bioinformatic approaches have provided insights into both its extremophilic lifestyle as well as fundamental cellular processes common to all life forms. Here, we review post-genomic research on this archaeon, including investigations of DNA replication and repair systems, phototrophic, anaerobic, and other physiological capabilities, acidity of the proteome for function at high salinity, and role of lateral gene transfer in its evolution.
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Affiliation(s)
- Shiladitya DasSarma
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Brian R Berquist
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - James A Coker
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Priya DasSarma
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Jochen A Müller
- Department of Biology, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA
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Berquist BR, Müller JA, DasSarma S. 27 Genetic Systems for Halophilic Archaea. J Microbiol Methods 2006. [DOI: 10.1016/s0580-9517(08)70030-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Bartlett MS. Determinants of transcription initiation by archaeal RNA polymerase. Curr Opin Microbiol 2005; 8:677-84. [PMID: 16249119 DOI: 10.1016/j.mib.2005.10.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 10/13/2005] [Indexed: 12/27/2022]
Abstract
Transcription in Archaea is catalyzed by an RNA polymerase that is most similar to eukaryotic RNA polymerases both in subunit composition and in transcription initiation factor requirements. Recent studies on archaeal transcription in diverse members of this domain have contributed new details concerning the functions of promoters and transcription factors in guiding initiation by RNA polymerase, and phylogenetic arguments have allowed modeling of archaeal transcription initiation complexes by comparison with recently described models of eukaryotic and bacterial transcription initiation complexes. Important new advances in reconstitution of archaeal transcription complexes from fully recombinant components is permitting testing of hypotheses derived from and informed by these structural models, and will help bring the study of archaeal transcription to the levels of understanding currently enjoyed by bacterial and eukaryotic RNA polymerase II transcription.
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Affiliation(s)
- Michael S Bartlett
- Department of Biology, Portland State University, SB2 Room 246, 1719 SW 10th Avenue, Portland, OR 97201, USA.
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Ouhammouch M, Langham GE, Hausner W, Simpson AJ, El-Sayed NMA, Geiduschek EP. Promoter architecture and response to a positive regulator of archaeal transcription. Mol Microbiol 2005; 56:625-37. [PMID: 15819620 DOI: 10.1111/j.1365-2958.2005.04563.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. Particular interest attaches to how these bacterial-type effectors, especially activators, regulate a eukaryote-like transcription system. The hyperthermophilic archaeon Methanocaldococcus jannaschii encodes a potent transcriptional activator, Ptr2, related to the Lrp/AsnC family of bacterial regulators. Ptr2 activates rubredoxin 2 (rb2) transcription through a bipartite upstream activating site (UAS), and conveys its stimulatory effects on its cognate transcription machinery through direct recruitment of the TATA binding protein (TBP). A functional dissection of the highly constrained architecture of the rb2 promoter shows that a 'one-site' minimal UAS suffices for activation by Ptr2, and specifies the required placement of this site. The presence of such a simplified UAS upstream of the natural rubrerythrin (rbr) promoter also suffices for positive regulation by Ptr2 in vitro, and TBP recruitment remains the primary means of transcriptional activation at this promoter.
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Affiliation(s)
- Mohamed Ouhammouch
- Division of Biological Sciences and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA.
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Weston AD, Baliga NS, Bonneau R, Hood L. Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:345-57. [PMID: 15338636 DOI: 10.1101/sqb.2003.68.345] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- A D Weston
- Institute for Systems Biology, Seattle, Washington 98103-8904, USA
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Wu HY, Fang M. DNA supercoiling and transcription control: a model from the study of suppression of the leu-500 mutation in Salmonella typhimurium topA- strains. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 73:43-68. [PMID: 12882514 DOI: 10.1016/s0079-6603(03)01002-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA supercoiling is known to modulate gene expression. The functional relationship between DNA supercoiling and transcription initiation has been established genetically and biochemically. The molecular mechanism whereby DNA supercoiling regulates gene expression remains unclear however. Quite commonly, the same gene responds to the same DNA supercoiling change differently when the gene is positioned at different locations. Such strong positional effects on gene expression suggest that rather than the overall DNA supercoiling change, the variation of DNA supercoiling at a local site might be important for transcription control. We have started to understand the local DNA supercoiling dynamic on the chromosome. As a primary source of local DNA supercoiling fluctuation, transcription-driven DNA supercoiling is important in determining the chromosome supercoiling dynamic and theoretically, therefore, for transcription control as well. Indeed, by studying the coordinated expression of genes in the ilvIH-leuO-leuABCD gene cluster, we found that transcription-driven DNA supercoiling governs the expression of a group of functionally related genes in a sequential manner. Based on the findings in this model system, we put forward the possible mechanisms whereby DNA supercoiling plays its role in transcription control.
