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[PMID]:29179671
[Au] Autor:Hudaiberdiev S; Shmakov S; Wolf YI; Terns MP; Makarova KS; Koonin EV
[Ad] Endereço:National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
[Ti] Título:Phylogenomics of Cas4 family nucleases.
[So] Source:BMC Evol Biol;17(1):232, 2017 Nov 28.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The Cas4 family endonuclease is a component of the adaptation module in many variants of CRISPR-Cas adaptive immunity systems. Unlike most of the other Cas proteins, Cas4 is often encoded outside CRISPR-cas loci (solo-Cas4) and is also found in mobile genetic elements (MGE-Cas4). RESULTS: As part of our ongoing investigation of CRISPR-Cas evolution, we explored the phylogenomics of the Cas4 family. About 90% of the archaeal genomes encode Cas4 compared to only about 20% of the bacterial genomes. Many archaea encode both the CRISPR-associated form (CAS-Cas4) and solo-Cas4, whereas in bacteria, this combination is extremely rare. The solo-cas4 genes are over-represented in environmental bacteria and archaea with small genomes that typically lack CRISPR-Cas, suggesting that Cas4 could perform uncharacterized defense or repair functions in these microbes. Phylogenomic analysis indicates that both the CRISPR-associated cas4 genes are often transferred horizontally but almost exclusively, as part of the adaptation module. The evolutionary integrity of the adaptation module sharply contrasts the rampant shuffling of CRISPR-cas modules whereby a given variant of the adaptation module can combine with virtually any effector module. The solo-cas4 genes evolve primarily via vertical inheritance and are subject only to occasional horizontal transfer. The selection pressure on cas4 genes does not substantially differ between CAS-Cas4 and solo-cas4, and is close to the genomic median. Thus, cas4 genes, similarly to cas1 and cas2, evolve similarly to 'regular' microbial genes involved in various cellular functions, showing no evidence of direct involvement in virus-host arms races. A notable feature of the Cas4 family evolution is the frequent recruitment of cas4 genes by various mobile genetic elements (MGE), particularly, archaeal viruses. The functions of Cas4 in these elements are unknown and potentially might involve anti-defense roles. CONCLUSIONS: Unlike most of the other Cas proteins, Cas4 family members are as often encoded by stand-alone genes as they are incorporated in CRISPR-Cas systems. In addition, cas4 genes were repeatedly recruited by MGE, perhaps, for anti-defense functions. Experimental characterization of the solo and MGE-encoded Cas4 nucleases is expected to reveal currently uncharacterized defense and anti-defense systems and their interactions with CRISPR-Cas systems.
[Mh] Termos MeSH primário: Sistemas CRISPR-Cas/genética
Endonucleases/genética
Genômica
Família Multigênica
[Mh] Termos MeSH secundário: Archaea/enzimologia
Archaea/genética
Bactérias/enzimologia
Bactérias/genética
Sequência de Bases
Elementos de DNA Transponíveis/genética
Transferência Genética Horizontal/genética
Loci Gênicos
Genoma Arqueal
Genoma Bacteriano
Filogenia
Seleção Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Transposable Elements); EC 3.1.- (Endonucleases)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171129
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1081-1


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[PMID]:28470848
[Au] Autor:Camprubi E; Jordan SF; Vasiliadou R; Lane N
[Ad] Endereço:Department of Genetics, Evolution and Environment, University College London, London, UK.
[Ti] Título:Iron catalysis at the origin of life.
[So] Source:IUBMB Life;69(6):373-381, 2017 06.
