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Guan L, Han Y, Zhu S, Lin J. Application of CRISPR-Cas system in gene therapy: Pre-clinical progress in animal model. DNA Repair (Amst) 2016; 46:1-8. [PMID: 27519625 DOI: 10.1016/j.dnarep.2016.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 07/29/2016] [Accepted: 07/29/2016] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated proteins (Cas) belong to the crucial adaptive immune system, which exist in archaea and bacteria. Currently, CRISPR-Cas9 system has been modified and widely used to edit genome. In this review, we summarized the discovery, classification and mechanism of CRISPR-Cas system and further discussed the application of CRISPR-Cas9 in gene therapy, mainly in disease models.
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Affiliation(s)
- Lihong Guan
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China; Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, Henan, 453003, China
| | - Yawei Han
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450002, China
| | - Shaoyi Zhu
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Juntang Lin
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China; Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, Henan, 453003, China; College of Biomedical Engineering, Xinxiang Medical University, Xinxiang, Henan, 453003, China.
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102
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Mojica FJM, Rodriguez-Valera F. The discovery of CRISPR in archaea and bacteria. FEBS J 2016; 283:3162-9. [PMID: 27234458 DOI: 10.1111/febs.13766] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 05/26/2016] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas are self-/nonself-discriminating systems found in prokaryotic cells. They represent a remarkable example of molecular memory that is hereditarily transmitted. Their discovery can be considered as one of the first fruits of the systematic exploration of prokaryotic genomes. Although this genomic feature was serendipitously discovered in molecular biology studies, it was the availability of multiple complete genomes that shed light about their role as a genetic immune system. Here we tell the story of how this discovery originated and was slowly and painstakingly advanced to the point of understating the biological role of what initially was just an odd genomic feature.
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Affiliation(s)
- Francisco J M Mojica
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain.,Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', Universidad de Alicante, Spain
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103
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Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR-Cas I-F systems. Nat Microbiol 2016; 1:16081. [PMID: 27573106 DOI: 10.1038/nmicrobiol.2016.81] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/28/2016] [Indexed: 11/09/2022]
Abstract
Archaea and bacteria harbour clustered regularly interspaced short palindromic repeats (CRISPR) loci. These arrays encode RNA molecules (crRNA), each containing a sequence of a single repeat-intervening spacer. The crRNAs guide CRISPR-associated (Cas) proteins to cleave nucleic acids complementary to the crRNA spacer, thus interfering with targeted foreign elements. Notably, pre-existing spacers may trigger the acquisition of new spacers from the target molecule by means of a primed adaptation mechanism. Here, we show that naturally occurring orphan CRISPR arrays that contain spacers matching sequences of the cognate (absent) cas genes are able to elicit both primed adaptation and direct interference against genetic elements carrying those genes. Our findings show the existence of an anti-cas mechanism that prevents the transfer of a fully equipped CRISPR-Cas system. Hence, they suggest that CRISPR immunity may be undesired by particular prokaryotes, potentially because they could limit possibilities for gaining favourable sequences by lateral transfer.
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104
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Hung SSC, McCaughey T, Swann O, Pébay A, Hewitt AW. Genome engineering in ophthalmology: Application of CRISPR/Cas to the treatment of eye disease. Prog Retin Eye Res 2016; 53:1-20. [PMID: 27181583 DOI: 10.1016/j.preteyeres.2016.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 12/12/2022]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and CRISPR-associated protein (Cas) system has enabled an accurate and efficient means to edit the human genome. Rapid advances in this technology could results in imminent clinical application, and with favourable anatomical and immunological profiles, ophthalmic disease will be at the forefront of such work. There have been a number of breakthroughs improving the specificity and efficacy of CRISPR/Cas-mediated genome editing. Similarly, better methods to identify off-target cleavage sites have also been developed. With the impending clinical utility of CRISPR/Cas technology, complex ethical issues related to the regulation and management of the precise applications of human gene editing must be considered. This review discusses the current progress and recent breakthroughs in CRISPR/Cas-based gene engineering, and outlines some of the technical issues that must be addressed before gene correction, be it in vivo or in vitro, is integrated into ophthalmic care. We outline a clinical pipeline for CRISPR-based treatments of inherited eye diseases and provide an overview of the important ethical implications of gene editing and how these may influence the future of this technology.
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Affiliation(s)
- Sandy S C Hung
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Tristan McCaughey
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia; Department of Surgery, Monash University, Victoria, Australia
| | - Olivia Swann
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia; Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Australia.
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105
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Miller DV, Brown AM, Xu H, Bevan DR, White RH. Purine salvage inMethanocaldococcus jannaschii: Elucidating the role of a conserved cysteine in adenine deaminase. Proteins 2016; 84:828-40. [DOI: 10.1002/prot.25033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/22/2016] [Accepted: 03/06/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Danielle V. Miller
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - Anne M. Brown
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - Huimin Xu
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - David R. Bevan
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
| | - Robert H. White
- Department of Biochemistry; Virginia Polytechnic Institute and State University; Blacksburg Virginia 24061
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Abstract
Many plasmids have been described in Euryarchaeota, one of the three major archaeal phyla, most of them in salt-loving haloarchaea and hyperthermophilic Thermococcales. These plasmids resemble bacterial plasmids in terms of size (from small plasmids encoding only one gene up to large megaplasmids) and replication mechanisms (rolling circle or theta). Some of them are related to viral genomes and form a more or less continuous sequence space including many integrated elements. Plasmids from Euryarchaeota have been useful for designing efficient genetic tools for these microorganisms. In addition, they have also been used to probe the topological state of plasmids in species with or without DNA gyrase and/or reverse gyrase. Plasmids from Euryarchaeota encode both DNA replication proteins recruited from their hosts and novel families of DNA replication proteins. Euryarchaeota form an interesting playground to test evolutionary hypotheses on the origin and evolution of viruses and plasmids, since a robust phylogeny is available for this phylum. Preliminary studies have shown that for different plasmid families, plasmids share a common gene pool and coevolve with their hosts. They are involved in gene transfer, mostly between plasmids and viruses present in closely related species, but rarely between cells from distantly related archaeal lineages. With few exceptions (e.g., plasmids carrying gas vesicle genes), most archaeal plasmids seem to be cryptic. Interestingly, plasmids and viral genomes have been detected in extracellular membrane vesicles produced by Thermococcales, suggesting that these vesicles could be involved in the transfer of viruses and plasmids between cells.
