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Maati J, Prazeres DM, Grąz M, Wiater A, Jarosz-Wilkołazka A, Smaali I. Heteroxylan hydrolysis by a recombinant cellulase-free GH10 xylanase from the alkaliphilic bacterium Halalkalibacterium halodurans C-125. Arch Microbiol 2024; 206:261. [PMID: 38753095 DOI: 10.1007/s00203-024-03982-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/13/2024] [Accepted: 04/25/2024] [Indexed: 06/18/2024]
Abstract
The search for affordable enzymes with exceptional characteristics is fundamental to overcoming industrial and environmental constraints. In this study, a recombinant GH10 xylanase (Xyn10-HB) from the extremely alkaliphilic bacterium Halalkalibacterium halodurans C-125 cultivated at pH 10 was cloned and expressed in E. coli BL21(DE3). Removal of the signal peptide improved the expression, and an overall activity of 8 U/mL was obtained in the cell-free supernatant. The molecular weight of purified Xyn10-HB was estimated to be 42.6 kDa by SDS-PAGE. The enzyme was active across a wide pH range (5-10) with optimal activity recorded at pH 8.5 and 60 °C. It also presented good stability with a half-life of 3 h under these conditions. Substrate specificity studies showed that Xyn10-HB is a cellulase-free enzyme that conventionally hydrolyse birchwood and oat spelts xylans (Apparent Km of 0.46 mg/mL and 0.54 mg/mL, respectively). HPLC analysis showed that both xylans hydrolysis produced xylooligosaccharides (XOS) with a degree of polymerization (DP) ranging from 2 to 9. The conversion yield was 77% after 24 h with xylobiose and xylotriose as the main end-reaction products. When assayed on alkali-extracted wheat straw heteroxylan, the Xyn10-HB produced active XOS with antioxidant activity determined by the DPPH radical scavenging method (IC50 of 0.54 mg/mL after 4 h). Owing to its various characteristics, Xyn10-HB xylanase is a promising candidate for multiple biotechnological applications.
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Affiliation(s)
- Jihene Maati
- University of Carthage, Laboratory of Protein Engineering and Bioactive Molecules (LIP-MB-LR11ES24), INSAT-BP 676, 1080, Tunis Cedex, Tunisia
| | - Duarte Miguel Prazeres
- Institute for Bioengineering and Biosciences-iBB, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
- Institute for Health and Bioeconomy-li4HB, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
| | - Marcin Grąz
- Department of Biochemistry and Biotechnology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Adrian Wiater
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Anna Jarosz-Wilkołazka
- Department of Biochemistry and Biotechnology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Issam Smaali
- University of Carthage, Laboratory of Protein Engineering and Bioactive Molecules (LIP-MB-LR11ES24), INSAT-BP 676, 1080, Tunis Cedex, Tunisia.
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Breaker RR, Harris KA, Lyon SE, Wencker FDR, Fernando CM. Evidence that OLE RNA is a component of a major stress-responsive ribonucleoprotein particle in extremophilic bacteria. Mol Microbiol 2023; 120:324-340. [PMID: 37469248 DOI: 10.1111/mmi.15129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/30/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
OLE RNA is a ~600-nucleotide noncoding RNA present in many Gram-positive bacteria that thrive mostly in extreme environments, including elevated temperature, salt, and pH conditions. The precise biochemical functions of this highly conserved RNA remain unknown, but it forms a ribonucleoprotein (RNP) complex that localizes to cell membranes. Genetic disruption of the RNA or its essential protein partners causes reduced cell growth under various stress conditions. These phenotypes include sensitivity to short-chain alcohols, cold intolerance, reduced growth on sub-optimal carbon sources, and intolerance of even modest concentrations of Mg2+ . Thus, many bacterial species appear to employ OLE RNA as a component of an intricate RNP apparatus to monitor fundamental cellular processes and make physiological and metabolic adaptations. Herein we hypothesize that the OLE RNP complex is functionally equivalent to the eukaryotic TOR complexes, which integrate signals from various diverse pathways to coordinate processes central to cell growth, replication, and survival.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Kimberly A Harris
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Seth E Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Freya D R Wencker
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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3
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de Jong SI, Sorokin DY, van Loosdrecht MCM, Pabst M, McMillan DGG. Membrane proteome of the thermoalkaliphile Caldalkalibacillus thermarum TA2.A1. Front Microbiol 2023; 14:1228266. [PMID: 37577439 PMCID: PMC10416648 DOI: 10.3389/fmicb.2023.1228266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Proteomics has greatly advanced the understanding of the cellular biochemistry of microorganisms. The thermoalkaliphile Caldalkalibacillus thermarum TA2.A1 is an organism of interest for studies into how alkaliphiles adapt to their extreme lifestyles, as it can grow from pH 7.5 to pH 11. Within most classes of microbes, the membrane-bound electron transport chain (ETC) enables a great degree of adaptability and is a key part of metabolic adaptation. Knowing what membrane proteins are generally expressed is crucial as a benchmark for further studies. Unfortunately, membrane proteins are the category of proteins hardest to detect using conventional cellular proteomics protocols. In part, this is due to the hydrophobicity of membrane proteins as well as their general lower absolute abundance, which hinders detection. Here, we performed a combination of whole cell lysate proteomics and proteomics of membrane extracts solubilised with either SDS or FOS-choline-12 at various temperatures. The combined methods led to the detection of 158 membrane proteins containing at least a single transmembrane helix (TMH). Within this data set we revealed a full oxidative phosphorylation pathway as well as an alternative NADH dehydrogenase type II (Ndh-2) and a microaerophilic cytochrome oxidase ba3. We also observed C. thermarum TA2.A1 expressing transporters for ectoine and glycine betaine, compounds that are known osmolytes that may assist in maintaining a near neutral internal pH when the external pH is highly alkaline.
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Affiliation(s)
- Samuel I. de Jong
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Dimitry Y. Sorokin
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | | | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
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4
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Khomyakova MA, Merkel AY, Segliuk VS, Slobodkin AI. Desulfatitalea alkaliphila sp. nov., an alkalipilic sulfate- and arsenate- reducing bacterium isolated from a terrestrial mud volcano. Extremophiles 2023; 27:12. [PMID: 37178152 DOI: 10.1007/s00792-023-01297-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
A novel alkaliphilic sulfate-reducing bacterium, strain M08butT, was isolated from a salsa lake of terrestrial mud volcano (Taman Peninsula, Russia). Cells were rod-shaped, motile and Gram-stain-negative. The temperature range for growth was 15-42 °C (optimum at 30 °C). The pH range for growth was 7.0-11.0, with an optimum at pH 8.5-9.0 Strain M08butT used sulfate, thiosulfate, sulfite, dimethyl sulfoxide and arsenate as electron acceptors. Acetate, formate, butyrate, fumarate, succinate, glycerol and pyruvate were utilized as electron donors with sulfate. Fermentative growth was observed with fumarate, pyruvate, crotonate. Strain M08butT grew chemolithoautotrophically with H2 and CO2. The G + C content of the genomic DNA was 60.1%. The fatty acid profile of strain M08butT was characterized by the presence of anteiso-C15:0 as the major component (68.8%). The closest phylogenetic relative of strain M08butT was Desulfatitalea tepidiphila (the order Desulfobacterales) with 96.3% 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08butT is considered to represent a novel species of the genus Desulfatitalea, with proposed name Desulfatitalea alkaliphila sp. nov. The type strain of Desulfatitalea alkaliphila is M08butT (= KCTC 25382T = VKM B-3560T = DSM 113909T = JCM 39202T = UQM 41473T).
