Genetics and potential biotechnological applications of thermophilic and extremely thermophilic micro-organisms

Simultaneous saccharification and lactic acid fermentation of the cellulosic fraction of municipal solid waste using Bacillus smithii

Objective

A primary drawback to simultaneous saccharification and fermentation (SSF) processes is the incompatibility of the temperature and pH optima for the hydrolysis and fermentation steps—with the former working best at 50–55 °C and pH 4.5–5.5. Here, nine thermophilic Bacillus and Parageobacillus spp. were evaluated for growth and lactic acid fermentation at high temperature and low pH. The most promising candidate was then carried forward to demonstrate SSF using the cellulosic fraction from municipal solid waste (MSW) as a feedstock.

Results

B. smithii SA8Eth was identified as the most promising candidate and in a batch SSF maintained at 55 °C and pH 5.0, using a cellulase dose of 5 FPU/g glucan, it produced 5.1 g/L lactic acid from 2% (w/v) MSW cellulosic pulp in TSB media.

Conclusion

This work has both scientific and industrial relevance, as it evaluates a number of previously untrialled bacterial hosts for their compatibility with lignocellulosic SSF for lactic acid production and successfully identifies B. smithii as a potential candidate for such a process.

Electronic supplementary material

The online version of this article (10.1007/s10529-020-03049-y) contains supplementary material, which is available to authorized users.

Thermophiles; or, the Modern Prometheus: The Importance of Extreme Microorganisms for Understanding and Applying Extracellular Electron Transfer

Approximately four billion years ago, the first microorganisms to thrive on earth were anaerobic chemoautotrophic thermophiles, a specific group of extremophiles that survive and operate at temperatures ∼50 – 125°C and do not use molecular oxygen (O₂) for respiration. Instead, these microorganisms performed respiration via dissimilatory metal reduction by transferring their electrons extracellularly to insoluble electron acceptors. Genetic evidence suggests that Gram-positive thermophilic bacteria capable of extracellular electron transfer (EET) are positioned close to the root of the Bacteria kingdom on the tree of life. On the contrary, EET in Gram-negative mesophilic bacteria is a relatively new phenomenon that is evolutionarily distinct from Gram-positive bacteria. This suggests that EET evolved separately in Gram-positive thermophiles and Gram-negative mesophiles, and that EET in these bacterial types is a result of a convergent evolutionary process leading to homoplasy. Thus, the study of dissimilatory metal reducing thermophiles provides a glimpse into some of Earth’s earliest forms of respiration. This will provide new insights for understanding biogeochemistry and the development of early Earth in addition to providing unique avenues for exploration and discovery in astrobiology. Lastly, the physiological composition of Gram-positive thermophiles, coupled with the kinetic and thermodynamic consequences of surviving at elevated temperatures, makes them ideal candidates for developing new mathematical models and designing innovative next-generation biotechnologies.

KEY CONCEPTS

Anaerobe: organism that does not require oxygen for growth.

Chemoautotroph: organism that obtains energy by oxidizing inorganic electron donors.

Convergent Evolution: process in which organisms which are not closely related independently evolve similar traits due to adapting to similar ecological niches and/or environments.

Dissimilatory Metal Reduction: reduction of a metal or metalloid that uses electrons from oxidized organic or inorganic electron donors.

Exoelectrogen: microorganism that performs dissimilatory metal reduction via extracellular electron transfer.

Extremophiles: organisms that thrive in physical or geochemical conditions that are considered detrimental to most life on Earth.

Homoplasy: a character shared by a set of species that is not shared by a common ancestor

Non-synonymous Substitutions (K_a): a substitution of a nucleotide that changes a codon sequence resulting in a change in the amino acid sequence of a protein.

Synonymous Substitutions (K_s): a substitution of a nucleotide that may change a codon sequence, but results in no change in the amino acid sequence of a protein.

Thermophiles: a specific group of extremophiles that survive and operate at temperatures ∼50–125°C.

Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives

Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO₂ and hydrogen. With hydrogen yields approaching the theoretical limit for dark fermentation of 4 mol hydrogen per mol hexose, this organism has proven itself to be an excellent candidate for biological hydrogen production. This review provides an overview of the research on C. saccharolyticus with respect to the hydrolytic capability, sugar metabolism, hydrogen formation, mechanisms involved in hydrogen inhibition, and the regulation of the redox and carbon metabolism. Analysis of currently available fermentation data reveal decreased hydrogen yields under non-ideal cultivation conditions, which are mainly associated with the accumulation of hydrogen in the liquid phase. Thermodynamic considerations concerning the reactions involved in hydrogen formation are discussed with respect to the dissolved hydrogen concentration. Novel cultivation data demonstrate the sensitivity of C. saccharolyticus to increased hydrogen levels regarding substrate load and nitrogen limitation. In addition, special attention is given to the rhamnose metabolism, which represents an unusual type of redox balancing. Finally, several approaches are suggested to improve biohydrogen production by C. saccharolyticus.

Isolation and characterization of Thermus bacteriophages

One-hundred-fifteen bacteriophage strains were isolated from alkaline hot springs in Iceland, New Zealand, Russia (Kamchatka), and the U.S.A. The phages belonged to the Myoviridae, Siphoviridae, Tectiviridae, and Inoviridae families. Over 50% of isolates were isometric or filamentous. One type of siphovirus had giant tails of over 800 nm in length. Phages were further characterized by host range, genome size, DNA restriction endonuclease digestion patterns, and temperature and pH sensitivity. Myoviruses and tectiviruses had a worldwide distribution. Most phages were narrowly host-specific and all were highly resistant against heating and alkaline and acidic pH. This is the first time that tectiviruses and filamentous phages are reported for bacteria of the Thermus-Deinococcus phylum. The presence of tectiviruses, inoviruses, and myoviruses is attributed to acquisition from ancestral gamma-proteobacteria by horizontal gene transfer.

The enzymes from extreme thermophiles: bacterial sources, thermostabilities and industrial relevance

This review on enzymes from extreme thermophiles (optimum growth temperature greater than 65 degrees C) concentrates on their characteristics, especially thermostabilities, and their commercial applicability. The enzymes are considered in general terms first, with comments on denaturation, stabilization and industrial processes. Discussion of the enzymes subsequently proceeds in order of their E.C. classification: oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases. The ramifications of cloned enzymes from extreme thermophiles are also discussed.

Studies on Bacillus stearothermophilus. Part II. Transformation of progesterone

Bacillus stearothermophilus, a thermophilic bacterium isolated from Kuwaiti desert, when incubated with exogenous progesterone for 10 days at 65 degrees C produced two new dihydroxy isomers of progesterone, and two known compounds, 5 alpha-pregnane-3,6,20-trione and 6-dehydroprogesterone, along with the earlier reported monohydroxylated metabolites and a B-Seco compound. The two new dihydroxy compounds were identified as 6 alpha,20 alpha-dihydroxyprogesterone and 6 beta,20 alpha-dihydroxyprogesterone. These metabolites were purified by TLC and HPLC followed by their identification through 1H, 13C NMR and other spectroscopic data.

A novel phenol hydroxylase and catechol 2,3-dioxygenase from the thermophilic Bacillus thermoleovorans strain A2: nucleotide sequence and analysis of the genes

The new thermophilic Bacillus thermoleovorans strain A2 degrades phenol and cresols via the meta cleavage pathway. The first two enzymes involved in this process, the phenol hydroxylase and catechol 2,3-dioxygenase, encoded by the pheA and pheB genes respectively, were cloned and sequenced. The deduced amino acid sequence of pheA contains 524 amino acids with a theoretical M(r) of 59,602 Da and displays less than 10% amino acid identity to known phenol hydroxylases. The greatest amino acid identity (54%) displayed by pheA is with the larger component of the two-component 4-hydroxyphenylacetic acid hydroxylase from Escherichia coli W encoded by hpaB. No second component was present on the 3.8-kb insert. The consensus sequence GXGXXG for FAD/NAD binding sites is not present in pheA. PheB encodes a new catechol 2,3-dioxygenase of 308 amino acids (M(r) 35,487 Da) which has greatest amino acid identity (43%) with the 3-methyl catechol 2,3-dioxygenase of Pseudomonas putida UCC2 encoded by tdnC. Both pheA and pheB encode new enzymes which display low sequence homology with those previously published.

