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Simon P, Pompe W, Gruner D, Sturm E, Ostermann K, Matys S, Vogel M, Rödel G. Nested Formation of Calcium Carbonate Polymorphs in a Bacterial Surface Membrane with a Graded Nanoconfinement: An Evolutionary Strategy to Ensure Bacterial Survival. ACS Biomater Sci Eng 2022; 8:526-539. [PMID: 34995442 PMCID: PMC8848282 DOI: 10.1021/acsbiomaterials.1c01280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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It is the intention
of this study to elucidate the nested formation
of calcium carbonate polymorphs or polyamorphs in the different nanosized
compartments. With these observations, it can be concluded how the
bacteria can survive in a harsh environment with high calcium carbonate
supersaturation. The mechanisms of calcium carbonate precipitation
at the surface membrane and at the underlying cell wall membrane of
the thermophilic soil bacterium Geobacillus stearothermophilus DSM 13240 have been revealed by high-resolution transmission electron
microscopy and atomic force microscopy. In this Gram-positive bacterium,
nanopores in the surface layer (S-layer) and in the supporting cell
wall polymers are nucleation sites for metastable calcium carbonate
polymorphs and polyamorphs. In order to observe the different metastable
forms, various reaction times and a low reaction temperature (4 °C)
have been chosen. Calcium carbonate polymorphs nucleate in the confinement
of nanosized pores (⌀ 3–5 nm) of the S-layer. The hydrous
crystalline calcium carbonate (ikaite) is formed initially with [110]
as the favored growth direction. It transforms into the anhydrous
metastable vaterite by a solid-state transition. In a following reaction
step, calcite is precipitated, caused by dissolution of vaterite in
the aqueous solution. In the larger pores of the cell wall (⌀
20–50 nm), hydrated amorphous calcium carbonate is grown, which
transforms into metastable monohydrocalcite, aragonite, or calcite.
Due to the sequence of reaction steps via various metastable phases,
the bacteria gain time for chipping the partially mineralized S-layer,
and forming a fresh S-layer (characteristic growth time about 20 min).
Thus, the bacteria can survive in solutions with high calcium carbonate
supersaturation under the conditions of forced biomineralization.
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Affiliation(s)
- Paul Simon
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany
| | - Wolfgang Pompe
- Institute of Materials Science, Technische Universität Dresden, Helmholtzstraße 7, 01069 Dresden, Germany
| | - Denise Gruner
- Institute of Genetics, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany.,Polymeric Microsystems, Technische Universität Dresden, Helmholtzstraße 100, 01069 Dresden, Germany
| | - Elena Sturm
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Straße 40, 01187 Dresden, Germany.,Physical Chemistry, University of Konstanz, POB 714, D-78457 Konstanz, Germany
| | - Kai Ostermann
- Institute of Genetics, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Sabine Matys
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzener Landstraße 400, 01328 Dresden, Germany
| | - Manja Vogel
- Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzener Landstraße 400, 01328 Dresden, Germany
| | - Gerhard Rödel
- Institute of Genetics, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
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2
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Timilsina PM, Pandey GR, Shrestha A, Ojha M, Karki TB. Purification and characterization of a noble thermostable algal starch liquefying alpha-amylase from Aeribacillus pallidus BTPS-2 isolated from geothermal spring of Nepal. ACTA ACUST UNITED AC 2020; 28:e00551. [PMID: 33240796 PMCID: PMC7674295 DOI: 10.1016/j.btre.2020.e00551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/18/2020] [Accepted: 10/29/2020] [Indexed: 11/29/2022]
Abstract
A thermophilic strain, Aeribacillus pallidus BTPS-2 was isolated from Bhurung geothermal spring of Nepal. The 16 s rRNA sequence showed 99.8 % similarity with the type strain Aeribacillus pallidus DSM 3670. The morphological, physiological and biochemical properties were similar to the type strain. Alpha-amylase from A. pallidus BTPS-2 was purified to 19-fold purification by DEAE-Cellulose ion exchange chromatography. The Km value of amylase on starch was 0.51 ± 0.05 mg/mL. The optimum pH and temperature were 7.0 and 70 °C. SDS-PAGE analysis showed a single band at 100 kDa. The half-life of the enzyme at 80 °C was 2.81 h. The enzyme showed an inhibitory effect in the presence of Fe2+, Pb2+, Sn2+ and Hg2+ at 10 mM concentrations. TLC analysis showed that the enzyme is a liquifying alpha-amylase. The enzyme reduced the viscosity of algal biomass suspension up to 74.2 ± 0.17 % which was more efficient than Bacillus amyloliquefaciens alpha-amylase (80.5 ± 0.2 %).
