Comparison of the structural basis for thermal stability between archaeal and bacterial proteins

Ding, Yanrui; Cai, Yujie; Han, Yonggang; Zhao, Bingqiang

doi:10.1007/s00792-011-0406-z

Cited by 12 publications

(7 citation statements)

References 69 publications

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“…8b) gave insight into some of the factors that may confer stability in the Mj enzyme. The amino acid substitutions and their locations in Mj are consistent with thermostabilization strategies adopted by hyperthermophilic enzymes [34, 37–39]. Thermostable enzymes typically have more ion pairs (salt bridges), especially in networks, more hydrophobic interactions in their interior, and a larger number of bulkier hydrophobic side chains as compared to their mesophilic counterparts.…”

Section: Discussionmentioning

confidence: 60%

Characterization of the Dihydroorotase from Methanococcus jannaschii

2017

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The gene that codes for the putative dihydroorotase in the hyperthermophilic archaeon Methanococcus jannaschii was subcloned in pET-21a and expressed in Escherichia coli. A purification protocol was devised. The purity of the protein was evaluated by SDS-PAGE and the protein was confirmed by sequencing using LC-MS. The calculated molecular mass is 48104 Da. SEC-LS suggested that the protein is a monomer in solution. ICP-MS showed that there are two Zn ions per monomer. Kinetic analysis of the recombinant protein gave hyperbolic kinetics with Vmax = 12.2 µmol min−1 mg−1 and Km = 0.14 mM at 25° C. Furthermore the activity of the protein increased with temperature consistent with the hyperthermophilic nature of the organism. A homology model was constructed using the mesophilic Bacillus anthracis protein as the template. Residues known to be critical for Zn and substrate binding were conserved. The activity of the enzyme at 85° C and 90° C was found to be relatively constant over 160 min and this correlates with the temperature of optimal growth of the organism of 85° C. The amino acid sequences and structures of the two proteins were compared and this gave insight into some of the factors that may confer thermostability – more Lys and Ile, fewer Ala, Thr, Gln and Gly residues, and shorter N- and C-termini. Additional and better insight into the thermostabilization strategies adopted by this enzyme will be provided when its crystal structure is determined.

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Section: Discussionmentioning

confidence: 60%

Characterization of the Dihydroorotase from Methanococcus jannaschii

2017

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“…A comparison of structural basis for thermal stability in archaeal and bacterial proteins revealed that increased salt bridge and Glu content are among the important stabilizing factors of heat-resistant bacterial proteins [81]. Most thermophilic proteins tend to have more salt bridges, and achieve higher thermostability by up-shifting and broadening their protein stability curves.…”

Section: Resultsmentioning

confidence: 99%

Expression and Properties of the Highly Alkalophilic Phenylalanine Ammonia-Lyase of Thermophilic Rubrobacter xylanophilus

et al. 2014

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The sequence of a phenylalanine ammonia-lyase (PAL; EC: 4.3.1.24) of the thermophilic and radiotolerant bacterium Rubrobacter xylanophilus (RxPAL) was identified by screening the genomes of bacteria for members of the phenylalanine ammonia-lyase family. A synthetic gene encoding the RxPAL protein was cloned and overexpressed in Escherichia coli TOP 10 in a soluble form with an N-terminal His6-tag and the recombinant RxPAL protein was purified by Ni-NTA affinity chromatography. The activity assay of RxPAL with l-phenylalanine at various pH values exhibited a local maximum at pH 8.5 and a global maximum at pH 11.5. Circular dichroism (CD) studies showed that RxPAL is associated with an extensive α-helical character (far UV CD) and two distinctive near-UV CD peaks. These structural characteristics were well preserved up to pH 11.0. The extremely high pH optimum of RxPAL can be rationalized by a three-dimensional homology model indicating possible disulfide bridges, extensive salt-bridge formation and an excess of negative electrostatic potential on the surface. Due to these properties, RxPAL may be a candidate as biocatalyst in synthetic biotransformations leading to unnatural l- or d-amino acids or as therapeutic enzyme in treatment of phenylketonuria or leukemia.

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“…The Halanaerobiales follow an experimentally confirmed salt-in strategy without an acidic proteome. Instead, they hydrolyze Glutamine (Q) and Asparagine (N) to compensate for the lack of acidic amino acids ( Bardavid and Oren 2012 ). However, the genome of Acethalobium arabaticum , a member of the Halanaerobiales , encodes a more acidic proteome, similar to Salinibacter and Salinicoccus ( supplementary fig.…”

Section: Discussionmentioning

confidence: 99%

The Evolutionary Origins of Extreme Halophilic Archaeal Lineages

Feng

Neri

Gosselin

et al. 2021

Genome Biology and Evolution

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Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; while the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (unrelated groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/non-catalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN.

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Comparison of the structural basis for thermal stability between archaeal and bacterial proteins

Cited by 12 publications

References 69 publications

Characterization of the Dihydroorotase from Methanococcus jannaschii

Characterization of the Dihydroorotase from Methanococcus jannaschii

Expression and Properties of the Highly Alkalophilic Phenylalanine Ammonia-Lyase of Thermophilic Rubrobacter xylanophilus

The Evolutionary Origins of Extreme Halophilic Archaeal Lineages

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