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia.
| | - A Yu Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
| | - V S Segliuk
- Gubkin University, Leninskiy Prospect, 65/1, 119991, Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, Bld. 2, 119071, Moscow, Russia
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5
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Kim SK, Min YH, Jin HJ. Characteristics of the ErmK Protein of Bacillus halodurans C-125. Microbiol Spectr 2023; 11:e0259822. [PMID: 36511701 PMCID: PMC9927578 DOI: 10.1128/spectrum.02598-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/13/2022] [Indexed: 12/15/2022] Open
Abstract
Bacillus halodurans C-125 is an alkaliphilic microorganism that grows best at pH 10 to 10.5. B. halodurans C-125 harbors the erm (erythromycin resistance methylase) gene as well as the mphB (macrolide phosphotransferase) and putative mef (macrolide efflux) genes, which confer resistance to macrolide, lincosamide, and streptogramin B (MLSB) antibiotics. The Erm protein expressed in B. halodurans C-125 could be classified as ErmK because it shares 66.2% and 61.2% amino acid sequence identity with the closest ErmD and Erm(34), respectively. ErmK can be regarded as a dimethylase, as evidenced by reverse transcriptase analysis and the antibiotic resistance profile exhibited by E. coli expressing ermK. Although ErmK showed one-third or less in vitro methylating activity compared to ErmC', E. coli cells expressing ErmK exhibited comparable resistance to erythromycin and tylosin, and a similar dimethylation proportion of 23S rRNA due to the higher expression rate in a T7 promoter-mediated expression system. The less efficient methylation activity of ErmK might reflect an adaption to mitigate the fitness cost caused by dimethylation through the Erm protein presumably because B. halodurans C-125 has less probability to encounter the antibiotics in its favorable growth conditions and grows retardedly in neutral environments. IMPORTANCE Erm proteins confer MLSB antibiotic resistance (minimal inhibitory concentration [MIC] value up to 4,096 μg/mL) on microorganisms ranging from antibiotic producers to pathogens, imposing one of the most pressing threats to clinics. Therefore, Erm proteins have long been speculated to be plausible targets for developing inhibitor(s). In our laboratory, it has been noticed that there are variations in enzymatic activity among the Erm proteins, Erm in antibiotic producers being better than that in pathogens. In this study, it has been observed that Erm protein in B. halodurans C-125 extremophile is a novel member of Erm protein and acts more laggardly, compared to that in pathogen. While this sluggishness of Erm protein in extremophile might be evolved to reduce the fitness cost incurred by Erm activity adapting to its environments, this feature could be exploited to develop the more potent and/or efficacious drug to combat formidably problematic antibiotic-resistant pathogens.
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Affiliation(s)
- Sung Keun Kim
- Department of Bioscience and Biotechnology, The University of Suwon, Hwaseong City, South Korea
| | - Yu Hong Min
- College of Health and Welfare, Daegu Haany University, Gyeongsangbuk-Do, South Korea
| | - Hyung Jong Jin
- Department of Bioscience and Biotechnology, The University of Suwon, Hwaseong City, South Korea
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6
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Application of Endoxylanases of Bacillus halodurans for Producing Xylooligosaccharides from Empty Fruit Bunch. Catalysts 2022. [DOI: 10.3390/catal13010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Endo-1,4-β-xylanase catalyzes the random hydrolysis of β-1,4-D-xylosidic bonds in xylan, resulting in the formation of oligomers of xylose. This study aims to demonstrate the promise of endoxylanases from alkaliphilic Bacillus halodurans for the production of xylooligosaccharides (XOS) from oil palm empty fruit bunch (EFB) at high pH. Two enzyme preparations were employed: recombinant endoxylanase Xyn45 (GH10 xylanase) and nonrecombinant endoxylanases, a mixture of two extracellular endo-1,4-β-xylanases Xyn45 and Xyn23 (GH11 xylanase) produced by B. halodurans. EFB was first treated with an alkaline solution. Then, the dissolved xylan-containing fraction was retained, and a prepared enzyme was added to react at pH 8 to convert xylan into XOS. Compared with the use of only Xyn45, the combined use of Xyn45 and Xyn23 resulted in a higher yield of XOS, suggesting the synergistic effect of the two endoxylanases. The yield of XOS obtained from EFB was as high as 46.77% ± 1.64% (w/w), with the xylobiose-to-xylotriose ratio being 6:5. However, when the enzyme activity dose was low, the product contained more xylotriose than xylobiose. Four probiotic lactobacilli and bifidobacteria grew well on a medium containing XOS from EFB. The presence of XOS increased cell mass and reduced pH, suggesting that XOS promoted the growth of probiotics.
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Salwan R, Sharma V. Genomics of Prokaryotic Extremophiles to Unfold the Mystery of Survival in Extreme Environments. Microbiol Res 2022; 264:127156. [DOI: 10.1016/j.micres.2022.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
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González-Tortuero E, Anthon C, Havgaard JH, Geissler AS, Breüner A, Hjort C, Gorodkin J, Seemann SE. The Bacillaceae-1 RNA motif comprises two distinct classes. Gene 2022; 841:146756. [PMID: 35905857 DOI: 10.1016/j.gene.2022.146756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/10/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis, we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches.
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Affiliation(s)
- Enrique González-Tortuero
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jakob H Havgaard
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Adrian S Geissler
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Stefan E Seemann
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
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9
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Allen WJ, Corey RA, Watkins DW, Oliveira ASF, Hards K, Cook GM, Collinson I. Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion. eLife 2022; 11:e77586. [PMID: 35486093 PMCID: PMC9110029 DOI: 10.7554/elife.77586] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/24/2022] Open
Abstract
Transport of proteins across and into membranes is a fundamental biological process with the vast majority being conducted by the ubiquitous Sec machinery. In bacteria, this is usually achieved when the SecY-complex engages the cytosolic ATPase SecA (secretion) or translating ribosomes (insertion). Great strides have been made towards understanding the mechanism of protein translocation. Yet, important questions remain - notably, the nature of the individual steps that constitute transport, and how the proton-motive force (PMF) across the plasma membrane contributes. Here, we apply a recently developed high-resolution protein transport assay to explore these questions. We find that pre-protein transport is limited primarily by the diffusion of arginine residues across the membrane, particularly in the context of bulky hydrophobic sequences. This specific effect of arginine, caused by its positive charge, is mitigated for lysine which can be deprotonated and transported across the membrane in its neutral form. These observations have interesting implications for the mechanism of protein secretion, suggesting a simple mechanism through which the PMF can aid transport by enabling a 'proton ratchet', wherein re-protonation of exiting lysine residues prevents channel re-entry, biasing transport in the outward direction.
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Affiliation(s)
- William J Allen
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Robin A Corey
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - A Sofia F Oliveira
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
- School of Chemistry, University of Bristol, University WalkBristolUnited Kingdom
| | - Kiel Hards
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of OtagoDunedinNew Zealand
| | - Ian Collinson
- School of Biochemistry, University of Bristol, University WalkBristolUnited Kingdom
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Tang K, Cui Y, Xiao J, Ding M, Chao H, Wu J, Han Z, Liu J, Li X, Yan D. Molecular cloning and characterization of a novel xylanase from Microbacterium imperiale YD-01. J Food Biochem 2021; 45:e13988. [PMID: 34730252 DOI: 10.1111/jfbc.13988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/25/2021] [Accepted: 10/13/2021] [Indexed: 11/27/2022]
Abstract
Xylaneses are very common xylanolytic enzymes, which are widely used in food, papermaking, and other industries. In this study, a xylanase-encoding gene xyn1923, which encodes a protein of 1352 amino acids, was identified through the whole genome analysis of Microbacterium imperiale YD-01. Bioinformatics analysis showed that Xyn1923 only had maximum similarity of 37% with the reported xylanase from Alkalihalobacillus halodurans C-125, indicating that Xyn1923 was a novel xylanase. The enzymatic properties of Xyn1923 were systematically analyzed after purification. The results showed that the specific activity of the enzyme was 10.582 ± 0.413 U/mg, while the optimum pH and temperature of the enzyme were 7.0 and 70°C, respectively. The enzyme is stable in the pH range of 6.0-9.0, and the enzyme activity could maintain more than 85% of the original activity after 16 hr incubation at pH 9.0. The enzyme activity is relatively stable in the range of 30-60°C, and its enzyme activity could maintain more than 89% of the original activity after treatment at 60°C for 30 min. Low concentrations (≤1 mM) of Co2+ , Ba2+ , Fe2+ , and Fe3+ metal ions exerted a stimulatory effect on the activity of Xyn1923. And in contrast, high concentrations (≥2 mM) of the above metal ions inhibit the activity of Xyn1923. Mg2+ , Ag+ , Cu2+ , Ca2+ , Mn2+ , and Pb2+ ions showed a negative effect on the activity of Xyn1923. Enzyme kinetic studies showed that Km and Vmax values for xylan were 7.842 ± 0.538 mg/ml and 15.208 ± 0.822 U/mg, respectively. Xyn1923 was found to be a weakly alkaline thermophilic xylanase through an enzymatic property analysis. PRACTICAL APPLICATIONS: Xylanases are widely used in food and feed, biofuels, papermaking, and other industries. However, their use is limited by poor performance under the conditions of pH and temperature. Therefore, the discovery of xylanases with the capability of working efficiently at alkaline pH and high temperature is the priority for its industrial applications. In this study, a novel xylanase-encoding gene xyn1923 from Microbacterium imperiale YD-01 was cloned and heterologously expressed in Escherichia coli. Enzymatic properties of this novel xylanase were investigated, indicating that the robust thermal stability and alkali resistance of Xyn1923 make it a potential candidate for the food and paper industries.