[Is] ISSN:1521-6551
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Iron-sulphur proteins are ancient and drive fundamental processes in cells, notably electron transfer and CO fixation. Iron-sulphur minerals with equivalent structures could have played a key role in the origin of life. However, the 'iron-sulphur world' hypothesis has had a mixed reception, with questions raised especially about the feasibility of a pyrites-pulled reverse Krebs cycle. Phylogenetics suggests that the earliest cells drove carbon and energy metabolism via the acetyl CoA pathway, which is also replete in Fe(Ni)S proteins. Deep differences between bacteria and archaea in this pathway obscure the ancestral state. These differences make sense if early cells depended on natural proton gradients in alkaline hydrothermal vents. If so, the acetyl CoA pathway diverged with the origins of active ion pumping, and ancestral CO fixation might have been equivalent to methanogens, which depend on a membrane-bound NiFe hydrogenase, energy converting hydrogenase. This uses the proton-motive force to reduce ferredoxin, thence CO . The mechanism suggests that pH could modulate reduction potential at the active site of the enzyme, facilitating the difficult reduction of CO by H . This mechanism could be generalised under abiotic conditions so that steep pH differences across semi-conducting Fe(Ni)S barriers drives not just the first steps of CO fixation to C1 and C2 organics such as CO, CH SH and CH COSH, but a series of similar carbonylation and hydrogenation reactions to form longer chain carboxylic acids such as pyruvate, oxaloacetate and α-ketoglutarate, as in the incomplete reverse Krebs cycle found in methanogens. We suggest that the closure of a complete reverse Krebs cycle, by regenerating acetyl CoA directly, displaced the acetyl CoA pathway from many modern groups. A later reliance on acetyl CoA and ATP eliminated the need for the proton-motive force to drive most steps of the reverse Krebs cycle. © 2017 IUBMB Life, 69(6):373-381, 2017.
[Mh] Termos MeSH primário: Acetilcoenzima A/química
Ferredoxinas/química
Proteínas com Ferro-Enxofre/química
Ferro/química
Origem da Vida
[Mh] Termos MeSH secundário: Acetilcoenzima A/metabolismo
Archaea/química
Archaea/metabolismo
Bactérias/química
Bactérias/metabolismo
Ciclo do Carbono
Dióxido de Carbono/química
Dióxido de Carbono/metabolismo
Catálise
Ciclo do Ácido Cítrico
Ferredoxinas/metabolismo
Concentração de Íons de Hidrogênio
Fontes Hidrotermais
Ferro/metabolismo
Proteínas com Ferro-Enxofre/metabolismo
Ácidos Cetoglutáricos/química
Ácidos Cetoglutáricos/metabolismo
Ácido Oxaloacético/química
Ácido Oxaloacético/metabolismo
Prótons
Ácido Pirúvico/química
Ácido Pirúvico/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Ferredoxins); 0 (Iron-Sulfur Proteins); 0 (Ketoglutaric Acids); 0 (Protons); 142M471B3J (Carbon Dioxide); 2F399MM81J (Oxaloacetic Acid); 72-89-9 (Acetyl Coenzyme A); 8558G7RUTR (Pyruvic Acid); 8ID597Z82X (alpha-ketoglutaric acid); E1UOL152H7 (Iron)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1002/iub.1632


  3 / 7781 MEDLINE  
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[PMID]:29478661
[Au] Autor:Ma W; Sun J; Li Y; Lun X; Shan D; Nie C; Liu M
[Ad] Endereço:College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China. Electronic address: mpeggy@163.com.
[Ti] Título:17α-Ethynylestradiol biodegradation in different river-based groundwater recharge modes with reclaimed water and degradation-associated community structure of bacteria and archaea.
[So] Source:J Environ Sci (China);64:51-61, 2018 Feb.