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McAllister TA, Meale SJ, Valle E, Guan LL, Zhou M, Kelly WJ, Henderson G, Attwood GT, Janssen PH. RUMINANT NUTRITION SYMPOSIUM: Use of genomics and transcriptomics to identify strategies to lower ruminal methanogenesis. J Anim Sci 2016; 93:1431-49. [PMID: 26020166 DOI: 10.2527/jas.2014-8329] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Globally, methane (CH4) emissions account for 40% to 45% of greenhouse gas emissions from ruminant livestock, with over 90% of these emissions arising from enteric fermentation. Reduction of carbon dioxide to CH4 is critical for efficient ruminal fermentation because it prevents the accumulation of reducing equivalents in the rumen. Methanogens exist in a symbiotic relationship with rumen protozoa and fungi and within biofilms associated with feed and the rumen wall. Genomics and transcriptomics are playing an increasingly important role in defining the ecology of ruminal methanogenesis and identifying avenues for its mitigation. Metagenomic approaches have provided information on changes in abundances as well as the species composition of the methanogen community among ruminants that vary naturally in their CH4 emissions, their feed efficiency, and their response to CH4 mitigators. Sequencing the genomes of rumen methanogens has provided insight into surface proteins that may prove useful in the development of vaccines and has allowed assembly of biochemical pathways for use in chemogenomic approaches to lowering ruminal CH4 emissions. Metagenomics and metatranscriptomic analysis of entire rumen microbial communities are providing new perspectives on how methanogens interact with other members of this ecosystem and how these relationships may be altered to reduce methanogenesis. Identification of community members that produce antimethanogen agents that either inhibit or kill methanogens could lead to the identification of new mitigation approaches. Discovery of a lytic archaeophage that specifically lyses methanogens is 1 such example. Efforts in using genomic data to alter methanogenesis have been hampered by a lack of sequence information that is specific to the microbial community of the rumen. Programs such as Hungate1000 and the Global Rumen Census are increasing the breadth and depth of our understanding of global ruminal microbial communities, steps that are key to using these tools to further define the science of ruminal methanogenesis.
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Turk SCHJ, Kloosterman WP, Ninaber DK, Kolen KPAM, Knutova J, Suir E, Schürmann M, Raemakers-Franken PC, Müller M, de Wildeman SMA, Raamsdonk LM, van der Pol R, Wu L, Temudo MF, van der Hoeven RAM, Akeroyd M, van der Stoel RE, Noorman HJ, Bovenberg RAL, Trefzer AC. Metabolic Engineering toward Sustainable Production of Nylon-6. ACS Synth Biol 2016; 5:65-73. [PMID: 26511532 DOI: 10.1021/acssynbio.5b00129] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nylon-6 is a bulk polymer used for many applications. It consists of the non-natural building block 6-aminocaproic acid, the linear form of caprolactam. Via a retro-synthetic approach, two synthetic pathways were identified for the fermentative production of 6-aminocaproic acid. Both pathways require yet unreported novel biocatalytic steps. We demonstrated proof of these bioconversions by in vitro enzyme assays with a set of selected candidate proteins expressed in Escherichia coli. One of the biosynthetic pathways starts with 2-oxoglutarate and contains bioconversions of the ketoacid elongation pathway known from methanogenic archaea. This pathway was selected for implementation in E. coli and yielded 6-aminocaproic acid at levels up to 160 mg/L in lab-scale batch fermentations. The total amount of 6-aminocaproic acid and related intermediates generated by this pathway exceeded 2 g/L in lab-scale fed-batch fermentations, indicating its potential for further optimization toward large-scale sustainable production of nylon-6.
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Affiliation(s)
| | - Wigard P. Kloosterman
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- University Medical Center Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands
| | - Dennis K. Ninaber
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | | | - Julia Knutova
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | - Erwin Suir
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- BioscienZ, Goeseelsstraat 10, 4817 MV Breda, The Netherlands
| | - Martin Schürmann
- DSM Innovative Synthesis, PO Box 18, 6160 MD Geleen, The Netherlands
| | | | - Monika Müller
- DSM Innovative Synthesis, PO Box 18, 6160 MD Geleen, The Netherlands
| | | | | | - Ruud van der Pol
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | - Liang Wu
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | | | | | - Michiel Akeroyd
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | | | - Henk J. Noorman
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- Synthetic
Biology and Cell Engineering, Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Axel C. Trefzer
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
- Life Technologies, GeneArt, Im Gewerbepark B35, 93059 Regensburg, Germany
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109
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Susanti D, Johnson EF, Lapidus A, Han J, Reddy TBK, Pilay M, Ivanova NN, Markowitz VM, Woyke T, Kyrpides NC, Mukhopadhyay B. Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. Stand Genomic Sci 2016; 11:3. [PMID: 26767090 PMCID: PMC4711178 DOI: 10.1186/s40793-015-0128-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/30/2015] [Indexed: 11/10/2022] Open
Abstract
This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and Desulfurococcus mucosus suggested that these two desulfurococci are two different strains of the same species.