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Affiliation(s)
- Keqin Tang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Yin Cui
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Jingyi Xiao
- City University of Hong Kong, Kowloon, China
| | - Mengyao Ding
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Hongjun Chao
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Jing Wu
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Zhenggang Han
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Jun Liu
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Xin Li
- School of life science and technology, Wuhan Polytechnic University, Wuhan, China
| | - Dazhong Yan
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,School of life science and technology, Wuhan Polytechnic University, Wuhan, China
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11
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Identification of pulvomycin as an inhibitor of the futalosine pathway. J Antibiot (Tokyo) 2021; 74:825-829. [PMID: 34417567 DOI: 10.1038/s41429-021-00465-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/12/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023]
Abstract
Menaquinone is an essential cofactor in the electron-transfer pathway for bacteria. Menaquinone is biosynthesized from chorismate using either the well-known canonical pathway established by pioneering studies in model microorganisms or the futalosine pathway, which we discovered in Streptomyces. Because Helicobacter pylori, which causes stomach cancer, uses the futalosine pathway and most beneficial intestinal bacteria including lactobacilli use the canonical pathway, the futalosine pathway will be a great target to develop antibiotics specific for H. pylori. Here, we searched for such compounds from metabolites produced by actinomycetes and identified pulvomycin from culture broth of Streptomyces sp. K18-0194 as a specific inhibitor of the futalosine pathway.
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12
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Krishna PS, Raghunathan S, Prakash JSS. Comparative genome analysis of Alkalihalobacillus okhensis Kh10-101 T reveals insights into adaptive mechanisms for halo-alkali tolerance. 3 Biotech 2021; 11:392. [PMID: 34350093 DOI: 10.1007/s13205-021-02938-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/22/2021] [Indexed: 11/26/2022] Open
Abstract
Alkalihalobacillus okhensis is a halo-alkaliphile with optimal growth at pH 10 and 5% NaCl. Phylogenetic analysis revealed habitat-dependent segregation of Bacilli, with all the alkalihalophiles forming a separate clade. It uses acidification of the external medium and pH-dependent cell wall reinforcement to survive sodic environments. Interestingly, comparative genome analysis revealed the genome encodes surface proteins with a high proportion of acidic amino acids compared to their orthologs of B. subtilis, a piece of direct evidence for adaptive evolution. It has a relatively higher number of genes involved in the metabolism of osmolytes and sodium-dependent transporters when compared to B. subtilis. Growth of Alkalihalobacillus okhensis strain Kh10-101 T (hereafter A. okhensis) is Na+ dependent, with a minimum of 4% NaCl at neutral pH, but 0.5% NaCl is enough at pH 10. It tolerated a sudden increase in salt concentration and exhibited an elongated phenotype but could not tolerate a sudden pH shift from 7 to 11. The cell envelope got damaged, confirming that the pH regulation through cell wall reinforcement is key to survival at a high-pH condition. We report for the first time a comprehensive genome analysis of Bacilli to delineate the mechanisms evolved for adaptation to halo-alkaline conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02938-x.
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Affiliation(s)
- Pilla Sankara Krishna
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
| | - Sarada Raghunathan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
| | - Jogadhenu S S Prakash
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046 India
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Ishihara M, Kikkawa M, Shimizu K, Suzuki H, Honda H. Simple stain-free screening method for pectinolytic microorganisms under alkalophilic conditions. Biotechnol Lett 2021; 43:1905-1911. [PMID: 34228234 DOI: 10.1007/s10529-021-03162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/28/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVES To develop a simple pectin-degrading microorganism screening method. RESULTS We developed a method utilizing the phenomenon whereby cooling an alkaline agar medium containing pectin causes the agar to become cloudy. This highly simplified method involves culturing the microorganisms on pectin-containing agar medium until colony formation is observed, and subsequent overnight cooling of the agar medium to 4 °C. Using this simple procedure, we successfully identified pectin-degrading microorganisms by observing colonies with halos on the clouded agar medium. We used alkaline pectinase and Bacillus halodurans, which is known to secrete alkaline pectinase, to establish the screening method. We demonstrated the screening of pectin-degrading microorganisms using the developed method and successfully isolated pectin-degrading microorganisms (Paenibacillus sp., Bacillus clausii, and Bacillus halodurans) from a soil sample. CONCLUSIONS The developed method is useful for identifying pectin-degrading microorganisms.
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Affiliation(s)
- Mai Ishihara
- New Field Pioneering Division, Toyota Boshoku Corporation, Kariya, Japan
| | - Masahiro Kikkawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Kazunori Shimizu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroaki Suzuki
- New Field Pioneering Division, Toyota Boshoku Corporation, Kariya, Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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14
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Freitas-Silva J, de Oliveira BFR, Vigoder FDM, Muricy G, Dobson ADW, Laport MS. Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha). Front Microbiol 2021; 11:592735. [PMID: 33488540 PMCID: PMC7820076 DOI: 10.3389/fmicb.2020.592735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/09/2020] [Indexed: 11/30/2022] Open
Abstract
Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The nearly complete genome of strain 64-1 consists of 3.6 Mbp (41.5% GC), which includes 3,705 coding sequences (CDS). An open pangenome was observed when limiting to the type strains of the B. pumilus group and aquatic-derived B. pumilus representatives. The genome appears to encode for at least 12 potential biosynthetic gene clusters (BGCs), including both types I and III polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and one NRPS-T1PKS hybrid, among others. In particular, bacilysin and other bacteriocin-coding genes were found and may be associated with the detected antimicrobial activity. Strain 64-1 also appears to possess a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes (CAZymes). A myriad of genes which may be involved in various process required by the strain in its marine habitat, such as those encoding for osmoprotectory transport systems and the biosynthesis of compatible solutes were also present. Several heavy metal tolerance genes are also present, together with various mobile elements including a region encoding for a type III-B Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, four prophage segments and transposase elements. This is the first report on the genomic characterization of a cultivable bacterial member of the Plakina cyanorosea holobiont.
