scholarly journals Cloning and characterization of two functionally diverse lipases from soil metagenome

2013 ◽  
Vol 59 (1) ◽  
pp. 21-31 ◽  
Author(s):  
Mahejibin Khan ◽  
K. Jithesh ◽  
R. Mookambikay
Keyword(s):  
Soil Metagenome ◽  
Functionally Diverse

Cloning and functional characterization of a superfamily of microbial inwardly rectifying potassium channels

2006 ◽  
Vol 26 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Si Sun ◽  
Jo Han Gan ◽  
Jennifer J. Paynter ◽  
Stephen J. Tucker
Keyword(s):  
Functional Properties ◽  
Functional Characterization ◽  
Unicellular Eukaryote ◽  
Channel Blockers ◽  
E Coli ◽  
Inwardly Rectifying Potassium Channels ◽  
Genes Encoding ◽  
Functionally Diverse ◽  
Inwardly Rectifying

Our understanding of the mammalian inwardly rectifying family of K+ channels (Kir family) has recently been advanced by X-ray crystal structures of two homologous prokaryotic orthologs (KirBac1.1 and KirBac3.1). However, the functional properties of these KirBac channels are still poorly understood. To address this problem, we cloned and characterized genes encoding KirBac orthologs from a wide variety of different prokaryotes and a simple unicellular eukaryote. The functional properties of these KirBacs were then examined by growth complementation in a K+ uptake-deficient strain of Escherichia coli (TK2420). Whereas some KirBac genes exhibited robust growth complementation, others either did not complement or showed temperature-dependent complementation including KirBac1.1 and KirBac3.1. In some cases, KirBac expression was also toxic to the growth of E. coli. The KirBac family exhibited a range of sensitivity to the K+ channel blockers Ba2+ and Cs+ as well as differences in their ability to grow on very low-K+ media, thus demonstrating major differences in their permeation properties. These results reveal the existence of a functionally diverse superfamily of microbial KirBac genes and present an excellent resource for the structural and functional analysis of this class of K+ channels. Furthermore, the complementation assay used in this study provides a simple and robust method for the functional characterization of a range of prokaryotic K+ channels that are difficult to study by traditional methods.

scholarly journals Atomic-level characterization of protein–protein association

2019 ◽  
Vol 116 (10) ◽  
pp. 4244-4249 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

scholarly journals Cloning and characterization of a thermostable and alkaline fibrinolytic enzyme from a soil metagenome

2013 ◽  
Vol 12 (45) ◽  
pp. 6389-6399 ◽  
Author(s):  
Leedagger; Sun-Yi ◽  
Yudagger; Sun-Nyoung ◽  
Choi Hak-Jong ◽  
Kim Kwang-Youn ◽  
Kim Sang-Hun ◽  
...  
Keyword(s):  
Fibrinolytic Enzyme ◽  
Soil Metagenome

scholarly journals Expression and characterization of a novel highly glucose-tolerant β-glucosidase from a soil metagenome

2013 ◽  
Vol 45 (8) ◽  
pp. 664-673 ◽  
Author(s):  
Jian Lu ◽  
Liqin Du ◽  
Yutuo Wei ◽  
Yuanyuan Hu ◽  
Ribo Huang
Keyword(s):  
Soil Metagenome ◽  
Glucose Tolerant

scholarly journals Identification of a novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative:Pseudomonas aeruginosaLdcA

2018 ◽  
Author(s):  
Diego Carriel-Lopez ◽  
Pierre Simon Garcia ◽  
Florence Castelli ◽  
Patricia Lamourette ◽  
François Fenaille ◽  
...  
Keyword(s):  
Amino Acid ◽  
Functional Characterization ◽  
Acid Stress ◽  
Basic Amino Acid ◽  
Multidrug Resistant ◽  
Human Pathogen ◽  
Short Forms ◽  
Charged Macromolecules ◽  
Functionally Diverse

SummaryPolyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by PLP-dependent amino acid decarboxylases referred to as LAOdcs (Lysine-Arginine-Ornithine decarboxylases). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancestral nature of their short forms inCyanobacteriaandFirmicutes,and emergence of distinct subfamilies of long LAOdcs inProteobacteria.We identified a novel subfamily of lysine decarboxylases, LdcA, ancestral inBetaproteobacteriaandPseudomortadaceae {Gammaproteobacteria).We analyzed the expression of LdcA fromPseudomonas aeruginosa,and uncovered its role, intimately linked to cadaverine production, in promoting growth and reducing persistence of this multidrug resistant human pathogen during carbenicillin treatment. Finally, we documented a certain redundancy in the function of the three main polyamines - cadaverine, putrescine and spermidine - inP. aeruginosaby demonstrating the link between their intracellular level, as well as the capacity of putrescine and spermidine to complement the growth phenotype of theIdcAmutant.