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Affiliation(s)
| | - Gyanu Raj Pandey
- Department of Biotechnology, Kathmandu University, Dhulikhel, 6250, Nepal.,Biotechnological Research and Developmental Center, Bharatpur, Chitwan, 44200, Nepal
| | - Asmita Shrestha
- Department of Biotechnology, Kathmandu University, Dhulikhel, 6250, Nepal.,Biotechnological Research and Developmental Center, Bharatpur, Chitwan, 44200, Nepal
| | - Manish Ojha
- Department of Biotechnology, Kathmandu University, Dhulikhel, 6250, Nepal
| | - Tika Bahadur Karki
- Department of Biotechnology, Kathmandu University, Dhulikhel, 6250, Nepal
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3
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Møller MS, Henriksen A, Svensson B. Structure and function of α-glucan debranching enzymes. Cell Mol Life Sci 2016; 73:2619-41. [PMID: 27137180 PMCID: PMC11108273 DOI: 10.1007/s00018-016-2241-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 10/21/2022]
Abstract
α-Glucan debranching enzymes hydrolyse α-1,6-linkages in starch/glycogen, thereby, playing a central role in energy metabolism in all living organisms. They belong to glycoside hydrolase families GH13 and GH57 and several of these enzymes are industrially important. Nine GH13 subfamilies include α-glucan debranching enzymes; isoamylase and glycogen debranching enzymes (GH13_11); pullulanase type I/limit dextrinase (GH13_12-14); pullulan hydrolase (GH13_20); bifunctional glycogen debranching enzyme (GH13_25); oligo-1 and glucan-1,6-α-glucosidases (GH13_31); pullulanase type II (GH13_39); and α-amylase domains (GH13_41) in two-domain amylase-pullulanases. GH57 harbours type II pullulanases. Specificity differences, domain organisation, carbohydrate binding modules, sequence motifs, three-dimensional structures and specificity determinants are discussed. The phylogenetic analysis indicated that GH13_39 enzymes could represent a "missing link" between the strictly α-1,6-specific debranching enzymes and the enzymes with dual specificity and α-1,4-linkage preference.
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Affiliation(s)
- Marie Sofie Møller
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 221 00, Lund, Sweden.
| | - Anette Henriksen
- Global Research Unit, Department of Large Protein Biophysics and Formulation, Novo Nordisk A/S, Novo Nordisk Park, 2760, Måløv, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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4
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Nisha M, Satyanarayana T. Characteristics, protein engineering and applications of microbial thermostable pullulanases and pullulan hydrolases. Appl Microbiol Biotechnol 2016; 100:5661-79. [DOI: 10.1007/s00253-016-7572-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/17/2022]
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5
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Brumm PJ, De Maayer P, Mead DA, Cowan DA. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. Front Microbiol 2015; 6:430. [PMID: 26029180 PMCID: PMC4428132 DOI: 10.3389/fmicb.2015.00430] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/22/2015] [Indexed: 11/13/2022] Open
Abstract
In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.
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Affiliation(s)
- Phillip J. Brumm
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
| | - Pieter De Maayer
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
- Department of Microbiology and Plant Pathology, University of PretoriaPretoria, South Africa
| | - David A. Mead
- C5•6 TechnologiesMiddleton, WI, USA
- Great Lakes Bioenergy Research Center, University of WisconsinMadison, WI, USA
- Lucigen CorporationMiddleton, WI, USA
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
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6
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Sleytr UB, Schuster B, Egelseer E, Pum D. S-layers: principles and applications. FEMS Microbiol Rev 2014; 38:823-64. [PMID: 24483139 PMCID: PMC4232325 DOI: 10.1111/1574-6976.12063] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 01/12/2023] Open
Abstract
Monomolecular arrays of protein or glycoprotein subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope components. S-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. The isoporous lattices completely covering the cell surface provide organisms with various selection advantages including functioning as protective coats, molecular sieves and ion traps, as structures involved in surface recognition and cell adhesion, and as antifouling layers. S-layers are also identified to contribute to virulence when present as a structural component of pathogens. In Archaea, most of which possess S-layers as exclusive wall component, they are involved in determining cell shape and cell division. Studies on structure, chemistry, genetics, assembly, function, and evolutionary relationship of S-layers revealed considerable application potential in (nano)biotechnology, biomimetics, biomedicine, and synthetic biology.