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Affiliation(s)
- Jéssyca Freitas-Silva
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Francesco Rodrigues de Oliveira
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,School of Microbiology, University College Cork, Cork, Ireland
| | - Felipe de Mello Vigoder
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Guilherme Muricy
- Department of Invertebrates, National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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15
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Dittoe DK, Barabote RD, Rothrock MJ, Ricke SC. Assessment of a Potential Role of Dickeya dadantii DSM 18020 as a Pectinase Producer for Utilization in Poultry Diets Based on in silico Analyses. Front Microbiol 2020; 11:751. [PMID: 32390987 PMCID: PMC7191031 DOI: 10.3389/fmicb.2020.00751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/30/2020] [Indexed: 01/17/2023] Open
Abstract
Currently, the poultry industry has been faced with consumer pressure to utilize only vegetable feedstuffs in poultry diets, eliminate antibiotics from poultry production, and rear poultry in free range systems. To maintain current production standards, the industry must determine ways to enhance nutrient uptake and utilization further. One possible solution is the supplementation of pectinase, an enzyme that degrades pectin within the cell walls of plants, in poultry diets. Therefore, the objective of the current study was to determine the potential role of a pectinase producer, Dickeya dadantii DSM 18020, as a commercially utilized pectinase producer in poultry diets against other known pectinase producers, in silico. In the current study, whole genomes of Dickeya dadantii DSM 18020 (Dd18020), D. dadantii 3937 (Dd3937), D. solani IPO 2222 (Ds2222), Bacillus halodurans C-125 (BhC125), and B. subtilis subsp. subtilis str. 168 (Bs168) were compared using bioinformatic approaches to compare the chromosomal genome size, GC content, protein coding genes (CDS), total genes, average protein length (a.a.) and determine the predicted metabolic pathways, predicted pectin degrading enzymes, and pectin-degradation pathways across pectinase producers. Due to insufficient information surrounding the genome of Dd18020 (lack of annotation), the genome of Dd3937, a 99% identical genome to Dd18020, was utilized to compare pectinase-associated enzymes and pathways. The results from the current study demonstrated that Dd3937 possessed the most significant proportion of pathways presented and the highest number of pathways related to degradation, assimilation, and utilization of pectin. Also, Dd18020 exhibited a high number of pectinase-related enzymes. Both Dd3937 and Dd2222 shared the pectin degradation I pathway via the EC 3.1.1.11, EC 3.2.1.82, and EC 4.2.2.- enzymes, but did not share this pathway with either Bacillus species. In conclusion, Dd18020 demonstrated the genetic potential to produce multiple pectinase enzymes that could be beneficial to the degradation of pectin in poultry diets. However, for Dd18020 to become a commercially viable enzyme producer for the poultry industry, further research quantifying the pectinase production in vitro and determining the stability of the produced pectinases during feed manufacturing are necessary.
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Affiliation(s)
- Dana K Dittoe
- Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR, United States
| | - Ravi D Barabote
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Steven C Ricke
- Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR, United States
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16
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Kim MJ, Jang MU, Nam GH, Shin H, Song JR, Kim TJ. Functional Expression and Characterization of Acetyl Xylan Esterases CE Family 7 from Lactobacillus antri and Bacillus halodurans. J Microbiol Biotechnol 2020; 30:155-162. [PMID: 31986559 PMCID: PMC9728288 DOI: 10.4014/jmb.2001.01004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acetyl xylan esterase (AXE; E.C. 3.1.1.72) is one of the accessory enzymes for xylan degradation, which can remove the terminal acetate residues from xylan polymers. In this study, two genes encoding putative AXEs (LaAXE and BhAXE) were cloned from Lactobacillus antri DSM 16041 and Bacillus halodurans C-125, and constitutively expressed in Escherichia coli. They possess considerable activities towards various substrates such as p-nitrophenyl acetate, 4-methylumbelliferyl acetate, glucose pentaacetate, and 7-amino cephalosporanic acid. LaAXE and BhAXE showed the highest activities at pH 7.0 and 8.0 at 50°C, respectively. These enzymes are AXE members of carbohydrate esterase (CE) family 7 with the cephalosporine-C deacetylase activity for the production of antibiotics precursors. The simultaneous treatment of LaAXE with Thermotoga neapolitana β-xylanase showed 1.44-fold higher synergistic degradation of beechwood xylan than the single treatment of xylanase, whereas BhAXE showed no significant synergism. It was suggested that LaAXE can deacetylate beechwood xylan and enhance the successive accessibility of xylanase towards the resulting substrates. The novel LaAXE originated from a lactic acid bacterium will be utilized for the enzymatic production of D-xylose and xylooligosaccharides.
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Affiliation(s)
- Min-Jeong Kim
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Myoung-Uoon Jang
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Gyeong-Hwa Nam
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Heeji Shin
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jeong-Rok Song
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Tae-Jip Kim
- Division of Animal, Horticultural and Food Sciences, Graduate School of Chungbuk National University, Cheongju 28644, Republic of Korea,Corresponding author Phone: +82-43-261-3354 Fax: +82-43-271-4412 E-mail:
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17
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Mamo G, Mattiasson B. Alkaliphiles: The Versatile Tools in Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 172:1-51. [PMID: 32342125 DOI: 10.1007/10_2020_126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The extreme environments within the biosphere are inhabited by organisms known as extremophiles. Lately, these organisms are attracting a great deal of interest from researchers and industrialists. The motive behind this attraction is mainly related to the desire for new and efficient products of biotechnological importance and human curiosity of understanding nature. Organisms living in common "human-friendly" environments have served humanity for a very long time, and this has led to exhaustion of the low-hanging "fruits," a phenomenon witnessed by the diminishing rate of new discoveries. For example, acquiring novel products such as drugs from the traditional sources has become difficult and expensive. Such challenges together with the basic research interest have brought the exploration of previously neglected or unknown groups of organisms. Extremophiles are among these groups which have been brought to focus and garnering a growing importance in biotechnology. In the last few decades, numerous extremophiles and their products have got their ways into industrial, agricultural, environmental, pharmaceutical, and other biotechnological applications.Alkaliphiles, organisms which thrive optimally at or above pH 9, are one of the most important classes of extremophiles. To flourish in their extreme habitats, alkaliphiles evolved impressive structural and functional adaptations. The high pH adaptation gave unique biocatalysts that are operationally stable at elevated pH and several other novel products with immense biotechnological application potential. Advances in the cultivation techniques, success in gene cloning and expression, metabolic engineering, metagenomics, and other related techniques are significantly contributing to expand the application horizon of these remarkable organisms of the 'bizarre' world. Studies have shown the enormous potential of alkaliphiles in numerous biotechnological applications. Although it seems just the beginning, some fantastic strides are already made in tapping this potential. This work tries to review some of the prominent applications of alkaliphiles by focusing such as on their enzymes, metabolites, exopolysaccharides, and biosurfactants. Moreover, the chapter strives to assesses the whole-cell applications of alkaliphiles including in biomining, food and feed supplementation, bioconstruction, microbial fuel cell, biofuel production, and bioremediation.
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Affiliation(s)
| | - Bo Mattiasson
- Department of Biotechnology, Lund University, Lund, Sweden
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18
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Noby N, Hussein A, Saeed H, Embaby AM. "Recombinant cold -adapted halotolerant, organic solvent-stable esterase (estHIJ) from Bacillus halodurans. Anal Biochem 2019; 591:113554. [PMID: 31863727 DOI: 10.1016/j.ab.2019.113554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/08/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
Esterases and lipases enduring harsh conditions, including low temperature and extreme tolerance to organic solvents, have attracted great attention in recent times. In the current study, a full open reading frame of 747 bp that encodes a novel, cold-adapted esterase (estHIJ) of 248 amino acids from Bacillus halodurans strain NAH-Egypt was heterologously cloned and expressed in E. coli BL21 (DE3) Rosetta. Amino acid sequence analysis revealed that estHIJ belongs to family XIII of lipolytic enzymes, with a characteristic pentapeptide motif (G-L-S-L-G). The recombinant estHIJ was purified using Ni-affinity chromatography to homogeneity with purification fold, yield, specific activity, and molecular weight (MW) of 3.5, 47.5%, 19.8 U/mg and 29 kDa, respectively. The enzyme showed preferential substrate specificity towards pNP-acetate (C2), with catalytic efficiency of 46,825 min-1 mM-1 estHIJ displayed optimal activity at 30 °C and pH (7.0-8.0). estHIJ demonstrated robust stability in the presence of 50% (v/v) non-polar solvents and 4 M NaCl after 15 h and 6 h of incubation, respectively. The promising features of the recombinant estHIJ underpin its potential in several fields, e.g., the synthesis of pharmaceutical compounds and the food industry.