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Affiliation(s)
- Dwi Susanti
- />Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061 USA
| | - Eric F. Johnson
- />Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Alla Lapidus
- />Centre for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
- />Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - James Han
- />US DOE Joint Genome Institute, Walnut Creek, California 94598 USA
| | - T. B. K. Reddy
- />US DOE Joint Genome Institute, Walnut Creek, California 94598 USA
| | - Manoj Pilay
- />Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | | | - Victor M. Markowitz
- />Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California USA
| | - Tanja Woyke
- />US DOE Joint Genome Institute, Walnut Creek, California 94598 USA
| | - Nikos C. Kyrpides
- />US DOE Joint Genome Institute, Walnut Creek, California 94598 USA
- />Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Biswarup Mukhopadhyay
- />Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061 USA
- />Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061 USA
- />Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061 USA
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111
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Lossouarn J, Dupont S, Gorlas A, Mercier C, Bienvenu N, Marguet E, Forterre P, Geslin C. An abyssal mobilome: viruses, plasmids and vesicles from deep-sea hydrothermal vents. Res Microbiol 2015; 166:742-52. [DOI: 10.1016/j.resmic.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/11/2023]
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112
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Novikova O, Jayachandran P, Kelley DS, Morton Z, Merwin S, Topilina NI, Belfort M. Intein Clustering Suggests Functional Importance in Different Domains of Life. Mol Biol Evol 2015; 33:783-99. [PMID: 26609079 PMCID: PMC4760082 DOI: 10.1093/molbev/msv271] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Inteins, also called protein introns, are self-splicing mobile elements found in all domains of life. A bioinformatic survey of genomic data highlights a biased distribution of inteins among functional categories of proteins in both bacteria and archaea, with a strong preference for a single network of functions containing replisome proteins. Many nonorthologous, functionally equivalent replicative proteins in bacteria and archaea carry inteins, suggesting a selective retention of inteins in proteins of particular functions across domains of life. Inteins cluster not only in proteins with related roles but also in specific functional units of those proteins, like ATPase domains. This peculiar bias does not fully fit the models describing inteins exclusively as parasitic elements. In such models, evolutionary dynamics of inteins is viewed primarily through their mobility with the intein homing endonuclease (HEN) as the major factor of intein acquisition and loss. Although the HEN is essential for intein invasion and spread in populations, HEN dynamics does not explain the observed biased distribution of inteins among proteins in specific functional categories. We propose that the protein splicing domain of the intein can act as an environmental sensor that adapts to a particular niche and could increase the chance of the intein becoming fixed in a population. We argue that selective retention of some inteins might be beneficial under certain environmental stresses, to act as panic buttons that reversibly inhibit specific networks, consistent with the observed intein distribution.
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Affiliation(s)
- Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany
| | | | - Danielle S Kelley
- Department of Biomedical Sciences, School of Public Health, University at Albany
| | - Zachary Morton
- Department of Biological Sciences and RNA Institute, University at Albany
| | | | - Natalya I Topilina
- Department of Biological Sciences and RNA Institute, University at Albany
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany Department of Biomedical Sciences, School of Public Health, University at Albany
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113
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Zhou H, Vonk B, Roubos JA, Bovenberg RAL, Voigt CA. Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor. Nucleic Acids Res 2015; 43:10560-70. [PMID: 26519464 PMCID: PMC4666358 DOI: 10.1093/nar/gkv1071] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/01/2015] [Indexed: 11/14/2022] Open
Abstract
Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advances in DNA assembly and gene insulation facilitate this approach by accelerating multi-gene pathway construction and the statistical interpretation of screening data. This is applied to a 6-aminocaproic acid (6-ACA) pathway in Escherichia coli consisting of six heterologous enzymes. A 32-member fraction factorial library is designed that simultaneously perturbs expression and media composition. This is compared to a 64-member full factorial library just varying expression (0.64 Mb of DNA assembly). Statistical analysis of the screening data from these libraries leads to different predictions as to whether the expression of enzymes needs to increase or decrease. Therefore, if genotype and media were varied separately this would lead to a suboptimal combination. This is applied to the design of a strain and media composition that increases 6-ACA from 9 to 48 mg/l in a single optimization step. This work introduces a generalizable platform to co-optimize genetic and non-genetic factors.
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Affiliation(s)
- Hui Zhou
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brenda Vonk
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands
| | | | - Roel A L Bovenberg
- DSM Biotechnology Center, PO Box 1, 2600 MA Delft, The Netherlands Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Sarmiento F, Peralta R, Blamey JM. Cold and Hot Extremozymes: Industrial Relevance and Current Trends. Front Bioeng Biotechnol 2015; 3:148. [PMID: 26539430 PMCID: PMC4611823 DOI: 10.3389/fbioe.2015.00148] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
The development of enzymes for industrial applications relies heavily on the use of microorganisms. The intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. Extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. These microorganisms have developed unique mechanisms and molecular means to cope with extreme temperatures, acidic and basic pH, high salinity, high radiation, low water activity, and high metal concentrations among other environmental conditions. Extremophile-derived enzymes, or extremozymes, are able to catalyze chemical reactions under harsh conditions, like those found in industrial processes, which were previously not thought to be conducive for enzymatic activity. Due to their optimal activity and stability under extreme conditions, extremozymes offer new catalytic alternatives for current industrial applications. These extremozymes also represent the cornerstone for the development of environmentally friendly, efficient, and sustainable industrial technologies. Many advances in industrial biocatalysis have been achieved in recent years; however, the potential of biocatalysis through the use of extremozymes is far from being fully realized. In this article, the adaptations and significance of psychrophilic, thermophilic, and hyperthermophilic enzymes, and their applications in selected industrial markets will be reviewed. Also, the current challenges in the development and mass production of extremozymes as well as future prospects and trends for their biotechnological application will be discussed.
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Affiliation(s)
| | - Rocío Peralta
- Fundación Científica y Cultural Biociencia , Santiago , Chile
| | - Jenny M Blamey
- Swissaustral USA , Athens, GA , USA ; Fundación Científica y Cultural Biociencia , Santiago , Chile
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115
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Baloglu MC, Ulu F, Altunoglu YC, Pekol S, Alagoz G, Ese O. Identification, molecular characterization and expression analysis ofRPL24genes in three Cucurbitaceae family members: cucumber, melon and watermelon. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1079144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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116
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Chellapandi P, Ranjani J. Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:97-106. [PMID: 26279704 DOI: 10.1007/s11693-015-9176-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 06/29/2015] [Accepted: 07/27/2015] [Indexed: 11/25/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) are direct features of the prokaryotic genomes involved in resistance to their bacterial viruses and phages. Herein, we have identified CRISPR loci together with CRISPR-associated sequences (CAS) genes to reveal their immunity against genome invaders in the thermophilic archaea and bacteria. Genomic survey of this study implied that genomic distribution of CRISPR-CAS systems was varied from strain to strain, which was determined by the degree of invading mobiloms. Direct repeats found to be equal in some extent in many thermopiles, but their spacers were differed in each strain. Phylogenetic analyses of CAS superfamily revealed that genes cmr, csh, csx11, HD domain, devR were belonged to the subtypes of cas gene family. The members in cas gene family of thermophiles were functionally diverged within closely related genomes and may contribute to develop several defense strategies. Nevertheless, genome dynamics, geological variation and host defense mechanism were contributed to share their molecular functions across the thermophiles. A thermophilic archaean, Thermococcus gammotolerans and thermophilic bacteria, Petrotoga mobilis and Thermotoga lettingae have shown superoperons-like appearance to cluster cas genes, which were typically evolved for their defense pathways. A cmr operon was identified with a specific promoter in a thermophilic archaean, Caldivirga maquilingensis. Overall, we concluded that knowledge-based genomic survey and phylogeny-based functional assignment have suggested for designing a reliable genetic regulatory circuit naturally from CRISPR-CAS systems, acquired defense pathways, to thermophiles in future synthetic biology.