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Affiliation(s)
- Hai-Young Wu
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, Michigan 48201, USA
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Affiliation(s)
- J Soppa
- Institute for Microbiology, Biocentre Niederursel, J. W. Goethe University Frankfurt, D-60439 Frankfurt, Germany
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Baliga NS. Promoter analysis by saturation mutagenesis. Biol Proced Online 2001; 3:64-69. [PMID: 12734578 PMCID: PMC145547 DOI: 10.1251/bpo24] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2001] [Revised: 12/15/2001] [Accepted: 12/17/2001] [Indexed: 11/23/2022] Open
Abstract
Gene expression and regulation are mediated by DNA sequences, in most instances, directly upstream to the coding sequences by recruiting transcription factors, regulators, and a RNA polymerase in a spatially defined fashion. Few nucleotides within a promoter make contact with the bound proteins. The minimal set of nucleotides that can recruit a protein factor is called a cis-acting element. This article addresses a powerful mutagenesis strategy that can be employed to define cis-acting elements at a molecular level. Technical details including primer design, saturation mutagenesis, construction of promoter libraries, phenotypic analysis, data analysis, and interpretation are discussed.
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Affiliation(s)
- Nitin S Baliga
- Institute for Systems Biology. 4225 Roosevelt way NE, Suite 200, Seattle, WA 98105. USA.
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Baliga NS, Kennedy SP, Ng WV, Hood L, DasSarma S. Genomic and genetic dissection of an archaeal regulon. Proc Natl Acad Sci U S A 2001; 98:2521-5. [PMID: 11226271 PMCID: PMC30170 DOI: 10.1073/pnas.051632498] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2000] [Indexed: 11/18/2022] Open
Abstract
The extremely halophilic archaeon Halobacterium sp. NRC-1 can grow phototrophically by means of light-driven proton pumping by bacteriorhodopsin in the purple membrane. Here, we show by genetic analysis of the wild type, and insertion and double-frame shift mutants of Bat that this transcriptional regulator coordinates synthesis of a structural protein and a chromophore for purple membrane biogenesis in response to both light and oxygen. Analysis of the complete Halobacterium sp. NRC-1 genome sequence showed that the regulatory site, upstream activator sequence (UAS), the putative binding site for Bat upstream of the bacterio-opsin gene (bop), is also present upstream to the other Bat-regulated genes. The transcription regulator Bat contains a photoresponsive cGMP-binding (GAF) domain, and a bacterial AraC type helix-turn-helix DNA binding motif. We also provide evidence for involvement of the PAS/PAC domain of Bat in redox-sensing activity by genetic analysis of a purple membrane overproducer. Five additional Bat-like putative regulatory genes were found, which together are likely to be responsible for orchestrating the complex response of this archaeon to light and oxygen. Similarities of the bop-like UAS and transcription factors in diverse organisms, including a plant and a gamma-proteobacterium, suggest an ancient origin for this regulon capable of coordinating light and oxygen responses in the three major branches of the evolutionary tree of life. Finally, sensitivity of four of five regulon genes to DNA supercoiling is demonstrated and correlated to presence of alternating purine-pyrimidine sequences (RY boxes) near the regulated promoters.
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Affiliation(s)
- N S Baliga
- Department of Microbiology, 203 Morrill Science Center IV-N, University of Massachusetts, Amherst, MA 01003, USA
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Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 2000; 97:12176-81. [PMID: 11016950 PMCID: PMC17314 DOI: 10.1073/pnas.190337797] [Citation(s) in RCA: 484] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into a large chromosome and 2 related minichromosomes. The Halobacterium NRC-1 genome codes for 2,630 predicted proteins, 36% of which are unrelated to any previously reported. Analysis of the genome sequence shows the presence of pathways for uptake and utilization of amino acids, active sodium-proton antiporter and potassium uptake systems, sophisticated photosensory and signal transduction pathways, and DNA replication, transcription, and translation systems resembling more complex eukaryotic organisms. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria. The ease of culturing Halobacterium and the availability of methods for its genetic manipulation in the laboratory, including construction of gene knockouts and replacements, indicate this halophile can serve as an excellent model system among the archaea.
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Affiliation(s)
- W V Ng
- Department of Molecular Biotechnology, University of Washington, Seattle, WA 98195, USA. tment of Microbiology, University of Massachusetts, Amherst, MA 01003; Centre for Extremophile Research, Department of Biology and Biochemistry, Univer
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