scholarly journals Characterization of a novel family VIII esterase EstM2 from soil metagenome capable of hydrolyzing estrogenic phthalates

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Jayita Sarkar ◽  
Arindam Dutta ◽  
Piyali Pal Chowdhury ◽  
Joydeep Chakraborty ◽  
Tapan K. Dutta
Keyword(s):  
Soil Metagenome

Applications of CRISPR-Cas systems in lactic acid bacteria

2020 ◽  
Vol 44 (5) ◽  
pp. 523-537 ◽  
Author(s):  
Avery Roberts ◽  
Rodolphe Barrangou
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Natural Environments ◽  
Gene Therapies ◽  
The Past ◽  
Food And Agriculture ◽  
Functionally Diverse

ABSTRACT As a phenotypically and phylogenetically diverse group, lactic acid bacteria are found in a variety of natural environments and occupy important roles in medicine, biotechnology, food and agriculture. The widespread use of lactic acid bacteria across these industries fuels the need for new and functionally diverse strains that may be utilized as starter cultures or probiotics. Originally characterized in lactic acid bacteria, CRISPR-Cas systems and derived molecular machines can be used natively or exogenously to engineer new strains with enhanced functional attributes. Research on CRISPR-Cas biology and its applications has exploded over the past decade with studies spanning from the initial characterization of CRISPR-Cas immunity in Streptococcus thermophilus to the use of CRISPR-Cas for clinical gene therapies. Here, we discuss CRISPR-Cas classification, overview CRISPR biology and mechanism of action, and discuss current and future applications in lactic acid bacteria, opening new avenues for their industrial exploitation and manipulation of microbiomes.

scholarly journals Structural and Biophysical Characterization of BoxC from Burkholderia xenovorans LB400

2009 ◽  
Vol 284 (24) ◽  
pp. 16377-16385 ◽  
Author(s):  
Jasleen Bains ◽  
Rafael Leon ◽  
Martin J. Boulanger
Keyword(s):  
Active Site ◽  
Mechanistic Model ◽  
Titration Calorimetry ◽  
Biophysical Characterization ◽  
Docking Simulations ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400 ◽  
C Terminus ◽  
Functionally Diverse

The mineralization of aromatic compounds by microorganisms relies on a structurally and functionally diverse group of ring-cleaving enzymes. The recently discovered benzoate oxidation pathway in Burkholderia xenovorans LB400 encodes a novel such ring-cleaving enzyme, termed BoxC, that catalyzes the conversion of 2,3-dihydro-2,3-dihydroxybenzoyl-CoA to 3,4-dehydroadipyl-CoA without the requirement for molecular oxygen. Sequence analysis indicates that BoxC is a highly divergent member of the crotonase superfamily and nearly double the size of the average superfamily member. The structure of BoxC determined to 1.5 Å resolution reveals an intriguing structural demarcation. A highly divergent region in the C terminus probably serves as a structural scaffold for the conserved N terminus that encompasses the active site and, in conjunction with a conserved C-terminal helix, mediates dimer formation. Isothermal titration calorimetry and molecular docking simulations contribute to a detailed view of the active site, resulting in a compelling mechanistic model where a pair of conserved glutamate residues (Glu146 and Glu168) work in tandem to deprotonate the dihydroxylated ring substrate, leading to cleavage. A final deformylation step incorporating a water molecule and Cys111 as a general base completes the formation of 3,4-dehydroadipyl-CoA product. Overall, this study establishes the basis for BoxC as one of the most divergent members of the crotonase superfamily and provides the first structural insight into the mechanism of this novel class of ring-cleaving enzymes.

Characterization of a Lichenase Isolated from Soil Metagenome

2014 ◽  
Vol 24 (12) ◽  
pp. 1699-1706 ◽  
Author(s):  
Sang-Yoon Kim ◽  
Doo-Byoung Oh ◽  
Ohsuk Kwon
Keyword(s):  
Soil Metagenome
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