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Affiliation(s)
- P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
| | - J Ranjani
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024 India
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117
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Abstract
SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.
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118
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Fujishiro T, Ataka K, Ermler U, Shima S. Towards a functional identification of catalytically inactive [Fe]-hydrogenase paralogs. FEBS J 2015; 282:3412-23. [PMID: 26094576 DOI: 10.1111/febs.13351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED [Fe]-hydrogenase (Hmd), an enzyme of the methanogenic energy metabolism, harbors an iron-guanylylpyridinol (FeGP) cofactor used for H2 cleavage. The generated hydride is transferred to methenyl-tetrahydromethanopterin (methenyl-H4MPT(+)). Most hydrogenotrophic methanogens contain the hmd-related genes hmdII and hmdIII. Their function is still elusive. We were able to reconstitute the HmdII holoenzyme of Methanocaldococcus jannaschii with recombinantly produced apoenzyme and the FeGP cofactor, which is a prerequisite for in vitro functional analysis. Infrared spectroscopic and X-ray structural data clearly indicated binding of the FeGP cofactor. Methylene-H4MPT binding was detectable in the significantly altered infrared spectra of the HmdII holoenzyme and in the HmdII apoenzyme-methylene-H4 MPT complex structure. The related binding mode of the FeGP cofactor and methenyl-H4MPT(+) compared with Hmd and their multiple contacts to the polypeptide highly suggest a biological role in HmdII. However, holo-HmdII did not catalyze the Hmd reaction, not even in a single turnover process, as demonstrated by kinetic measurements. The found inactivity can be rationalized by an increased contact area between the C- and N-terminal folding units in HmdII compared with in Hmd, which impairs the catalytically necessary open-to-close transition, and by an exchange of a crucial histidine to a tyrosine. Mainly based on the presented data, a function of HmdII as Hmd isoenzyme, H2 sensor, FeGP-cofactor storage protein and scaffold protein for FeGP-cofactor biosynthesis could be excluded. Inspired by the recently found binding of HmdII to aminoacyl-tRNA synthetases and tRNA, we tentatively consider HmdII as a regulatory protein for protein synthesis that senses the intracellular methylene-H4 MPT concentration. DATABASE Structural data are available in the Protein Data Bank under the accession numbers 4YT8; 4YT2; 4YT4 and 4YT5.
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Affiliation(s)
- Takashi Fujishiro
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Germany
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Frankfurt/Main, Germany
| | - Seigo Shima
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany.,PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
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119
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Identification of the Final Two Genes Functioning in Methanofuran Biosynthesis in Methanocaldococcus jannaschii. J Bacteriol 2015; 197:2850-8. [PMID: 26100040 DOI: 10.1128/jb.00401-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED All methanofuran structural variants contain a basic core structure of 4-[N-(γ-l-glutamyl)-p-(β-aminoethyl)phenoxymethyl]-(aminomethyl)furan (APMF-Glu) but have different side chains depending on the source organism. Recently, we identified four genes (MfnA, MfnB, MfnC, and MfnD) that are responsible for the biosynthesis of the methanofuran precursor γ-glutamyltyramine and 5-(aminomethyl)-3-furanmethanol-phosphate (F1-P) from tyrosine, glutamate, glyceraldehyde-3-P, and alanine in Methanocaldococcus jannaschii. How γ-glutamyltyramine and F1-P couple together to form the core structure of methanofuran was previously unknown. Here, we report the identification of two enzymes encoded by the genes mj0458 and mj0840 that catalyze the formation of F1-PP from ATP and F1-P and the condensation of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. We have annotated these enzymes as MfnE and MfnF, respectively, representing the fifth and sixth enzymes in the methanofuran biosynthetic pathway to be identified. Although MfnE was previously reported as an archaeal adenylate kinase, our present results show that MfnE is a promiscuous enzyme and that its possible physiological role is to produce F1-PP. Unlike other enzymes catalyzing coupling reactions involving pyrophosphate as the leaving group, MfnF exhibits a distinctive α/β two-layer sandwich structure. By comparing MfnF with thiamine synthase and dihydropteroate synthase, a substitution nucleophilic unimolecular (SN-1) reaction mechanism is proposed for MfnF. With the identification of MfnE and MfnF, the biosynthetic pathway for the methanofuran core structure APMF-Glu is complete. IMPORTANCE This work describes the identification of the final two enzymes responsible for catalyzing the biosynthesis of the core structure of methanofuran. The gene products of mj0458 and mj0840 catalyze the formation of F1-PP and the coupling of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. Although the chemistry of such a coupling reaction is widespread in biochemistry, we provide here the first evidence that such a mechanism is used in methanofuran biosynthesis. MfnF belongs to the hydantoinase A family (PF01968) and exhibits a unique α/β two-layer sandwich structure that is different from the enzymes catalyzing similar reactions. Our results show that MfnF catalyzes the formation of an ether bond during methanofuran biosynthesis. Therefore, this work further expands the functionality of this enzyme family.
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120
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Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies. BIOMED RESEARCH INTERNATIONAL 2015; 2015:904541. [PMID: 26125026 PMCID: PMC4466500 DOI: 10.1155/2015/904541] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/01/2015] [Accepted: 04/01/2015] [Indexed: 02/07/2023]
Abstract
Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.
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121
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Zhang B, Jiang CY, Liu YM, Liu C, Liu SJ. Engineering of a hybrid route to enhance shikimic acid production in Corynebacterium glutamicum. Biotechnol Lett 2015; 37:1861-8. [DOI: 10.1007/s10529-015-1852-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/01/2015] [Indexed: 11/28/2022]
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122
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Allen KD, Miller DV, Rauch BJ, Perona JJ, White RH. Homocysteine Is Biosynthesized from Aspartate Semialdehyde and Hydrogen Sulfide in Methanogenic Archaea. Biochemistry 2015; 54:3129-32. [DOI: 10.1021/acs.biochem.5b00118] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kylie D. Allen
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Danielle V. Miller
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Benjamin J. Rauch
- Department
of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
| | - John J. Perona
- Department
of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239-3098, United States
- Department
of Chemistry, Portland State University, 1719 Southwest 10th Avenue, Portland, Oregon 97201, United States
| | - Robert H. White
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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123
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Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 2015; 521:173-179. [PMID: 25945739 PMCID: PMC4444528 DOI: 10.1038/nature14447] [Citation(s) in RCA: 701] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/01/2015] [Indexed: 12/22/2022]
Abstract
The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.
