Biocatalysts: application and engineering for industrial purposes

Jemli, Sonia; Ayadi-Zouari, Dorra; Hlima, Hajer Ben; Béjar, Samír

doi:10.3109/07388551.2014.950550

Cited by 189 publications

(145 citation statements)

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“…Thus, only a tiny fraction of the Earth's biosphere has been explored for the purpose of enzyme discovery, despite the fact that natural microbial diversity has been recognized to be the major source of new microbes (7). Such diversity also contains novel genes and functions (8) whose activities remain mostly unknown but whose potential to contribute to an innovation-based economy is recognized (9,10).…”

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confidence: 99%

Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

Alcaide

Tchigvintsev

Martínez-Martínez

et al. 2015

Appl Environ Microbiol

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iThe shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (<52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (<356 U mg ؊1 ) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities. Metagenomics provides a means for the discovery of entirely new enzymes in microorganisms and their communities without the need to culture these microorganisms as individual species, which is technically very difficult (1-5). Although the discovery of new enzyme activities has progressed considerably (6), it has not managed to go beyond the effective identification of enzymatic activities at a rather limited number of environmental sites. While an extensive search in the specialized literature and public databases indicated that microbial communities from approximately 1,800 different sites worldwide have been examined for their genomic content, only in approximately 200 of those locations (11% of the total) have new active clones or enzymes been identified and/or partially characterized. Thus, only a tiny fraction of the Earth's biosphere has been explored for the purpose of enzyme discovery, despite the fact that natural microbial diversity has been recognized to be the major source of new microbes (7). Such diversity also contains novel genes and functions (8) whose activities remain mostly unknown but whose potential to contribute to an innovation-based economy is recognized (9, 10).One of the habitats less explored to date in terms of examining enzyme repertoires is the deep-sea realm, where...

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Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

Alcaide

Tchigvintsev

Martínez-Martínez

et al. 2015

Appl Environ Microbiol

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“…V současnosti jsou proteasy nejvíce využívanými enzymy 1, 2, 6). V detergentech se využívají jako složka čistících prostředku do domácnosti, přípravků pro čištění kontaktních čoček, čističů zubních protéz a pracích prášků (19)(20)(21). Čtvrtinu celosvětového komerčního obratu proteas tvoří právě výroba pracích prášků.…”

Section: Průmyslové Aplikaceunclassified

“…Současné metody, které využívá kožešnický průmysl, pracují s nebezpečnými chemikáliemi, jenž mají velký dopad na životní prostředí. Enzymy představují jejich šetrnou alternativu, protože jsou schopné zároveň zlepšit kvalitu kůže a redukovat znečištění životního prostředí (19,20). V potravinářském průmyslu se proteasy využívají již od antiky, např.…”

Section: Průmyslové Aplikaceunclassified

Microbial Proteases and Their Applications

Válek¹,

Pohanka²

2018

Mil. Med. Sci. Lett.