[Is] ISSN:1001-0742
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:This study investigated 17α-ethynylestradiol (EE2) biodegradation process and primary metabolic pathways associated with community structures of microorganism during groundwater recharge using reclaimed water. The attenuation rate is 1.58 times higher in wetting and drying alternative recharge (WDAR) than in continual recharge (CR). The primary biotransformation pathways of EE2 in WDAR system began with the oxidation of C-17 on ring D to form a ketone group, and D-ring was subsequently hydroxylated and cleaved. In the CR system, the metabolic pathway changed from the oxidation of C-17 on ring D to hydroxylation of C-4 on ring A, and ring A or B subsequently cleaved; this transition was related to DO, and the microbial community structure. Four hundred fifty four pyrosequencing of 16s rRNA genes indicated that the bacterial communities in the upper layer of the WDAR system were more diverse than those found in the bottom layer of the CR system; this result was reversed for archaea. Unweighted UniFrac and taxonomic analyses were conducted to relate the change in bacterial community structure to the metabolic pathway. Microorganism community diversity and structure were related to the concentrations of dissolved oxygen, EE2 and its intermediates in the system. Five known bacterial classes and one known archaeal class, five major bacterial genera and one major archaeal genus might be involved in EE2 degradation. The findings of this study provide an understanding of EE2 biodegradation in groundwater recharge areas under different recharging modes and can facilitate the prediction of the fate of EE2 in underground aquifers.
[Mh] Termos MeSH primário: Etinilestradiol/metabolismo
Água Subterrânea/microbiologia
Rios/microbiologia
Poluentes Químicos da Água/metabolismo
[Mh] Termos MeSH secundário: Archaea/fisiologia
Bactérias/metabolismo
Etinilestradiol/análise
Água Subterrânea/química
Rios/química
Microbiologia da Água
Poluentes Químicos da Água/análise
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Water Pollutants, Chemical); 423D2T571U (Ethinyl Estradiol)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180301
[Lr] Data última revisão:
180301
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180227
[St] Status:MEDLINE


  4 / 7781 MEDLINE  
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[PMID]:29478633
[Au] Autor:Zhu J; Chen L; Zhang Y; Zhu X
[Ad] Endereço:School of Environment, Tsinghua University, Beijing 100084, China. Electronic address: a5130751@126.com.
[Ti] Título:Revealing the anaerobic acclimation of microbial community in a membrane bioreactor for coking wastewater treatment by Illumina Miseq sequencing.
[So] Source:J Environ Sci (China);64:139-148, 2018 Feb.
[Is] ISSN:1001-0742
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:The dynamic change of microbial community during sludge acclimation from aerobic to anaerobic in a MBR for coking wastewater treatment was revealed by Illumina Miseq sequencing in this study. The diversity of both Bacteria and Archaea showed an increase-decrease trajectory during acclimation, and exhibited the highest at the domestication interim. Ignavibacteria changed from a tiny minority (less than 1%) to the dominant bacterial group (54.0%) along with acclimation. The relative abundance of Betaproteobacteria kept relatively steady, as in this class some species increased coupled with some other species decreased during acclimation. The dominant Archaea shifted from Halobacteria in initial aerobic sludge to Methanobacteria in the acclimated anaerobic sludge. The dominant bacterial and archaeal groups in different acclimation stages were indigenous microorganisms in the initial sludge, though some of them were very rare. This study supported that the species in "rare biosphere" might eventually become dominant in response to environmental change.
[Mh] Termos MeSH primário: Aclimatação/genética
Reatores Biológicos/microbiologia
Eliminação de Resíduos Líquidos/métodos
Águas Residuais/microbiologia
[Mh] Termos MeSH secundário: Anaerobiose
Archaea/fisiologia
Bactérias/metabolismo
Análise da Demanda Biológica de Oxigênio
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Waste Water)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180301
[Lr] Data última revisão:
180301
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180227
[St] Status:MEDLINE


  5 / 7781 MEDLINE  
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[PMID]:28460196
[Au] Autor:Warinner C; Herbig A; Mann A; Fellows Yates JA; Weiß CL; Burbano HA; Orlando L; Krause J
[Ad] Endereço:Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email: warinner@shh.mpg.de.
[Ti] Título:A Robust Framework for Microbial Archaeology.
[So] Source:Annu Rev Genomics Hum Genet;18:321-356, 2017 Aug 31.
[Is] ISSN:1545-293X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field.