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Affiliation(s)
- Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Steffen L Jørgensen
- Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway
| | | | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Anders E Lind
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Roel van Eijk
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway.,Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Lionel Guy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
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124
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Abstract
All living organisms require protein degradation to terminate biological processes and remove damaged proteins. One such machine is the 20S proteasome, a specialized barrel-shaped and compartmentalized multicatalytic protease. The activity of the 20S proteasome generally requires the binding of regulators/proteasome activators (PAs), which control the entrance of substrates. These include the PA700 (19S complex), which assembles with the 20S and forms the 26S proteasome and allows the efficient degradation of proteins usually labeled by ubiquitin tags, PA200 and PA28, which are involved in proteolysis through ubiquitin-independent mechanisms and PI31, which was initially identified as a 20S inhibitor in vitro. Unlike 20S proteasome, shown to be present in all Eukaryotes and Archaea, the evolutionary history of PAs remained fragmentary. Here, we made a comprehensive survey and phylogenetic analyses of the four types of regulators in 17 clades covering most of the eukaryotic supergroups. We found remarkable conservation of each PA700 subunit in all eukaryotes, indicating that the current complex PA700 structure was already set up in the last eukaryotic common ancestor (LECA). Also present in LECA, PA200, PA28, and PI31 showed a more contrasted evolutionary picture, because many lineages have subsequently lost one or two of them. The paramount conservation of PA700 composition in all eukaryotes and the dynamic evolution of PA200, PA28, and PI31 are discussed in the light of current knowledge on their physiological roles.
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Affiliation(s)
- Philippe Fort
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
| | - Andrey V Kajava
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France Institut de Biologie Computationnelle, Montpellier, France
| | - Fredéric Delsuc
- Université de Montpellier, France CNRS, IRD, Institut des Sciences de l'Evolution, UMR 5554, Montpellier, France
| | - Olivier Coux
- CNRS, CRBM, UMR5237, Montpellier, France Université de Montpellier, France
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125
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Miraula M, Ciurli S, Zambelli B. Intrinsic disorder and metal binding in UreG proteins from Archae hyperthermophiles: GTPase enzymes involved in the activation of Ni(II) dependent urease. J Biol Inorg Chem 2015; 20:739-55. [PMID: 25846143 DOI: 10.1007/s00775-015-1261-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/20/2015] [Indexed: 02/03/2023]
Abstract
Urease is a Ni(II) enzyme present in every domain of life, in charge for nitrogen recycling through urea hydrolysis. Its activity requires the presence of two Ni(II) ions in the active site. These are delivered by the concerted action of four accessory proteins, named UreD, UreF, UreG and UreE. This process requires protein flexibility at different levels and some disorder-to-order transition events that coordinate the mechanism of protein-protein interaction. In particular, UreG, the GTPase in charge of nucleotide hydrolysis required for urease activation, presents a significant degree of intrinsic disorder, existing as a conformational ensemble featuring characteristics that recall a molten globule. Here, the folding properties of UreG were explored in Archaea hyperthermophiles, known to generally feature significantly low level of structural disorder in their proteome. UreG proteins from Methanocaldococcus jannaschii (Mj) and Metallosphaera sedula (Ms) were structurally and functionally analyzed by integrating circular dichroism, NMR, light scattering and enzymatic assays. Metal-binding properties were studied using isothermal titration calorimetry. The results indicate that, as the mesophilic counterparts, both proteins contain a significant amount of secondary structure but maintain a flexible fold and a low GTPase activity. As opposed to other UreGs, secondary structure is lost at high temperatures (68 and 75 °C, respectively) with an apparent two-state mechanism. Both proteins bind Zn(II) and Ni(II), with affinities two orders of magnitude higher for Zn(II) than for Ni(II). No major modifications of the average conformational ensemble are observed, but binding of Zn(II) yields a more compact dimeric form in MsUreG.
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Affiliation(s)
- Manfredi Miraula
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy
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126
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Stewart LC, Jung JH, Kim YT, Kwon SW, Park CS, Holden JF. M
ethanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2015; 65:1280-1283. [DOI: 10.1099/ijs.0.000097] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hyperthermophilic methanogen, strain JH146T, was isolated from 26 °C hydrothermal vent fluid emanating from a crack in basaltic rock at Marker 113 vent, Axial Seamount in the northeastern Pacific Ocean. It was identified as an obligate anaerobe that uses only H2 and CO2 for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is more than 97 % similar to other species of the genus
Methanocaldococcus
. Therefore, overall genome relatedness index analyses were performed to establish that strain JH146T represents a novel species. For each analysis, strain JH146T was most similar to
Methanocaldococcus sp.
FS406-22, which can fix N2 and also comes from Marker 113 vent. However, strain JH146T differs from strain FS406-22 in that it cannot fix N2. The average nucleotide identity score for strain JH146T was 87 %, the genome-to-genome direct comparison score was 33–55 % and the species identification score was 93 %. For each analysis, strain JH146T was below the species delineation cut-off. Full-genome gene synteny analysis showed that strain JH146T and strain FS406-22 have 97 % genome synteny, but strain JH146T was missing the operons necessary for N2 fixation and assimilatory nitrate reduction that are present in strain FS406-22. Based on its whole genome sequence, strain JH146T is suggested to represent a novel species of the genus
Methanocaldococcus
for which the name Methanocaldococcus
bathoardescens is proposed. The type strain is JH146T ( = DSM 27223T = KACC 18232T).
