Evolution of Protein Molecules

Manual for the Identification of Medical Bacteria.

The yeast cell wall is a strong, but elastic, structure that is essential not only for the maintenance of cell shape and integrity, but also for progression through the cell cycle. During growth and morphogenesis, and in response to environmental challenges, the cell wall is remodeled in a highly regulated and polarized manner, a process that is principally under the control of the cell wall integrity (CWI) signaling pathway. This pathway transmits wall stress signals from the cell surface to the Rho1 GTPase, which mobilizes a physiologic response through a variety of effectors. Activation of CWI signaling regulates the production of various carbohydrate polymers of the cell wall, as well as their polarized delivery to the site of cell wall remodeling. This review article centers on CWI signaling in Saccharomyces cerevisiae through the cell cycle and in response to cell wall stress. The interface of this signaling pathway with other pathways that contribute to the maintenance of cell wall integrity is also discussed.

https://www.genetics.org/content/genetics/189/4/1145.full.pdf

Regulation of Cell Wall Biogenesis in Saccharomyces cerevisiae: The Cell Wall Integrity Signaling Pathway

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

/pdf/genome-based-taxonomic-classification-of-the-phylum-4uc1zrzg88.pdf

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Keratinases are exciting proteolytic enzymes that display the capability to degrade the insoluble protein keratin. These enzymes are produced by diverse microorganisms belonging to the Eucarya, Bacteria, and Archea domains. Keratinases display a great diversity in their biochemical and biophysical properties. Most keratinases are optimally active at neutral to alkaline pH and 40–60°C, but examples of microbial keratinolysis at alkalophilic and thermophilic conditions have been well documented. Several keratinases have been associated to the subtilisin family of serine-type proteases by analysis of their protein sequences. Studies with specific substrates and inhibitors indicated that keratinases are often serine or metalloproteases with preference for hydrophobic and aromatic residues at the P1 position. Keratinolytic enzymes have several current and potential applications in agroindustrial, pharmaceutical, and biomedical fields. Their use in biomass conversion into biofuels may address the increasing concern on energy conservation and recycling.

Biochemical features of microbial keratinases and their production and applications.

A xylanase with broad pH and temperature adaptability from Streptomyces megasporus DSM 41476, and its potential application in brewing industry

A novel cold-active xylanase gene from the environmental DNA of goat rumen contents: Direct cloning, expression and enzyme characterization

We have identified a highly pH-adaptable and stable xylanase (XynA4) from the thermoacidophilic Alicyclobacillus sp. A4, a strain that was isolated from a hot spring in Yunnan Province, China. The gene (xynA4) that encodes this xylanase was cloned, sequenced, and expressed in Escherichia coli. It encodes a 338-residue polypeptide with a calculated molecular mass of 42.5 kDa. The deduced amino acid sequence is most similar to (53% identity) an endo-1,4-β-xylanase from Geobacillus stearothermophilus that belongs to family 10 of the glycoside hydrolases. Purified recombinant XynA4 exhibited maximum activity at 55°C and pH 7.0, had broad pH adaptability (>40% activity at pH 3.8–9.4) and stability (retaining >80% activity after incubation at pH 2.6–12.0 for 1 h at 37°C), and was highly thermostable (retaining >90% activity after incubation at 60°C for 1 h at pH 7.0). These properties make XynA4 promising for application in the paper industry. This is the first report that describes cloning and expression of a xylanase gene from the genus Alicyclobacillus.

A new xylanase from thermoacidophilic Alicyclobacillus sp. A4 with broad-range pH activity and pH stability.

A β-mannanase gene, man5AP13, was cloned from Phialophora sp. P13 and expressed in Pichia pastoris. The deduced amino acid sequence of the mature enzyme, MAN5AP13, had highest identity (53%) with the glycoside hydrolase family 5 β-mannanase from Bispora sp. MEY-1. The purified recombinant β-mannanase was acidophilic and acid stable, exhibiting maximal activity at pH 1.5 and retaining >60% of the initial activity over the pH range 1.5−7.0. The optimum temperature was 60 °C. The specific activity, Km and Vmax for locust bean gum substrate were 851 U/mg, 2.5 mg/mL, and 1667.7 U/min·mg, respectively. The enzyme had excellent activity and stability under simulated gastric conditions, and the released reducing sugar of locust bean gum was significantly enhanced by one-fold in simulated gastric fluid containing pepsin in contrast to that without pepsin. All these properties make MAN5AP13 a potential additive for use in the food and feed industries.

An Acidophilic and Acid-Stable β-Mannanase from Phialophora sp. P13 with High Mannan Hydrolysis Activity under Simulated Gastric Conditions

A thermophilic α-galactosidase from Neosartorya fischeri P1 with high specific activity, broad substrate specificity and significant hydrolysis ability of soymilk.

Peilong Yang

Papers

A xylanase with broad pH and temperature adaptability from Streptomyces megasporus DSM 41476, and its potential application in brewing industry

A novel cold-active xylanase gene from the environmental DNA of goat rumen contents: Direct cloning, expression and enzyme characterization

A new xylanase from thermoacidophilic Alicyclobacillus sp. A4 with broad-range pH activity and pH stability.

An Acidophilic and Acid-Stable β-Mannanase from Phialophora sp. P13 with High Mannan Hydrolysis Activity under Simulated Gastric Conditions

A thermophilic α-galactosidase from Neosartorya fischeri P1 with high specific activity, broad substrate specificity and significant hydrolysis ability of soymilk.