[Mh] Termos MeSH primário: Archaea/isolamento & purificação
Bactérias/isolamento & purificação
DNA Antigo/análise
Metagenômica/métodos
Microbiota/genética
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Archaea/genética
Arqueologia/métodos
Bactérias/genética
Genoma Arqueal
Genoma Bacteriano
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (DNA, Ancient)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180228
[Lr] Data última revisão:
180228
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1146/annurev-genom-091416-035526


  6 / 7781 MEDLINE  
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[PMID]:29251473
[Au] Autor:Dong L; Meng Y; Wang J; Sun G
[Ti] Título:Effects of Transgenic Bt+CpTI cotton on the abundance and diversity of rhizosphere ammonia oxidizing bacteria and archaea.
[So] Source:J Environ Biol;37(5):881-8, 2016 09.
[Is] ISSN:0254-8704
[Cp] País de publicação:India
[La] Idioma:eng
[Ab] Resumo:Genetically modified crops (GMCs) hold great promise for improving agricultural output, but at the same time present challenges in terms of environmental safety assessment. Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and archaea (AOA), are very important functional microbial groups in nitrogen cycle. The abundance and diversity of AOA and AOB in the rhizosphere of genetically modified cotton (SGK321) and non-GM cotton (SY321) across growth stages were investigated using real time quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP). Results showed that cotton genotype had a significant effect on the change in abundance of AOA and AOB, as indicated by amoA copy number. Variations in AOB abundance in rhizosphere of SY321 differed from those in SGK321. The number of AOB in the rhizosphere of SY321 fluctuated considerably: It dramatically decreased from 1.2?106 copies g-1 dry soil to 3?105 copies g-1 dry soil during the flowering stage and then increased to 1.1?106 copies g-1 and 1.5?106 copies g-1 at the belling and boll opening stages, respectively. However, abundance of AOB in the rhizosphere of SGK321 was relatively stable during all the stages of growth. The effect of SGK321 and SY321 on AOA number was quite similar to that of AOB: AOA abundance in SGK321 increased smoothly from 1.0 ?105 copies g-1 dry soil to 1.4?106 copies g-1 dry soil during growth, but that in SY321 fluctuated. Correspondence analysis (CA), canonical CA (CCA), and partial CCA (pCCA) of T-RFLP profiles of AOA and AOB showed that AOB community changed across growth stages in both cotton genotypes, and cotton genotype was the most important factor affecting the AOA community. In conclusion, the current findings indicated no adverse effect of GM cotton on functional microorganisms.
[Mh] Termos MeSH primário: Amônia/metabolismo
Archaea/metabolismo
Bactérias/metabolismo
Gossypium/genética
Microbiologia do Solo
[Mh] Termos MeSH secundário: Archaea/classificação
Bactérias/classificação
DNA Arqueal/genética
DNA Bacteriano/genética
Oxirredução
Raízes de Plantas
Plantas Geneticamente Modificadas
Solo
[Pt] Tipo de publicação:RESEARCH SUPPORT, NON-U.S. GOV'T; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Archaeal); 0 (DNA, Bacterial); 0 (Soil); 7664-41-7 (Ammonia)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171219
[St] Status:MEDLINE


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[PMID]:28749735
[Au] Autor:Borges AL; Davidson AR; Bondy-Denomy J
[Ad] Endereço:Department of Microbiology and Immunology, University of California, San Francisco, California 94158; email: joseph.bondy-denomy@ucsf.edu.
[Ti] Título:The Discovery, Mechanisms, and Evolutionary Impact of Anti-CRISPRs.
[So] Source:Annu Rev Virol;4(1):37-59, 2017 Sep 29.
[Is] ISSN:2327-0578
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Bacteria and archaea use CRISPR-Cas adaptive immune systems to defend themselves from infection by bacteriophages (phages). These RNA-guided nucleases are powerful weapons in the fight against foreign DNA, such as phages and plasmids, as well as a revolutionary gene editing tool. Phages are not passive bystanders in their interactions with CRISPR-Cas systems, however; recent discoveries have described phage genes that inhibit CRISPR-Cas function. More than 20 protein families, previously of unknown function, have been ascribed anti-CRISPR function. Here, we discuss how these CRISPR-Cas inhibitors were discovered and their modes of action were elucidated. We also consider the potential impact of anti-CRISPRs on bacterial and phage evolution. Finally, we speculate about the future of this field.