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Affiliation(s)
- Uwe B. Sleytr
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bernhard Schuster
- Institute of Synthetic BiologyDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Eva‐Maria Egelseer
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Dietmar Pum
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
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A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization. Int J Mol Sci 2013; 14:11302-18. [PMID: 23759984 PMCID: PMC3709733 DOI: 10.3390/ijms140611302] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/03/2013] [Accepted: 05/14/2013] [Indexed: 11/21/2022] Open
Abstract
An amylopullulanase of the thermophilic Anoxybacillus sp. SK3-4 (ApuASK) was purified to homogeneity and characterized. Though amylopullulanases larger than 200 kDa are rare, the molecular mass of purified ApuASK appears to be approximately 225 kDa, on both SDS-PAGE analyses and native-PAGE analyses. ApuASK was stable between pH 6.0 and pH 8.0 and exhibited optimal activity at pH 7.5. The optimal temperature for ApuASK enzyme activity was 60 °C, and it retained 54% of its total activity for 240 min at 65 °C. ApuASK reacts with pullulan, starch, glycogen, and dextrin, yielding glucose, maltose, and maltotriose. Interestingly, most of the previously described amylopullulanases are unable to produce glucose and maltose from these substrates. Thus, ApuASK is a novel, high molecular-mass amylopullulanase able to produce glucose, maltose, and maltotriose from pullulan and starch. Based on whole genome sequencing data, ApuASK appeared to be the largest protein present in Anoxybacillus sp. SK3-4. The α-amylase catalytic domain present in all of the amylase superfamily members is present in ApuASK, located between the cyclodextrin (CD)-pullulan-degrading N-terminus and the α-amylase catalytic C-terminus (amyC) domains. In addition, the existence of a S-layer homology (SLH) domain indicates that ApuASK might function as a cell-anchoring enzyme and be important for carbohydrate utilization in a streaming hot spring.
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8
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Rich RL, Myszka DG. Survey of the 2009 commercial optical biosensor literature. J Mol Recognit 2012; 24:892-914. [PMID: 22038797 DOI: 10.1002/jmr.1138] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We took a different approach to reviewing the commercial biosensor literature this year by inviting 22 biosensor users to serve as a review committee. They set the criteria for what to expect in a publication and ultimately decided to use a pass/fail system for selecting which papers to include in this year's reference list. Of the 1514 publications in 2009 that reported using commercially available optical biosensor technology, only 20% passed their cutoff. The most common criticism the reviewers had with the literature was that "the biosensor experiments could have been done better." They selected 10 papers to highlight good experimental technique, data presentation, and unique applications of the technology. This communal review process was educational for everyone involved and one we will not soon forget.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT, USA
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9
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S-layer homology domain proteins Csac_0678 and Csac_2722 are implicated in plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Appl Environ Microbiol 2011; 78:768-77. [PMID: 22138994 DOI: 10.1128/aem.07031-11] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Caldicellulosiruptor contains extremely thermophilic bacteria that grow on plant polysaccharides. The genomes of Caldicellulosiruptor species reveal certain surface layer homology (SLH) domain proteins that have distinguishing features, pointing to a role in lignocellulose deconstruction. Two of these proteins in Caldicellulosiruptor saccharolyticus (Csac_0678 and Csac_2722) were examined from this perspective. In addition to three contiguous SLH domains, the Csac_0678 gene encodes a glycoside hydrolase family 5 (GH5) catalytic domain and a family 28 carbohydrate-binding module (CBM); orthologs to Csac_0678 could be identified in all genome-sequenced Caldicellulosiruptor species. Recombinant Csac_0678 was optimally active at 75°C and pH 5.0, exhibiting both endoglucanase and xylanase activities. SLH domain removal did not impact Csac_0678 GH activity, but deletion of the CBM28 domain eliminated binding to crystalline cellulose and rendered the enzyme inactive on this substrate. Csac_2722 is the largest open reading frame (ORF) in the C. saccharolyticus genome (predicted molecular mass of 286,516 kDa) and contains two putative sugar-binding domains, two Big4 domains (bacterial domains with an immunoglobulin [Ig]-like fold), and a cadherin-like (Cd) domain. Recombinant Csac_2722, lacking the SLH and Cd domains, bound to cellulose and had detectable carboxymethylcellulose (CMC) hydrolytic activity. Antibodies directed against Csac_0678 and Csac_2722 confirmed that these proteins bound to the C. saccharolyticus S-layer. Their cellular localization and functional biochemical properties indicate roles for Csac_0678 and Csac_2722 in recruitment and hydrolysis of complex polysaccharides and the deconstruction of lignocellulosic biomass. Furthermore, these results suggest that related SLH domain proteins in other Caldicellulosiruptor genomes may also be important contributors to plant biomass utilization.
