Emerging Fields in Functional Metagenomics and Its Industrial Relevance: Overcoming Limitations and Redirecting the Search for Novel Biocatalysts

Perner, Mirjam; Ilmberger, Nele; Köhler, Hans Ulrich; Chow, Jennifer; Streit, Wolfgang R.

doi:10.1002/9781118010549.ch47

Cited by 9 publications

(10 citation statements)

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“…Commonly, the heterologous expression of (hydrogenase) enzymes (i.e., the expression in a foreign host) is limited by promoter recognition, diverging codon-usage, translation and the incompatibility or a lack of the respective maturation and assembly apparatus (cf. Perner et al, 2011b ). In E. coli for example, the exchange of a carboxy-terminal extension of the large subunit of a [NiFe]-hydrogenase with that from an isoenzyme resulted in the abortion of the protein maturation.…”

Section: Hydrogenase Genesmentioning

confidence: 99%

“…However, compared to some enzymes like esterases, which are considered as one of the most important industrial biocatalysts (cf. Perner et al, 2011b ), hydrogenases have only rarely been in the focus of metagenomic studies. Moreover, in most cases the metagenomic datasets were merely screened for the presence of [NiFe]-hydrogenase genes (e.g., Brazelton et al, 2012 ; Dahle et al, 2013 ; Perner et al, 2014 ; Fortunato and Huber, 2016 ).…”

Section: Hydrogenase Genesmentioning

confidence: 99%

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Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents

Adam

Perner

2018

Front. Microbiol.

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Deep-sea hydrothermal vents may provide one of the largest reservoirs on Earth for hydrogen-oxidizing microorganisms. Depending on the type of geological setting, hydrothermal environments can be considerably enriched in hydrogen (up to millimolar concentrations). As hot, reduced hydrothermal fluids ascend to the seafloor they mix with entrained cold, oxygenated seawater, forming thermal and chemical gradients along their fluid pathways. Consequently, in these thermally and chemically dynamic habitats biochemically distinct hydrogenases (adapted to various temperature regimes, oxygen and hydrogen concentrations) from physiologically and phylogenetically diverse Bacteria and Archaea can be expected. Hydrogen oxidation is one of the important inorganic energy sources in these habitats, capable of providing relatively large amounts of energy (237 kJ/mol H2) for driving ATP synthesis and autotrophic CO2 fixation. Therefore, hydrogen-oxidizing organisms play a key role in deep-sea hydrothermal vent ecosystems as they can be considerably involved in light-independent primary biomass production. So far, the specific role of hydrogen-utilizing microorganisms in deep-sea hydrothermal ecosystems has been investigated by isolating hydrogen-oxidizers, measuring hydrogen consumption (ex situ), studying hydrogenase gene distribution and more recently by analyzing metatranscriptomic and metaproteomic data. Here we summarize this available knowledge and discuss the advent of new techniques for the identification of novel hydrogen-uptake and -evolving enzymes from hydrothermal vent microorganisms.

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Section: Hydrogenase Genesmentioning

confidence: 99%

Section: Hydrogenase Genesmentioning

confidence: 99%

Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents

Adam

Perner

2018

Front. Microbiol.

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“…Even though drawbacks exist when expressing environmental DNA in a surrogate host (troubles are associated with e.g., recognition of intrinsic promoters, codon usage, translation, assembly and folding of enzymes etc.) [13], it is the only way to discover truly novel enzymes [14].…”

Section: Introductionmentioning

confidence: 99%

Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments

Böhnke

Perner

2019

The ISME Journal

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Almost all the inorganic carbon on Earth is converted into biomass via the Calvin-Benson-Bassham (CBB) cycle. Here, the central carboxylation reaction is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which can be found in numerous primary producers including plants, algae, cyanobacteria, and many autotrophic bacteria. Although RubisCO possesses a crucial role in global biomass production, it is not a perfect catalyst. Therefore, research interest persists on accessing the full potential of yet unexplored RubisCOs. We recently developed an activity-based screen suited to seek active recombinant RubisCOs from the environment-independent of the native host's culturability. Here, we applied this screen to twenty pre-selected genomic fosmid clones from six cultured proteobacteria to demonstrate that a broad range of phylogenetically distinct RubisCOs can be targeted. We then screened 12,500 metagenomic fosmid clones from six distinct hydrothermal vents and identified forty active RubisCOs. Additional sequence-based screening uncovered eight further RubisCOs, which could then also be detected by a modified version of the screen. Seven were active form III RubisCOs from yet uncultured Archaea. This indicates the potential of the activity-based screen to detect RubisCO enzymes even from organisms that would not be expected to be targeted.

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“…The primary disadvantage of this screening method is that gene expression may fail due to difficulties in promoter recognition, low translation efficiency, lack of specific cofactors in certain expression hosts, protein misfolding and post-translational modification defects of the desired proteins. However, all these issues can be solved using vectors with a wide host range that enables expression in a variety of hosts, vectors that are adapted to a large insert size and Rosetta strains of Escherichia coli, which contains transfer ribonucleic acid (tRNA) for rare amino acid codons [17,23]. Consequently, the function-based metagenomic approach is now the most frequently used technique for screening for novel extremozymes from the deep sea [24][25][26][27].…”

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Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review

et al. 2019

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The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.Nearly three-quarters of the Earth's surface area is covered by ocean, the average depth of which is 3800 m, implying that the vast majority of our planet comprises deep-sea environments. The deep sea is one of the most mysterious and unexplored environments on the Earth, and it supports diverse microbial communities that play important roles in biogeochemical cycles [1]. The deep sea is also recognised as an extreme environment, as it is characterised by the absence of sunlight and the presence of predominantly low temperatures and high hydrostatic pressures, and these environmental conditions become even more challenging in particular habitats, such as deep-sea hydrothermal vents with their extremely high temperatures of >400 • C, deep hypersaline anoxic basins (DHABs) with their extremely high salinities and abysses of up to 11 km depth with their extremely high pressures.Deep-sea extremophiles are living organisms that can survive and proliferate in deep-sea environments that have extreme physical (pressure and temperature) and geochemical (pH, salinity and redox potential) conditions that are lethal to other organisms. The majority of deep-sea extremophiles belong to the prokaryotes, which are microorganisms in the domains of Archaea and Bacteria [2,3].These extremophilic microorganisms are functionally diverse and widely distributed in taxonomy [4], and they are classified into thermophiles (55 • C to 121 • C), psychrophiles (−2 • C to 20 • C), halophiles (2-5 M NaCl or KCl), piezophiles (>500 atmospheres), alkalophiles (pH > 8), acidophiles (pH < 4) and metalophiles (high concentrations of metals, e.g., copper, zinc, cadmium and arsenic) according to the extreme environments in which they grow and the extreme conditions they can tolerate. Ma...

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Emerging Fields in Functional Metagenomics and Its Industrial Relevance: Overcoming Limitations and Redirecting the Search for Novel Biocatalysts

Cited by 9 publications

References 149 publications

Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents

Microbially Mediated Hydrogen Cycling in Deep-Sea Hydrothermal Vents

Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments

Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review

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