[Mh] Termos MeSH primário: Bactérias/genética
Bacteriófagos/genética
Bacteriófagos/fisiologia
Sistemas CRISPR-Cas
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas
Evolução Molecular
[Mh] Termos MeSH secundário: Archaea/genética
Bactérias/virologia
Bacteriófagos/metabolismo
Edição de Genes
Proteínas Virais/genética
Proteínas Virais/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Viral Proteins)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180217
[Lr] Data última revisão:
180217
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170728
[St] Status:MEDLINE
[do] DOI:10.1146/annurev-virology-101416-041616


  8 / 7781 MEDLINE  
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[PMID]:27771364
[Au] Autor:Loder AJ; Han Y; Hawkins AB; Lian H; Lipscomb GL; Schut GJ; Keller MW; Adams MWW; Kelly RM
[Ad] Endereço:Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, United States.
[Ti] Título:Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO fixation cycle in extremely thermoacidophilic archaea.
[So] Source:Metab Eng;38:446-463, 2016 11.
[Is] ISSN:1096-7184
[Cp] País de publicação:Belgium
[La] Idioma:eng
[Ab] Resumo:The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35-65% split of carbon flux through the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxypropionate.
[Mh] Termos MeSH primário: Dióxido de Carbono/metabolismo
Hidroxibutiratos/metabolismo
Ácido Láctico/análogos & derivados
Análise do Fluxo Metabólico/métodos
Redes e Vias Metabólicas/fisiologia
Modelos Biológicos
Sulfolobaceae/metabolismo
[Mh] Termos MeSH secundário: Archaea/metabolismo
Extremófilos/metabolismo
Cinética
Ácido Láctico/metabolismo
Taxa de Depuração Metabólica
Transdução de Sinais/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Hydroxybutyrates); 142M471B3J (Carbon Dioxide); 30IW36W5B2 (4-hydroxybutyric acid); 33X04XA5AT (Lactic Acid); C4ZF6XLD2X (hydracrylic acid)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180214
[Lr] Data última revisão:
180214
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161025
[St] Status:MEDLINE


  9 / 7781 MEDLINE  
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[PMID]:28822812
[Au] Autor:Harris KL; Thomson RES; Strohmaier SJ; Gumulya Y; Gillam EMJ
[Ad] Endereço:School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia.
[Ti] Título:Determinants of thermostability in the cytochrome P450 fold.
[So] Source:Biochim Biophys Acta;1866(1):97-115, 2018 01.