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Affiliation(s)
- Nehad Noby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Ahmed Hussein
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Hesham Saeed
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt.
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19
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Abstract
Despite the typical human notion that the Earth is a habitable planet, over three quarters of our planet is uninhabitable by us without assistance. The organisms that live and thrive in these “inhospitable” environments are known by the name extremophiles and are found in all Domains of Life. Despite our general lack of knowledge about them, they have already assisted humans in many ways and still have much more to give. In this review, I describe how they have adapted to live/thrive/survive in their niches, helped scientists unlock major scientific discoveries, advance the field of biotechnology, and inform us about the boundaries of Life and where we might find it in the Universe.
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Affiliation(s)
- James A Coker
- Department of Sciences, University of Maryland Global Campus, Adelphi, MD, USA
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20
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Halmschlag B, Steurer X, Putri SP, Fukusaki E, Blank LM. Tailor-made poly-γ-glutamic acid production. Metab Eng 2019; 55:239-248. [DOI: 10.1016/j.ymben.2019.07.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/16/2019] [Accepted: 07/20/2019] [Indexed: 10/26/2022]
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21
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Suberu Y, Akande I, Samuel T, Lawal A, Olaniran A. Cloning, expression, purification and characterisation of serine alkaline protease from Bacillus subtilis RD7. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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22
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Kadnikov VV, Mardanov AV, Ivasenko DA, Antsiferov DV, Beletsky AV, Karnachuk OV, Ravin NV. A Novel Bacteriophage of the Order Caudovirales from the Soil Metagenome in the Area of an Underground Coal Seam Fire. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719020152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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23
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Mahmood MS, Rasul F, Saleem M, Afroz A, Malik MF, Ashraf NM, Rashid U, Naz S, Zeeshan N. Characterization of recombinant endo-1,4-β-xylanase of Bacillus halodurans C-125 and rational identification of hot spot amino acid residues responsible for enhancing thermostability by an in-silico approach. Mol Biol Rep 2019; 46:3651-3662. [PMID: 31079316 DOI: 10.1007/s11033-019-04751-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/08/2019] [Indexed: 12/11/2022]
Abstract
Increased demand of enzymes for industrial use has led the scientists towards protein engineering techniques. In different protein engineering strategies, rational approach has emerged as the most efficient method utilizing bioinformatics tools to produce enzymes with desired reaction kinetics; physiochemical (temperature, pH, half life, etc) and biological (selectivity, specificity, etc.) characteristics. Xylanase is one of the widely used enzymes in paper and food industry to degrade xylan component present in plant pulp. In this study endo 1,4-β-xylanase (Xyl-11A) from Bacillus halodurans C-125 was cloned in pET-22b (+) vector and expressed in Escherichia coli BL21 (DE3) expression strain. The enzyme had Michaelis constant Km of 1.32 mg ml-1 birchwoodxylan (soluble form) and maximum reaction velocity (Vmax) 73.53 mmol min-1 mg-1 with an optimum temperature of 75 °C and pH 9.0. The thermostability analysis showed that enzyme retained more than 80% of its residual activity when incubated at 75 °C for 2 h. In addition, to increase Xyl-11A thermostability, an in-silico analysis was performedto identify the hot spot amino acid residues. Consensus-based amino acid substitution was applied to evaluate multiple sequence alignment of homologs and identified 20 amino acids positions by following Jensen-Shnnon Divergence method. 3D models of 20 selected mutants were analyzed for conformational transition in protein structures by using NMSim server. Two selected mutants T6K and I17M of Xyl-11A retained 40, 60% residual activity respectively, at 85 °C for 120 min as compared to wild type enzyme which retained 37% initial activity under same conditions, confirming the enhanced thermostability of mutants. The present study showed a good approach for the identification of promising amino acid residues responsible for enhancing the thermostability of enzymes of industrial importance.
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Affiliation(s)
- Malik Siddique Mahmood
- Institute of Biochemistry and Biotechnology, University of the Punjab, P. O Box No, 54590, Lahore, Pakistan
| | - Faiz Rasul
- Department of Biochemistry and Molecular Biology, University of Science and Technology, Hefei, China
| | - Mahjabeen Saleem
- Institute of Biochemistry and Biotechnology, University of the Punjab, P. O Box No, 54590, Lahore, Pakistan
| | - Amber Afroz
- Department of Biochemistry and Biotechnology, University of Gujrat, P. O Box No. 50700, Gujrat, Pakistan
| | - Muhammad Faheem Malik
- Department of Biochemistry and Biotechnology, University of Gujrat, P. O Box No. 50700, Gujrat, Pakistan
| | - Naeem Mehmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, P. O Box No. 50700, Gujrat, Pakistan
| | - Umar Rashid
- Department of Biochemistry and Biotechnology, University of Gujrat, P. O Box No. 50700, Gujrat, Pakistan
| | - Shumaila Naz
- Department of Biosciences, University of Gujrat, Gujrat, Pakistan
| | - Nadia Zeeshan
- Department of Biochemistry and Biotechnology, University of Gujrat, P. O Box No. 50700, Gujrat, Pakistan.
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24
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Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Niu L, Zhu W, Liang J, Huang Y, Wang B, Wu X, Liang H, Xu J. Paraliobacillus zengyii sp. nov., a slightly halophilic and extremely halotolerant bacterium isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2019; 69:1426-1432. [PMID: 30860460 DOI: 10.1099/ijsem.0.003333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Two rod-shaped, slightly halophilic and extremely halotolerant bacterial strains (X-1125T and X-1174), which were Gram-stain-positive, facultatively anaerobic and motile with peritrichous flagella, were isolated from the faeces of Tibetan antelopes. Their optimal temperature, NaCl concentration and pH for growth were 28 °C, 3 % (w/v) NaCl and pH 7.5, respectively. Based on the results of 16S rRNA gene sequences, and phylogenetic and phylogenomic analyses, their nearest phylogenetic neighbours were Paraliobacillussediminis KCTC 33762T (98.4 % similarity), Paraliobacillusquinghaiensis CGMCC 1.6333T (96.9 %) and Paraliobacillusryukyuensis NBRC 100001T (95.9 %) while the 16S rRNA genes of strains X-1125T and X-1174 were highly similar (99.7 %) to each other. The polar lipids comprised diphosphatidylglycerol, two unidentified phospholipids and four unidentified lipids. MK-7 was the sole menaquinone (100 %). The cell wall contained alanine, glycine, glutamic acid and meso-diaminopimelic acid. The major fatty acids (>9 %) were anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 1ω11c. The in silico DNA-DNA hybridization value between strains X-1125T and X-1174 was 97.8 % (well above the species threshold), but their values were lower than the 70 % threshold with the three closely related type strains. Strains X-1125T and X-1174 had DNA G+C contents (mol%) of 35.2 and 35.1 %, respectively. Based on the presented data, strains X-1125T and X-1174 hereby represent a novel species of the genus Paraliobacillus, for which the name Paraliobacillus zengyii sp. nov. is proposed. The type strain is X-1125T (=DSM 107811T=CGMCC 1.16464T).