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Affiliation(s)
- Lucy C. Stewart
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - You-Tae Kim
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Soon-Wo Kwon
- National Agrobiodiversity Center, National Academy of Agricultural Science, Suwon 441-707, Republic of Korea
| | - Cheon-Seok Park
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - James F. Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
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127
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Wang I, Chen SY, Hsu STD. Unraveling the Folding Mechanism of the Smallest Knotted Protein, MJ0366. J Phys Chem B 2015; 119:4359-70. [DOI: 10.1021/jp511029s] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Iren Wang
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Szu-Yu Chen
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Shang-Te Danny Hsu
- Institute
of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan University, 1, Section
4, Roosevelt Road, Taipei 10617, Taiwan
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128
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Wong TY, Schwartzbach SD. Protein Mis-Termination Initiates Genetic Diseases, Cancers, and Restricts Bacterial Genome Expansion. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2015; 33:255-285. [PMID: 26087060 DOI: 10.1080/10590501.2015.1053461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein termination is an important cellular process. Protein termination relies on the stop-codons in the mRNA interacting properly with the releasing factors on the ribosome. One third of inherited diseases, including cancers, are associated with the mutation of the stop-codons. Many pathogens and viruses are able to manipulate their stop-codons to express their virulence. The influence of stop-codons is not limited to the primary reading frame of the genes. Stop-codons in the second and third reading frames are referred as premature stop signals (PSC). Stop-codons and PSCs together are collectively referred as stop-signals. The ratios of the stop-signals (referred as translation stop-signals ratio or TSSR) of genetically related bacteria, despite their great differences in gene contents, are much alike. This nearly identical Genomic-TSSR value of genetically related bacteria may suggest that bacterial genome expansion is limited by their unique stop-signals bias. We review the protein termination process and the different types of stop-codon mutation in plants, animals, microbes, and viruses, with special emphasis on the role of PSCs in directing bacterial evolution in their natural environments. Knowing the limit of genomic boundary could facilitate the formulation of new strategies in controlling the spread of diseases and combat antibiotic-resistant bacteria.
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Affiliation(s)
- Tit-Yee Wong
- a Department of Biological Sciences , University of Memphis , Memphis , Tennessee , USA
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129
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Smollett K, Blombach F, Werner F. Transcription in Archaea: preparation of Methanocaldococcus jannaschii transcription machinery. Methods Mol Biol 2015; 1276:291-303. [PMID: 25665571 DOI: 10.1007/978-1-4939-2392-2_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Archaeal RNA polymerase and general transcription factors are more closely related to those of eukaryotes than of bacteria. As such the study of transcription of archaea is important both in terms of examination of the evolution of the transcriptional machinery and as a simplified tool for eukaryotic transcription. In particular, the hyperthermophilic Methanocaldococcus jannaschii provides us with a fully recombinant RNA polymerase system allowing for much more detailed in vitro examination of the roles of different components during the transcription cycle than otherwise possible. The individual subunits of M. jannaschii enzyme are easily expressed and purified from heterologous expression systems. Forming functional RNA polymerase involves simply combining the different subunits under denaturing conditions and slowly removing the denaturant.
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Affiliation(s)
- Katherine Smollett
- Institute of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London, WC1E 6BT, UK,
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130
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Jain K, Krause K, Grewe F, Nelson GF, Weber APM, Christensen AC, Mower JP. Extreme features of the Galdieria sulphuraria organellar genomes: a consequence of polyextremophily? Genome Biol Evol 2014; 7:367-80. [PMID: 25552531 PMCID: PMC4316638 DOI: 10.1093/gbe/evu290] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nuclear genome sequencing from extremophilic eukaryotes has revealed clues about the mechanisms of adaptation to extreme environments, but the functional consequences of extremophily on organellar genomes are unknown. To address this issue, we assembled the mitochondrial and plastid genomes from a polyextremophilic red alga, Galdieria sulphuraria strain 074 W, and performed a comparative genomic analysis with other red algae and more broadly across eukaryotes. The mitogenome is highly reduced in size and genetic content and exhibits the highest guanine–cytosine skew of any known genome and the fastest substitution rate among all red algae. The plastid genome contains a large number of intergenic stem-loop structures but is otherwise rather typical in size, structure, and content in comparison with other red algae. We suggest that these unique genomic modifications result not only from the harsh conditions in which Galdieria lives but also from its unusual capability to grow heterotrophically, endolithically, and in the dark. These conditions place additional mutational pressures on the mitogenome due to the increased reliance on the mitochondrion for energy production, whereas the decreased reliance on photosynthesis and the presence of numerous stem-loop structures may shield the plastome from similar genomic stress.
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Affiliation(s)
- Kanika Jain
- Center for Plant Science Innovation, University of Nebraska - Lincoln School of Biological Sciences, University of Nebraska - Lincoln
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Felix Grewe
- Center for Plant Science Innovation, University of Nebraska - Lincoln Department of Agronomy and Horticulture, University of Nebraska - Lincoln
| | - Gaven F Nelson
- Center for Plant Science Innovation, University of Nebraska - Lincoln School of Biological Sciences, University of Nebraska - Lincoln
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | | | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska - Lincoln Department of Agronomy and Horticulture, University of Nebraska - Lincoln
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131
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Potassium stress growth characteristics and energetics in the haloarchaeon Haloarcula marismortui. Extremophiles 2014; 19:315-25. [PMID: 25503059 PMCID: PMC4339784 DOI: 10.1007/s00792-014-0716-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/21/2014] [Indexed: 10/25/2022]
Abstract
Growth characteristics surrounding halophilic archaeal organisms are extremely limited in the scientific literature, with studies tending toward observing changes in cellular generation times under growth conditions limited to changes in temperature and sodium chloride concentrations. Currently, knowledge of the ionic stress experienced by haloarchaeal species through an excess or depletion of other required ions is lacking at best. The halophilic archaeon, Haloarcula marismortui, was analyzed under extreme ionic stress conditions with a specific focus on induced potassium ion stress using growth curves and analysis of the intracellular ion concentrations. Generation times were determined under potassium chloride concentrations ranging from 8 to 720 mM, and also in the presence of the alternative monovalent cations of lithium, rubidium, and cesium under limiting potassium conditions. Intracellular ion concentrations, as determined by inductively coupled mass spectrometry (ICP-MS), indicate a minimum intracellular total ion requirement of 1.13 M while tolerating up to 2.43 M intracellular concentrations. The presence of intracellular rubidium and cesium indicates that monovalent ion transport is important for energy production. Comparison of eight archaeal genomes indicates an increased diversity of potassium transport complex subunits in the halophilic organisms. Analysis of the generation times, intracellular concentrations and genome survey shows Har. marismortui exhibits an ability to cope with monovalent cation concentration changes in its native environment and provides insight into the organisms ion transport capability and specificity.