[Is] ISSN:0006-3002
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Cytochromes P450 are found throughout the biosphere in a wide range of environments, serving a multitude of physiological functions. The ubiquity of the P450 fold suggests that it has been co-opted by evolution many times, and likely presents a useful compromise between structural stability and conformational flexibility. The diversity of substrates metabolized and reactions catalyzed by P450s makes them attractive starting materials for use as biocatalysts of commercially useful reactions. However, process conditions impose different requirements on enzymes to those in which they have evolved naturally. Most natural environments are relatively mild, and therefore most P450s have not been selected in Nature for the ability to withstand temperatures above ~40°C, yet industrial processes frequently require extended incubations at much higher temperatures. Thus, there has been considerable interest and effort invested in finding or engineering thermostable P450 systems. Numerous P450s have now been identified in thermophilic organisms and analysis of their structures provides information as to mechanisms by which the P450 fold can be stabilized. In addition, protein engineering, particularly by directed or artificial evolution, has revealed mutations that serve to stabilize particular mesophilic enzymes of interest. Here we review the current understanding of thermostability as it applies to the P450 fold, gleaned from the analysis of P450s characterized from thermophilic organisms and the parallel engineering of mesophilic forms for greater thermostability. We then present a perspective on how this information might be used to design stable P450 enzymes for industrial application. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
[Mh] Termos MeSH primário: Archaea/enzimologia
Bactérias/enzimologia
Sistema Enzimático do Citocromo P-450/química
Engenharia de Proteínas/métodos
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Archaea/genética
Bactérias/genética
Biocatálise
Estabilidade Enzimática
Expressão Gênica
Seres Humanos
Modelos Moleculares
Conformação Proteica em alfa-Hélice
Conformação Proteica em Folha beta
Dobramento de Proteína
Alinhamento de Sequência
Homologia de Sequência de Aminoácidos
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; REVIEW
[Nm] Nome de substância:
9035-51-2 (Cytochrome P-450 Enzyme System)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170821
[St] Status:MEDLINE


  10 / 7781 MEDLINE  
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[PMID]:28502748
[Au] Autor:Nelson DR
[Ad] Endereço:University of Tennessee Health Science Center, Dept. of Microbiology, Immunology and Biochemistry, 858 Madison Ave. Suite G01, Memphis, TN 38163, USA. Electronic address: dnelson@uthsc.edu.
[Ti] Título:Cytochrome P450 diversity in the tree of life.
[So] Source:Biochim Biophys Acta;1866(1):141-154, 2018 01.
[Is] ISSN:0006-3002
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Sequencing in all areas of the tree of life has produced >300,000 cytochrome P450 (CYP) sequences that have been mined and collected. Nomenclature has been assigned to >41,000 CYP sequences and the majority of the remainder has been sorted by BLAST searches into clans, families and subfamilies in preparation for naming. The P450 sequence space is being systematically explored and filled in. Well-studied groups like vertebrates are covered in greater depth while new insights are being added into uncharted territories like horseshoe crab (Limulus polyphemus), tardigrades (Hypsibius dujardini), velvet worm (Euperipatoides_rowelli), and basal land plants like hornworts, liverworts and mosses. CYPs from the fungi, one of the most diverse groups, are being explored and organized as nearly 800 fungal species are now sequenced. The CYP clan structure in fungi is emerging with 805 CYP families sorting into 32 CYP clans. >3000 bacterial sequences are named, mostly from terrestrial or freshwater sources. Of 18,379 bacterial sequences downloaded from the CYPED database, all are >43% identical to named CYPs. Therefore, they fit in the 602 named P450 prokaryotic families. Diversity in this group is becoming saturated, however 25% of 3305 seawater bacterial P450s did not match known P450 families, indicating marine bacterial CYPs are not as well sampled as land/freshwater based bacterial CYPs. Future sequencing plans of the Genome 10K project, i5k and GIGA (Global Invertebrate Genomics Alliance) are expected to produce more than one million cytochrome P450 sequences by 2020. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
[Mh] Termos MeSH primário: Sistema Enzimático do Citocromo P-450/classificação
Sistema Enzimático do Citocromo P-450/genética
Variação Genética
Genoma
Filogenia
[Mh] Termos MeSH secundário: Animais
Archaea/classificação
Archaea/enzimologia
Archaea/genética
Artrópodes/classificação
Artrópodes/enzimologia
Artrópodes/genética
Bactérias/classificação
Bactérias/enzimologia
Bactérias/genética
Evolução Biológica
Aves/classificação
Aves/genética
Aves/metabolismo
Sistema Enzimático do Citocromo P-450/metabolismo
Fungos/classificação
Fungos/enzimologia
Fungos/genética
Expressão Gênica
Seres Humanos
Família Multigênica
Plantas/classificação
Plantas/enzimologia
Plantas/genética
Tardígrados/classificação
Tardígrados/enzimologia
Tardígrados/genética
Vírus/classificação
Vírus/enzimologia
Vírus/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9035-51-2 (Cytochrome P-450 Enzyme System)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170516
[St] Status:MEDLINE



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