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Affiliation(s)
- Xiaoxia Wang
- 1Guangxi Key Laboratory of AIDS Prevention and Treatment and the Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China.,2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- 2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,3Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Shan Lu
- 2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,3Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Xin-He Lai
- 4School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China
| | - Dong Jin
- 2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,3Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Ji Pu
- 2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Lina Niu
- 5Department of Pathogen Biology, School of Basic Medicine and Life Science, Hainan Medical University; Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University); Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou 571199, PR China
| | - Wentao Zhu
- 3Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China
| | - Junrong Liang
- 2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ying Huang
- 2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Bin Wang
- 6Guizhou Center for Disease Control and Prevention, Guiyang 550000, PR China
| | - Xiaomin Wu
- 7Shaanxi Institute of Zoology, Xi'an 710032, PR China
| | - Hao Liang
- 1Guangxi Key Laboratory of AIDS Prevention and Treatment and the Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Jianguo Xu
- 1Guangxi Key Laboratory of AIDS Prevention and Treatment and the Guangxi Collaborative Innovation Center for Biomedicine, School of Public Health, Guangxi Medical University, Nanning 530021, Guangxi, PR China.,3Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai 201508, PR China.,2State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
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25
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Searching for potent and specific antibiotics against pathogenic Helicobacter and Campylobacter strains. ACTA ACUST UNITED AC 2019; 46:409-414. [DOI: 10.1007/s10295-018-2108-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/08/2018] [Indexed: 12/14/2022]
Abstract
Abstract
Menaquinone is an obligatory component of the electron-transfer pathway in microorganisms. Its biosynthetic pathway was established by pioneering studies with Escherichia coli and it was revealed to be derived from chorismate by Men enzymes. However, we identified an alternative pathway, the futalosine pathway, operating in some microorganisms including Helicobacter pylori and Campylobacter jejuni, which cause gastric carcinoma and diarrhea, respectively. Because some useful intestinal bacteria, such as lactobacilli, use the canonical pathway, the futalosine pathway is an attractive target for development of chemotherapeutics for the abovementioned pathogens. In this mini-review, we summarize compounds that inhibit Mqn enzymes involved in the futalosine pathway discovered to date.
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26
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Lebre PH, Cowan DA. Genomics of Alkaliphiles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 172:135-155. [PMID: 30796503 DOI: 10.1007/10_2018_83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alkalinicity presents a challenge for life due to a "reversed" proton gradient that is unfavourable to many bioenergetic processes across the membranes of microorganisms. Despite this, many bacteria, archaea, and eukaryotes, collectively termed alkaliphiles, are adapted to life in alkaline ecosystems and are of great scientific and biotechnological interest due to their niche specialization and ability to produce highly stable enzymes. Advances in next-generation sequencing technologies have propelled not only the genomic characterization of many alkaliphilic microorganisms that have been isolated from nature alkaline sources but also our understanding of the functional relationships between different taxa in microbial communities living in these ecosystems. In this review, we discuss the genetics and molecular biology of alkaliphiles from an "omics" point of view, focusing on how metagenomics and transcriptomics have contributed to our understanding of these extremophiles. Graphical Abstract.
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Affiliation(s)
- Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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FERNANDA SHANNI, ABINAWANTO ABINAWANTO, HELIANTI IS. Isolation of a Functional Gene Encoding Homologous Lysophospholipase from Indonesian Indigenous Bacillus halodurans CM1. MICROBIOLOGY INDONESIA 2019. [DOI: 10.5454/mi.13.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Khan MF, Patra S. Deciphering the rationale behind specific codon usage pattern in extremophiles. Sci Rep 2018; 8:15548. [PMID: 30341344 PMCID: PMC6195531 DOI: 10.1038/s41598-018-33476-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/21/2018] [Indexed: 12/03/2022] Open
Abstract
Protein stability is affected at different hierarchies – gene, RNA, amino acid sequence and structure. Gene is the first level which contributes via varying codon compositions. Codon selectivity of an organism differs with normal and extremophilic milieu. The present work attempts at detailing the codon usage pattern of six extremophilic classes and their harmony. Homologous gene datasets of thermophile-mesophile, psychrophile-mesophile, thermophile-psychrophile, acidophile-alkaliphile, halophile-nonhalophile and barophile-nonbarophile were analysed for filtering statistically significant attributes. Relative abundance analysis, 1–9 scale ranking, nucleotide compositions, attribute weighting and machine learning algorithms were employed to arrive at findings. AGG in thermophiles and barophiles, CAA in mesophiles and psychrophiles, TGG in acidophiles, GAG in alkaliphiles and GAC in halophiles had highest preference. Preference of GC-rich and G/C-ending codons were observed in halophiles and barophiles whereas, a decreasing trend was reflected in psychrophiles and alkaliphiles. GC-rich codons were found to decrease and G/C-ending codons increased in thermophiles whereas, acidophiles showed equal contents of GC-rich and G/C-ending codons. Codon usage patterns exhibited harmony among different extremophiles and has been detailed. However, the codon attribute preferences and their selectivity of extremophiles varied in comparison to non-extremophiles. The finding can be instrumental in codon optimization application for heterologous expression of extremophilic proteins.
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Affiliation(s)
- Mohd Faheem Khan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Zeeshan N, Naz S, Naz S, Afroz A, Zahur M, Zia S. Heterologous expression and enhanced production of β-1,4-glucanase of Bacillus halodurans C-125 in Escherichia coli. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Zapata-Pérez R, Martínez-Moñino AB, García-Saura AG, Cabanes J, Takami H, Sánchez-Ferrer Á. Biochemical characterization of a new nicotinamidase from an unclassified bacterium thriving in a geothermal water stream microbial mat community. PLoS One 2017; 12:e0181561. [PMID: 28750065 PMCID: PMC5531466 DOI: 10.1371/journal.pone.0181561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/03/2017] [Indexed: 12/19/2022] Open
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.
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Affiliation(s)
- Rubén Zapata-Pérez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Murcia, Spain
| | - Ana-Belén Martínez-Moñino
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Murcia, Spain
| | - Antonio-Ginés García-Saura
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Murcia, Spain
| | - Juana Cabanes
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Murcia, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
| | - Hideto Takami
- Microbial Genome Research Group, Yokohama Institute, JAMSTEC, Kanazawa, Yokohama, Japan
| | - Álvaro Sánchez-Ferrer
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Murcia, Spain
- Murcia Biomedical Research Institute (IMIB), Murcia, Spain
- * E-mail:
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Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars. ISME JOURNAL 2017; 11:2584-2598. [PMID: 28731475 DOI: 10.1038/ismej.2017.111] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 01/19/2023]
Abstract
Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (Eh<-550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.
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Functional characterization of hormone sensitive-like lipase from Bacillus halodurans: synthesis and recovery of pNP-laurate with high yields. Extremophiles 2017; 21:871-889. [DOI: 10.1007/s00792-017-0949-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/23/2017] [Indexed: 12/13/2022]
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Wang P, Wang F, Yang J. De novo assembly and analysis of the Pugionium cornutum (L.) Gaertn. transcriptome and identification of genes involved in the drought response. Gene 2017; 626:290-297. [PMID: 28552570 DOI: 10.1016/j.gene.2017.05.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/28/2017] [Accepted: 05/24/2017] [Indexed: 01/12/2023]
Abstract
Pugionium cornutum (L.) Gaertn. is a xerophytic plant species widely distributed in sandy and desert habitats in northwest China. However, the molecular mechanism of drought tolerance in P. cornutum has received little attention. At present, there is limited available transcriptome information for P. cormutum in public databases. Illumina sequencing was used to identify drought-responsive genes and to further characterize the molecular basis of drought tolerance in P. cornutum. In total, 51,385 unigenes with an average length of 825.32bp were obtained by de novo transcriptome assembly. Among these unigenes, 35,276 were annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic pathways. In addition, the results showed that differentially expressed genes (DEGs) were mainly involved in photosynthesis, nitrogen metabolism, and plant hormone signal transduction pathways, notably ascorbate and aldarate metabolism, which could be an alternative pathway to enhance antioxidant capacity in P. cornutum in response to drought stress. These results provide an important clue about the effects of accumulation of ROS on ascorbic acid biosynthesis in P. cornutum. In addition, we found that transcription of most genes involved in ascorbic acid metabolism was altered under drought stress. Additionally, 93 drought-inducible transcription factor genes were identified in the DEGs under drought conditions; these included DREB, AP2/EREBP, B-2a, ERF2, MYB and Zinc finger family. The results of this study provide further insight into the molecular mechanisms of stress tolerance in P. cornutum, and also identify some attractive candidate genes and valuable information for improving drought stress tolerance in other species through genetic engineering.
