Biochemical characterization of a new nicotinamidase from an unclassified bacterium thriving in a geothermal water stream microbial mat community

PLoS One. 2017 Jul 27;12(7):e0181561. doi: 10.1371/journal.pone.0181561. eCollection 2017.

Abstract

Nicotinamidases are amidohydrolases that convert nicotinamide into nicotinic acid, contributing to NAD+ homeostasis in most organisms. In order to increase the number of nicotinamidases described to date, this manuscript characterizes a nicotinamidase obtained from a metagenomic library fosmid clone (JFF054_F02) obtained from a geothermal water stream microbial mat community in a Japanese epithermal mine. The enzyme showed an optimum temperature of 90°C, making it the first hyperthermophilic bacterial nicotinamidase to be characterized, since the phylogenetic analysis of this fosmid clone placed it in a clade of uncultured geothermal bacteria. The enzyme, named as UbNic, not only showed an alkaline optimum pH, but also a biphasic pH dependence of its kcat, with a maximum at pH 9.5-10.0. The two pKa values obtained were 4.2 and 8.6 for pKes1 and pKes2, respectively. These results suggest a possible flexible catalytic mechanism for nicotinamidases, which reconciles the two previously proposed mechanisms. In addition, the enzyme showed a high catalytic efficiency, not only toward nicotinamide, but also toward other nicotinamide analogs. Its mutational analysis showed that a tryptophan (W83) is needed in one of the faces of the active site to maintain low Km values toward all the substrates tested. Furthermore, UbNic proved to contain a Fe2+ ion in its metal binding site, and was revealed to belong to a new nicotinamidase subgroup. All these characteristics, together with its high pH- and thermal stability, distinguish UbNic from previously described nicotinamidases, and suggest that a wide diversity of enzymes remains to be discovered in extreme environments.

MeSH terms

  • Aldehydes / metabolism
  • Amino Acid Sequence
  • Bacteria / enzymology*
  • Enzyme Inhibitors / pharmacology
  • Enzyme Stability / drug effects
  • Hot Springs / microbiology*
  • Hydrogen-Ion Concentration
  • Kinetics
  • Microbiota*
  • Models, Molecular
  • Mutant Proteins / metabolism
  • Nicotinamidase / antagonists & inhibitors
  • Nicotinamidase / chemistry
  • Nicotinamidase / metabolism*
  • Phylogeny
  • Rivers / microbiology*
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Temperature
  • Water Microbiology*

Substances

  • Aldehydes
  • Enzyme Inhibitors
  • Mutant Proteins
  • 3-pyridinaldehyde
  • Nicotinamidase

Grants and funding

This study was partially supported by Spanish grants from MINECO/AEI/FEDER (BIO2013-45336-R) and from the Ayudas a los Grupos y Unidades de Excelencia Científica de la Región de Murcia, Fundación Séneca – Agencia de Ciencia y Tecnología de la Región de Murcia (19893/GERM/15, Programa de Apoyo a la Investigación 2014). This study was also supported in part by Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan to HT (no. 20310124). A-GG-S is supported by the corresponding predoctoral fellowships (FPU-UMU) from the University of Murcia. A-BM-M and RZ-P have a predoctoral research fellowship associated with the above MINECO/AEI/FEDER (BIO2013-45336-R) project.