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Kinns H, Badelt-Lichtblau H, Egelseer EM, Sleytr UB, Howorka S. Identifying assembly-inhibiting and assembly-tolerant sites in the SbsB S-layer protein from Geobacillus stearothermophilus. J Mol Biol 2009; 395:742-53. [PMID: 19836402 DOI: 10.1016/j.jmb.2009.10.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2009] [Revised: 10/07/2009] [Accepted: 10/08/2009] [Indexed: 10/20/2022]
Abstract
Surface layer (S-layer) proteins self-assemble into two-dimensional crystalline lattices that cover the cell wall of all archaea and many bacteria. We have generated assembly-negative protein variants of high solubility that will facilitate high-resolution structure determination. Assembly-negative versions of the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2 were obtained using an insertion mutagenesis screen. The haemagglutinin epitope tag was inserted at 23 amino acid positions known to be located on the monomer protein surface from a previous cysteine accessibility screen. Limited proteolysis, circular dichroism, and fluorescence were used to probe whether the epitope insertion affected the secondary and tertiary structures of the monomer, while electron microscopy and size-exclusion chromatography were employed to examine proteins' ability to self-assemble. The screen not only identified assembly-compromised mutants with native fold but also yielded correctly folded, self-assembling mutants suitable for displaying epitopes for biomedical and biophysical applications, as well as cryo-electron microscopy imaging. Our study marks an important step in the analysis of the S-layer structure. In addition, the approach of concerted insertion and cysteine mutagenesis can likely be applied for other supramolecular assemblies.
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Affiliation(s)
- Helen Kinns
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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11
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Kroutil M, Pavkov T, Birner-Gruenberger R, Tesarz M, Sleytr UB, Egelseer EM, Keller W. Towards the structure of the C-terminal part of the S-layer protein SbsC. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1042-7. [PMID: 19851018 PMCID: PMC2765897 DOI: 10.1107/s1744309109035386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Accepted: 09/02/2009] [Indexed: 11/10/2022]
Abstract
The S-layer protein SbsC from Geobacillus stearothermophilus ATCC 12980 is the most prevalent single protein produced by the bacterium and covers the complete bacterial surface in the form of a two-dimensional crystalline monolayer. In order to elucidate the structural features of the assembly domains, several N-terminally truncated fragments of SbsC have been crystallized. Crystals obtained from recombinant fragments showed anisotropic diffraction to a maximum of 3.5 A resolution using synchrotron radiation. The best diffracting crystals were obtained from rSbsC(755-1099), an unintentional in situ proteolytic degradation product of rSbsC(447-1099). Crystals were obtained in two different space groups, P2(1) and P4(1)2(1)2, and diffracted to 2.6 and 3 A resolution, respectively. Native and heavy-atom derivative data have been collected. The structure of the C-terminal part will yield atomic resolution information for the domains that are crucial for the assembly of the two-dimensional lattice.
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Affiliation(s)
- Markus Kroutil
- Karl-Franzens University, Institute of Molecular Biosciences, Graz, Austria
| | - Tea Pavkov
- Karl-Franzens University, Institute of Molecular Biosciences, Graz, Austria
| | - Ruth Birner-Gruenberger
- Medical University of Graz, Center for Medical Research, Proteomics Core Facility, Graz, Austria
| | - Manfred Tesarz
- Department of NanoBiotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Uwe B. Sleytr
- Department of NanoBiotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Eva M. Egelseer
- Department of NanoBiotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Walter Keller
- Karl-Franzens University, Institute of Molecular Biosciences, Graz, Austria
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