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Affiliation(s)
- Ping Wang
- College of Agronomy, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Huhhot 010019, China.
| | - Fengfeng Wang
- College of Agronomy, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Huhhot 010019, China
| | - Jing Yang
- College of Agronomy, Inner Mongolia Agricultural University, Inner Mongolia Autonomous Region Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Huhhot 010019, China
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Walid AL, Neveen MAEK, Ebaa EES, Ehab REH. Isolation and characterization of a haloalkaliphilic protease producer bacterium from Wadi Natrun in Egypt. ACTA ACUST UNITED AC 2017. [DOI: 10.5897/ajb2017.15984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Baindara P, Kapoor A, Korpole S, Grover V. Cysteine-rich low molecular weight antimicrobial peptides from Brevibacillus and related genera for biotechnological applications. World J Microbiol Biotechnol 2017; 33:124. [DOI: 10.1007/s11274-017-2291-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 05/20/2017] [Indexed: 11/28/2022]
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Wang HL, Sun L. Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields. World J Microbiol Biotechnol 2017; 33:86. [DOI: 10.1007/s11274-017-2255-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 03/31/2017] [Indexed: 01/14/2023]
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Ogasawara Y, Kondo K, Ikeda A, Harada R, Dairi T. Identification of tirandamycins as specific inhibitors of the futalosine pathway. J Antibiot (Tokyo) 2017; 70:798-800. [DOI: 10.1038/ja.2017.22] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 02/06/2023]
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Zhao X, Kuipers OP. Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. BMC Genomics 2016; 17:882. [PMID: 27821051 PMCID: PMC5100339 DOI: 10.1186/s12864-016-3224-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. RESULTS We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. CONCLUSIONS Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.
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Affiliation(s)
- Xin Zhao
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.
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Deyasi K, Banerjee A, Deb B. Phylogeny of metabolic networks: a spectral graph theoretical approach. J Biosci 2016; 40:799-808. [PMID: 26564980 DOI: 10.1007/s12038-015-9562-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many methods have been developed for finding the commonalities between different organisms in order to study their phylogeny. The structure of metabolic networks also reveals valuable insights into metabolic capacity of species as well as into the habitats where they have evolved. We constructed metabolic networks of 79 fully sequenced organisms and compared their architectures. We used spectral density of normalized Laplacian matrix for comparing the structure of networks. The eigenvalues of this matrix reflect not only the global architecture of a network but also the local topologies that are produced by different graph evolutionary processes like motif duplication or joining. A divergence measure on spectral densities is used to quantify the distances between various metabolic networks, and a split network is constructed to analyse the phylogeny from these distances. In our analysis, we focused on the species that belong to different classes, but appear more related to each other in the phylogeny. We tried to explore whether they have evolved under similar environmental conditions or have similar life histories. With this focus, we have obtained interesting insights into the phylogenetic commonality between different organisms.
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Affiliation(s)
- Krishanu Deyasi
- Department of Mathematics and Statistics, Indian Institute of Science Education and Research, Kolkata, Mohanpur 741 246, India
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Bosma EF, Koehorst JJ, van Hijum SAFT, Renckens B, Vriesendorp B, van de Weijer AHP, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg R. Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T). Stand Genomic Sci 2016; 11:52. [PMID: 27559429 PMCID: PMC4995803 DOI: 10.1186/s40793-016-0172-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 08/09/2016] [Indexed: 11/10/2022] Open
Abstract
Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. Being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. We determined the complete genomic sequence of the B. smithii type strain DSM 4216(T), which consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880 genes. Genome annotation via RAST was complemented by a protein domain analysis. Some unique features of B. smithii central metabolism in comparison to related organisms included the lack of a standard acetate production pathway with no apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes, while acetate was the second fermentation product.
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Affiliation(s)
- Elleke F. Bosma
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
- Present address: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, 2800 Denmark
| | - Jasper J. Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | | | - Bernadet Renckens
- CMBI, NCMLS, Geert-Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
| | | | | | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
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A Novel Glycoside Hydrolase Family 5 β-1,3-1,6-Endoglucanase from Saccharophagus degradans 2-40T and Its Transglycosylase Activity. Appl Environ Microbiol 2016; 82:4340-4349. [PMID: 27208098 DOI: 10.1128/aem.00635-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/30/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED In this study, we characterized Gly5M, originating from a marine bacterium, as a novel β-1,3-1,6-endoglucanase in glycoside hydrolase family 5 (GH5) in the Carbohydrate-Active enZyme database. The gly5M gene encodes Gly5M, a newly characterized enzyme from GH5 subfamily 47 (GH5_47) in Saccharophagus degradans 2-40(T) The gly5M gene was cloned and overexpressed in Escherichia coli Through analysis of the enzymatic reaction products by thin-layer chromatography, high-performance liquid chromatography, and matrix-assisted laser desorption ionization-tandem time of flight mass spectrometry, Gly5M was identified as a novel β-1,3-endoglucanase (EC 3.2.1.39) and bacterial β-1,6-glucanase (EC 3.2.1.75) in GH5. The β-1,3-endoglucanase and β-1,6-endoglucanase activities were detected by using laminarin (a β-1,3-glucan with β-1,6-glycosidic linkages derived from brown macroalgae) and pustulan (a β-1,6-glucan derived from fungal cell walls) as the substrates, respectively. This enzyme also showed transglycosylase activity toward β-1,3-oligosaccharides when laminarioligosaccharides were used as the substrates. Since laminarin is the major form of glucan storage in brown macroalgae, Gly5M could be used to produce glucose and laminarioligosaccharides, using brown macroalgae, for industrial purposes. IMPORTANCE In this study, we have discovered a novel β-1,3-1,6-endoglucanase with a unique transglycosylase activity, namely, Gly5M, from a marine bacterium, Saccharophagus degradans 2-40(T) Gly5M was identified as the newly found β-1,3-endoglucanase and bacterial β-1,6-glucanase in GH5. Gly5M is capable of cleaving glycosidic linkages of both β-1,3-glucans and β-1,6-glucans. Gly5M also possesses a transglycosylase activity toward β-1,3-oligosacchrides. Due to the broad specificity of Gly5M, this enzyme can be used to produce glucose or high-value β-1,3- and/or β-1,6-oligosaccharides.
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Evolution of the SpoIISABC Toxin-Antitoxin-Antitoxin System in Bacilli. Toxins (Basel) 2016; 8:toxins8060180. [PMID: 27294956 PMCID: PMC4926146 DOI: 10.3390/toxins8060180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/01/2016] [Accepted: 06/02/2016] [Indexed: 11/23/2022] Open
Abstract
Programmed cell death in bacteria is generally associated with two-component toxin-antitoxin systems. The SpoIISABC system, originally identified in Bacillus subtilis, consists of three components: a SpoIISA toxin and the SpoIISB and SpoIISC antitoxins. SpoIISA is a membrane-bound protein, while SpoIISB and SpoIISC are small cytosolic antitoxins, which are able to bind SpoIISA and neutralize its toxicity. In the presented bioinformatics analysis, a taxonomic distribution of the genes of the SpoIISABC system is investigated; their conserved regions and residues are identified; and their phylogenetic relationships are inferred. The SpoIISABC system is part of the core genome in members of the Bacillus genus of the Firmicutes phylum. Its presence in some non-bacillus species is likely the result of horizontal gene transfer. The SpoIISB and SpoIISC antitoxins originated by gene duplications, which occurred independently in the B. subtilis and B. cereus lineages. In the B. cereus lineage, the SpoIIS module is present in two different architectures.