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132
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Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol 2014; 5:634. [PMID: 25520705 PMCID: PMC4253957 DOI: 10.3389/fmicb.2014.00634] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/05/2014] [Indexed: 11/21/2022] Open
Abstract
Methane (CH4) is a valuable fuel, constituting 70–95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing “gold standards” for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).
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Affiliation(s)
- Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Jane Lomax
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory Hinxton, UK
| | - João C Setubal
- Department of Biochemistry, Universidade de São Paulo São Paulo, Brazil ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Center for Genome Research and Biocomputing, Oregon State University Corvallis, OR, USA
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Department of Biological Sciences, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
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133
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One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia. J Bacteriol 2014; 197:717-26. [PMID: 25448816 DOI: 10.1128/jb.02365-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In cells, N(10)-formyltetrahydrofolate (N(10)-fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis of N(10)-fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We used Escherichia coli, which naturally lacks fhs, as our model. We show that in E. coli, the essential function of folD could be replaced by Clostridium perfringens fhs when it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. The fhs-supported folD deletion (ΔfolD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N(10)-fTHF in the ΔfolD strain (supported by plasmid-borne fhs) were limiting despite the high capacity of the available Fhs to synthesize N(10)-fTHF in vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The ΔfolD strain (harboring fhs on the chromosome) showed a high NADP(+)-to-NADPH ratio and hypersensitivity to trimethoprim. The presence of fhs in E. coli was disadvantageous for its aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. The computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria.
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134
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Peng L, Pei J, Pang H, Guo Y, Lin L, Huang R. Whole genome sequencing reveals a novel CRISPR system in industrial Clostridium acetobutylicum. J Ind Microbiol Biotechnol 2014; 41:1677-85. [PMID: 25217846 DOI: 10.1007/s10295-014-1507-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
Clostridium acetobutylicum is an important organism for biobutanol production. Due to frequent exposure to bacteriophages during fermentation, industrial C. acetobutylicum strains require a strong immune response against foreign genetic invaders. In the present study, a novel CRISPR system was reported in a C. acetobutylicum GXAS18-1 strain by whole genome sequencing, and several specific characteristics of the CRISPR system were revealed as follows: (1) multiple CRISPR loci were confirmed within the whole bacterial genome, while only one cluster of CRISPR-associated genes (Cas) was found in the current strain; (2) similar leader sequences at the 5' end of the multiple CRISPR loci were identified as promoter elements by promoter prediction, suggesting that these CRISPR loci were under the control of the same transcriptional factor; (3) homology analysis indicated that the present Cas genes shared only low sequence similarity with the published Cas families; and (4) concerning gene similarity and gene cluster order, these Cas genes belonged to the csm family and originated from the euryarchaeota by horizontal gene transfer.
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Affiliation(s)
- Lixin Peng
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Guangxi Key Laboratory of Biorefinery, Nanning, Guangxi, 530007, People's Republic of China
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135
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Ishino S, Ishino Y. DNA polymerases as useful reagents for biotechnology - the history of developmental research in the field. Front Microbiol 2014; 5:465. [PMID: 25221550 PMCID: PMC4148896 DOI: 10.3389/fmicb.2014.00465] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/15/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerase is a ubiquitous enzyme that synthesizes complementary DNA strands according to the template DNA in living cells. Multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. In addition to their fundamental role in maintaining genome integrity during replication and repair, DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, labeling, mutagenesis, and other purposes. The fundamental ability of DNA polymerases to synthesize a deoxyribonucleotide chain is conserved. However, the more specific properties, including processivity, fidelity (synthesis accuracy), and substrate nucleotide selectivity, differ among the enzymes. The distinctive properties of each DNA polymerase may lead to the potential development of unique reagents, and therefore searching for novel DNA polymerase has been one of the major focuses in this research field. In addition, protein engineering techniques to create mutant or artificial DNA polymerases have been successfully developing powerful DNA polymerases, suitable for specific purposes among the many kinds of DNA manipulations. Thermostable DNA polymerases are especially important for PCR-related techniques in molecular biology. In this review, we summarize the history of the research on developing thermostable DNA polymerases as reagents for genetic manipulation and discuss the future of this research field.
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Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
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136
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Guy L, Saw JH, Ettema TJG. The archaeal legacy of eukaryotes: a phylogenomic perspective. Cold Spring Harb Perspect Biol 2014; 6:a016022. [PMID: 24993577 DOI: 10.1101/cshperspect.a016022] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to reevaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling of archaeal genomes in this superphylum will certainly provide a better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.
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Affiliation(s)
- Lionel Guy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
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137
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Stierle AA, Stierle DB. Bioactive Secondary Metabolites from Acid Mine Waste Extremophiles. Nat Prod Commun 2014. [DOI: 10.1177/1934578x1400900738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The extremophilic microbes of the Berkeley Pit Lake are a valuable source of new and interesting secondary metabolites. It is of particular interest that these acidophilic microbes produce small molecule inhibitors of pathways associated with low pH and high Eh. These same small molecules also inhibit molecular pathways induced by reactive oxygen species (ROS) and inflammation in mammalian cells. Low pH is a hallmark of inflammation and high Eh is one of ROS, so the suitability of this collection as a source of bioactive metabolites is actually quite biorational. Compound isolation was guided by inhibition of caspase-1 and matrix metalloproteinase-3, and active compounds were sent to the National Cancer Institute-Developmental Therapeutics Program and Memorial Sloan Kettering Cancer center for evaluation as either antiproliferative or cytotoxic agents.