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Přijato 6. listopadu 2017. Zrevidováno 4. ledna 2018. Zveřejněno 9. března 2018. ÚvodProteasy jsou hydrolytické enzymy běžně se vyskytující v těle živočichů, rostlin, hub a mikroorganismů včetně virů (1, 2). Majoritně se využívají v průmyslu a biotechnologiích, kde je lze označit za významnou komoditu. Celosvětový obchod s enzymy byl v roce 2015 odhadován na 7 mld. USD, z toho proteasy tvoří 60% celosvětového prodeje enzymů (3). V současné době jsou z proteas nejvíce využívány mikrobiální proteasy, které tvoří 40 % celkového obchodního obratu a poptávka se neustále zvyšuje v souvislosti s tím, jak roste zájem o aplikační využití (2, 3). Vzhledem k nízké efektivitě produkce proteas z rostlin a živočichů se začaly, jako producenti velkého množství, využívat mikroorganismy (2). Existuje mnoho mikroorganismů schopných produkovat proteasy, ale jen malé procento z nich je vhodné k průmyslovému, medicínskému a jinému aplikačnímu využití (4). Proteasy mohou katalyzovat řadu odlišných reakcí a je zapotřebí vybrat právě ty, jež splňují kritéria pro využití v analytické chemii, medicíně či biotechnologiích (2). Většina komerčně využívaných proteas pochází z mikroorganismů rodu Bacillus. Využití mikrobiálních forem života pro produkci enzymů má několik výhod: produkce velkého množství enzymu Univerzita obrany, Fakulta vojenského zdravotnictví, Katedra molekulární patologie a biologie (K-308), Třebešská 1575, 50001 Hradec Králové miroslav.pohanka@gmail.com SouhrnProteasy jsou skupina enzymů mikrobiálního, rostlinného i živočišného původu s nezastupitelným významem v základním metabolismu. Jedná se však i o materiál, který je vhodný k biotechnologickým aplikacím v širokém spektru oblastí jako je potravinový průmysl, výroba čistících prostředků a medicínské využití. Tento přehledový článek shrnuje základní informace o proteasach a nastiňuje příklady jejich použití. Klíčová slova: proteasy; enzym; biotechnologie; mikrobiální SummaryProteases are enzymes microbial, plant or animal origin with crucial importance in the basic metabolism. It is also a suitable material for biotechnological applications in a wide range of fields of interests like food industry, cleaning agents and medicine applications. This review paper surveys basic data about proteases and provides representative examples of their application.

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“…This is one of the reasons why engineering enzymes for biocatalysis is an incessantly growing field [8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution

Monza

Acebes

Lucas

et al. 2017

Directed Enzyme Evolution: Advances and Applications

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Directed evolution creates diversity in subsequent rounds of mutagenesis in the quest of increased protein stability, substrate binding and catalysis. Although this technique does not require any structural/mechanistic knowledge of the system, the frequency of improved mutations is usually low. For this reason, computational tools are increasingly used to focus the search in sequence space, enhancing the efficiency of laboratory evolution. In particular, molecular modeling methods provide a unique tool to grasp the sequence/structure/function relationship The final publication is available at Springer via https://link.springer.com/chapter/10.1007/978-3-319-50413-1_10/fulltext.html of the protein to evolve, with the only condition that a structural model is provided. With this book chapter, we tried to guide the reader through the state of art of molecular modeling, discussing their strengths, limitations and directions. In addition, we suggest a possible future template for in silico directed evolution where we underline two main points: a hierarchical computational protocol combining several different techniques, and a synergic effort between simulations and experimental validation. IntroductionBiotechnology needs catalysts that can work under harsh conditions, catalyze a broad range of substrates, generate maximum amount of product, and tolerate changes in the environment. Enzymes, which are biodegradable and reusable catalysts [1], in addition to remarkable reaction rates, can work in environmentally friendly pH and temperature ranges, and display control over stereochemistry and regioselectivity which makes them ideal for many applications [2,3]. When thinking about enzymes, people normally associate them to expressions such as "perfect catalysts" or "outstanding reaction rate". In fact, there are examples of enzymes that catalyze reactions at extremely high rates such as triose phosphate isomerase, superoxide dismutase or carbonic anhydrase [4]. These are often limited only by the rate of ligand diffusion into the active site (diffusion-controlled rate). Nevertheless, an extensive analysis by Bar-Even et al., of nearly 2000 enzymes, showed that the median maximal turnover rate value over all measured enzymes is about 10 s −1 nowhere close to the values of 10 5 or 10 6 normally associated with catalysts [5,6].So, it would appear that natural enzymes are "just good enough" for the function they must perform in a given organism [7]. One might conclude that if they had evolved to their optimum performance then trying to improve them (from a kinetic point of view) would be attempting the impossible. On the contrary, as seen by the distribution of reaction rates, k cat , most enzymes function at a lower rate than the diffusion-limit and thus, there is space to further increase their kinetic properties to meet industrial needs. Additionally, we need enzymes capable of catalyzing reactions for which no known enzymes exist, to work with different substrates and for particular conditions that are industrially...

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Biocatalysts: application and engineering for industrial purposes

Cited by 189 publications

References 122 publications

Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics

Microbial Proteases and Their Applications

Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution

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