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Peculiarities of the interaction of the restriction endonuclease BspD6I with DNA containing its recognition site. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1072-1082. [PMID: 27216152 DOI: 10.1016/j.bbapap.2016.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 04/08/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND Nicking endonucleases are enzymes that recognize specific sites in double-stranded DNA and cleave only one strand at a predetermined position. These enzymes are involved in DNA replication and repair; they can also function as subunits of bacterial heterodimeric restriction endonucleases. One example of such a proteins is the restriction endonuclease BspD6I (R.BspD6I) from Bacillus species strain D6, which consists of the large subunit - nicking endonuclease BspD6I (Nt.BspD6I), and the small subunit (ss.BspD6I). Nt.BspD6I can function independently. Similar enzymes are now widely used in numerous biotechnological applications. The aim of this study was to investigate the fundamental properties of two subunits of R.BspD6I and their interdependence in the course of R.BspD6I activity. METHODS The binding and hydrolysis of DNA duplexes by R.BspD6I are primary analyzed by gel electrophoresis. To elucidate the difference between Nt.BspD6I interaction with the substrate and product of hydrolysis, the thickness shear mode acoustic method is used. RESULTS AND CONCLUSIONS The thermodynamic and kinetic parameters of the Nt.BspD6I interaction with DNA are determined. For the first time we demonstrated that Nt.BspD6I bends the DNA during complex formation. Nt.BspD6I is able to form complexes with the product nicked in the top strand and ss.BspD6I cleaves the bottom strand of the DNA consecutively. Furthermore, the influence of dA methylation in the R.BspD6I recognition site on ss.BspD6I activity is analyzed. GENERAL SIGNIFICANCE The obtained results provide evidence that Nt.BspD6I coordinates the activity of R.BspD6I by strictly coupling of the bottom strand cleavage by ss.BspD6I to the top strand cleavage.
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Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree. Appl Environ Microbiol 2016; 82:2854-2861. [PMID: 26944845 DOI: 10.1128/aem.00483-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. IMPORTANCE Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.
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Lylloff JE, Hansen LBS, Jepsen M, Sanggaard KW, Vester JK, Enghild JJ, Sørensen SJ, Stougaard P, Glaring MA. Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases. Microb Biotechnol 2016; 9:245-56. [PMID: 26834075 PMCID: PMC4767292 DOI: 10.1111/1751-7915.12343] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Proteases active at low temperature or high pH are used in many commercial applications, including the detergent, food and feed industries, and bacteria specifically adapted to these conditions are a potential source of novel proteases. Environments combining these two extremes are very rare, but offer the promise of proteases ideally suited to work at both high pH and low temperature. In this report, bacteria from two cold and alkaline environments, the ikaite columns in Greenland and alkaline ponds in the McMurdo Dry Valley region, Antarctica, were screened for extracellular protease activity. Two isolates, Arsukibacterium ikkense from Greenland and a related strain, Arsukibacterium sp. MJ3, from Antarctica, were further characterized with respect to protease production. Genome sequencing identified a range of potential extracellular proteases including a number of putative secreted subtilisins. An extensive liquid chromatography–tandem mass spectrometry analysis of proteins secreted by A. ikkense identified six subtilisin‐like proteases as abundant components of the exoproteome in addition to other peptidases potentially involved in complete degradation of extracellular protein. Screening of Arsukibacterium genome libraries in Escherichia coli identified two orthologous secreted subtilisins active at pH 10 and 20°C, which were also present in the A. ikkense exoproteome. Recombinant production of both proteases confirmed the observed activity.
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Affiliation(s)
- Jeanette E Lylloff
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Lea B S Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Morten Jepsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Kristian W Sanggaard
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jan K Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Jan J Enghild
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
| | - Mikkel A Glaring
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, 1871, Denmark
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Bakunina IY, Balabanova LA, Pennacchio A, Trincone A. Hooked on α-d-galactosidases: from biomedicine to enzymatic synthesis. Crit Rev Biotechnol 2015; 36:233-45. [PMID: 25394540 DOI: 10.3109/07388551.2014.949618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
α-d-Galactosidases (EC 3.2.1.22) are enzymes employed in a number of useful bio-based applications. We have depicted a comprehensive general survey of α-d-galactosidases from different origin with special emphasis on marine example(s). The structures of natural α-galactosyl containing compounds are described. In addition to 3D structures and mechanisms of action of α-d-galactosidases, different sources, natural function and genetic regulation are also covered. Finally, hydrolytic and synthetic exploitations as free or immobilized biocatalysts are reviewed. Interest in the synthetic aspects during the next years is anticipated for access to important small molecules by green technology with an emphasis on alternative selectivity of this class of enzymes from different sources.
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Affiliation(s)
- Irina Yu Bakunina
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Larissa A Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok , Russia and
| | - Angela Pennacchio
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
| | - Antonio Trincone
- b Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , Pozzuoli , Napoli , Italy
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Abstract
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
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The phosphoenolpyruvate:sugar phosphotransferase system is involved in sensitivity to the glucosylated bacteriocin sublancin. Antimicrob Agents Chemother 2015; 59:6844-54. [PMID: 26282429 DOI: 10.1128/aac.01519-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/11/2015] [Indexed: 12/25/2022] Open
Abstract
The mode of action of a group of glycosylated antimicrobial peptides known as glycocins remains to be elucidated. In the current study of one glycocin, sublancin, we identified the phosphoenolpyruvate:sugar phosphotransferase system (PTS) of Bacillus species as a key player in bacterial sensitivity. Sublancin kills several Gram-positive bacteria, such as Bacillus species and Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA). Unlike other classes of bacteriocins for which the PTS is involved in their mechanism of action, we show that the addition of PTS-requiring sugars leads to increased resistance rather than increased sensitivity, suggesting that sublancin has a distinct mechanism of action. Collectively, our present mutagenesis and genomic studies demonstrate that the histidine-containing phosphocarrier protein (HPr) and domain A of enzyme II (PtsG) in particular are critical determinants for bacterial sensitivity to sublancin.
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Vicedo E, Schlessinger A, Rost B. Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes. PLoS One 2015; 10:e0133990. [PMID: 26252577 PMCID: PMC4529154 DOI: 10.1371/journal.pone.0133990] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 07/03/2015] [Indexed: 12/24/2022] Open
Abstract
Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. Here, we revealed that some differences in organisms surviving in extreme habitats correlate with a simple single feature, namely the fraction of proteins predicted to have long disordered regions. We predicted disorder with different methods for 46 completely sequenced organisms from diverse habitats and found a correlation between protein disorder and the extremity of the environment. More specifically, the overall percentage of proteins with long disordered regions tended to be more similar between organisms of similar habitats than between organisms of similar taxonomy. For example, predictions tended to detect substantially more proteins with long disordered regions in prokaryotic halophiles (survive high salt) than in their taxonomic neighbors. Another peculiar environment is that of high radiation survived, e.g. by Deinococcus radiodurans. The relatively high fraction of disorder predicted in this extremophile might provide a shield against mutations. Although our analysis fails to establish causation, the observed correlation between such a simplistic, coarse-grained, microscopic molecular feature (disorder content) and a macroscopic variable (habitat) remains stunning.
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Affiliation(s)
- Esmeralda Vicedo
- TUM, Department of Informatics, Bioinformatics & Computational Biology—i12, Boltzmannstr. 3, 85748 Garching, Munich, Germany
- TUM Graduate School of Information Science in Health (GSISH), Boltzmannstr. 11, 85748 Garching, Munich, Germany
- * E-mail:
| | - Avner Schlessinger
- Icahn School of Medicine at Mount Sinai, Department of Pharmacology and Systems Therapeutics, One Gustave L. Levy Place, Box 1603, New York, New York, 10029, United States of America
| | - Burkhard Rost
- TUM, Department of Informatics, Bioinformatics & Computational Biology—i12, Boltzmannstr. 3, 85748 Garching, Munich, Germany
- Institute of Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748 Garching, Munich, Germany
- Institute for Food and Plant Sciences WZW Weihenstephan, Alte Akademie 8, Freising, Germany
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