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Affiliation(s)
- Andrea A. Stierle
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, Montana 59812, USA
| | - Donald B. Stierle
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, Montana 59812, USA
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138
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Total protein extraction for metaproteomics analysis of methane producing biofilm: the effects of detergents. Int J Mol Sci 2014; 15:10169-84. [PMID: 24914765 PMCID: PMC4100146 DOI: 10.3390/ijms150610169] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 02/07/2023] Open
Abstract
Protein recovery is crucial for shotgun metaproteomics to study the in situ functionality of microbial populations from complex biofilms but still poorly addressed by far. To fill this knowledge gap, we systematically evaluated the sample preparation with extraction buffers comprising four detergents for the metaproteomics analysis of a terephthalate-degrading methanogenic biofilm using an on-line two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) system. Totally, 1018 non-repeated proteins were identified with the four treatments. On the whole, each treatment could recover the biofilm proteins with specific distributions of molecular weight, hydrophobicity, and isoelectric point. The extraction buffers containing zwitterionic and anionic detergents were found to harvest the proteins with better efficiency and quality, allowing identification up to 76.2% of total identified proteins with the LC-MS/MS analysis. According to the annotation with a relevant metagenomic database, we further observed different taxonomic profiles of bacterial and archaeal members and discriminable patterns of the functional expression among the extraction buffers used. Overall, the finding of the present study provides first insight to the effect of the detergents on the characteristics of extractable proteins from biofilm and the developed protocol combined with nano 2D-LC/MS/MS analysis can improve the metaproteomics studies on microbial functionality of biofilms in the wastewater treatment systems.
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139
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Abstract
One efficient approach to assigning function to unannotated genes is to establish the enzymes that are missing in known biosynthetic pathways. One group of such pathways is those involved in coenzyme biosynthesis. In the case of the methanogenic archaeon Methanocaldococcus jannaschii as well as most methanogens, none of the expected enzymes for the biosynthesis of the β-alanine and pantoic acid moieties required for coenzyme A are annotated. To identify the gene(s) for β-alanine biosynthesis, we have established the pathway for the formation of β-alanine in this organism after experimentally eliminating other known and proposed pathways to β-alanine from malonate semialdehyde, l-alanine, spermine, dihydrouracil, and acryloyl-coenzyme A (CoA). Our data showed that the decarboxylation of aspartate was the only source of β-alanine in cell extracts of M. jannaschii. Unlike other prokaryotes where the enzyme producing β-alanine from l-aspartate is a pyruvoyl-containing l-aspartate decarboxylase (PanD), the enzyme in M. jannaschii is a pyridoxal phosphate (PLP)-dependent l-aspartate decarboxylase encoded by MJ0050, the same enzyme that was found to decarboxylate tyrosine for methanofuran biosynthesis. A Km of ∼0.80 mM for l-aspartate with a specific activity of 0.09 μmol min(-1) mg(-1) at 70°C for the decarboxylation of l-aspartate was measured for the recombinant enzyme. The MJ0050 gene was also demonstrated to complement the Escherichia coli panD deletion mutant cells, in which panD encoding aspartate decarboxylase in E. coli had been knocked out, thus confirming the function of this gene in vivo.
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140
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Ettema TJG, Lindås AC, Hjort K, Poplawski AB, Kaessmann H, Grogan DW, Kelman Z, Andersson AF, Pelve EA, Lundgren M, Svärd SG. Rolf Bernander (1956-2014): pioneer of the archaeal cell cycle. Mol Microbiol 2014; 92:903-9. [PMID: 24865634 DOI: 10.1111/mmi.12608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2014] [Indexed: 11/29/2022]
Abstract
On 19 January 2014 Rolf ('Roffe') Bernander passed away unexpectedly. Rolf was a dedicated scientist; his research aimed at unravelling the cell biology of the archaeal domain of life, especially cell cycle-related questions, but he also made important contributions in other areas of microbiology. Rolf had a professor position in the Molecular Evolution programme at Uppsala University, Sweden for about 8 years, and in January 2013 he became chair professor at the Department of Molecular Biosciences, The Wenner-Gren Institute at Stockholm University in Sweden. Rolf was an exceptional colleague and will be deeply missed by his family and friends, and the colleagues and co-workers that he leaves behind in the scientific community. He will be remembered for his endless enthusiasm for science, his analytical mind, and his quirky sense of humour.
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Affiliation(s)
- Thijs J G Ettema
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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141
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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142
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Characteristics of the new plasmid, pMTB1, from the metagenome of the microbial community of underground thermal waters of Western Siberia. BIOL BULL+ 2014. [DOI: 10.1134/s1062359014030054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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143
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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144
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145
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146
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147
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148
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 584] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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149
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Singh S, Zhang J, Huber TD, Sunkara M, Hurley K, Goff RD, Wang G, Zhang W, Liu C, Rohr J, Van Lanen SG, Morris AJ, Thorson JS. Facile chemoenzymatic strategies for the synthesis and utilization of S-adenosyl-(L)-methionine analogues. Angew Chem Int Ed Engl 2014; 53:3965-9. [PMID: 24616228 PMCID: PMC4076696 DOI: 10.1002/anie.201308272] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/16/2013] [Indexed: 01/22/2023]
Abstract
A chemoenzymatic platform for the synthesis of S-adenosyl-L-methionine (SAM) analogues compatible with downstream SAM-utilizing enzymes is reported. Forty-four non-native S/Se-alkylated Met analogues were synthesized and applied to probing the substrate specificity of five diverse methionine adenosyltransferases (MATs). Human MAT II was among the most permissive of the MATs analyzed and enabled the chemoenzymatic synthesis of 29 non-native SAM analogues. As a proof of concept for the feasibility of natural product "alkylrandomization", a small set of differentially-alkylated indolocarbazole analogues was generated by using a coupled hMAT2-RebM system (RebM is the sugar C4'-O-methyltransferase that is involved in rebeccamycin biosynthesis). The ability to couple SAM synthesis and utilization in a single vessel circumvents issues associated with the rapid decomposition of SAM analogues and thereby opens the door for the further interrogation of a wide range of SAM utilizing enzymes.
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Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Jianjun Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Tyler D. Huber
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, Gill Heart Institute, University of Kentucky, Lexington, KY 40536 (USA)
| | - Katherine Hurley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53705 (USA)
| | - Randal D. Goff
- Western Wyoming Community College, 2500 College Dr. Rock Springs, WY 82902-0428
| | - Guojun Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Wen Zhang
- Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, University of Kentucky, Lexington, KY 40536 (USA)
| | - Chunming Liu
- Molecular and Cellular Biochemistry, University of Kentucky, College of Medicine, University of Kentucky, Lexington, KY 40536 (USA)
| | - Jürgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, Gill Heart Institute, University of Kentucky, Lexington, KY 40536 (USA)
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536 (USA). Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536 (USA)
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150
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Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149-70. [PMID: 23807207 PMCID: PMC11114072 DOI: 10.1007/s00018-013-1388-z] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 05/27/2013] [Indexed: 10/26/2022]
Abstract
α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia,
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