A thermophilic nitrate reductase is responsible for the strain specific anaerobic growth of Thermus thermophilus HB8

T. thermophilus HB8 contains a nitrate reductase gene cluster which is absent from closely related strains. This cluster encodes 4 ORFs (a-d) similar in organization and protein sequence to those encoded by respiratory nitrate reductase operons (narGHJI) of Escherichia coli, Bacillus subtilis, Pseudomonas fluorescens, and Thiosphaera pantothropha. The highest similarity is shown between the proteins encoded by the ORFa, ORFb and ORFd, and the structural components of the mesophilic nitrate reductases NarG (alpha), NarH (beta), and NarI (gamma) proteins, whilst ORFc encodes a protein which showed lower similarity to NarJ, a protein of unknown function encoded between narH and narI genes in all the nar cluster so far sequenced. This T. thermophilus HB8 narGHJI cluster is strongly induced by the combined effect of nitrate and low oxygen concentration, giving rise to the synthesis of an enzyme whose optimal temperature and pH was determined to be 80 degrees C, and pH 10, respectively. We also demonstrate that insertional inactivation of the narG and narH genes of this cluster results in strictly aerobic mutants, showing its sole responsibility in the strain specific ability of T. thermophilus HB8 to grow anaerobically.

Structure of peptidoglycan from Thermus thermophilus HB8

The composition and structure of peptidoglycan (murein) extracted from the extreme thermophilic eubacterium Thermus thermophilus HB8 are presented. The structure of 29 muropeptides, accounting for more than 85% of total murein, is reported. The basic monomeric subunit consists of N-acetylglucosamine-N-acetylmuramic acid-L-Ala-D-Glu-L-Orn-D-Ala-D-Ala, acylated at the delta-NH2 group of Orn by a Gly-Gly dipeptide. In a significant proportion (about 23%) of total muropeptides, the N-terminal Gly is substituted by a residue of phenylacetic acid. This is the first time phenylacetic acid is described as a component of bacterial murein. Possible implications for murein physiology and biosynthesis are discussed. Murein cross-linking is mediated by D-Ala-Gly-Gly peptide cross-bridges. Glycan chains are apparently terminated by (1-->6) anhydro N-acetylmuramic acid residues. Neither reducing sugars nor murein-bound macromolecules were detected. Murein from T. thermophilus presents an intermediate complexity between those of gram-positive and gram-negative organisms. The murein composition and peptide cross-bridges of T. thermophilus are typical for a gram-positive bacterium. However, the murein content, degree of cross-linkage, and glycan chain length for T. thermophilus are closer to those for gram-negative organisms and could explain the gram-negative character of Thermus spp.

Characterization of the Bacillus stearothermophilus BR219 phenol hydroxylase gene

The catabolic genes pheA and pheB, coding for the conversion of phenol to catechol and catechol to 2-hydroxymuconic semialdehyde, respectively, have been cloned from Bacillus stearothermophilus BR219 into Escherichia coli. Following its localization on the 11-kb B. stearothermophilus DNA insert by deletion and expression analysis, the phenol hydroxylase gene pheA was subcloned as a 2-kb HindIII fragment, whose transformant expressed the enzyme after phenol induction and even more strongly after o-, m-, and p-cresol induction. In vitro transcription-translation experiments indicated that the phenol hydroxylase and catechol 2,3-dioxygenase enzymes are constituted of single subunits with molecular weights of 44,000 and 33,000, respectively. Nucleotide sequencing of the pheA gene revealed a strong similarity to flavin hydroxylases from Rhodococcus and Streptomyces species. Hybridization experiments indicated that the fragment containing PheA and PheB is located on a 66-kb plasmid in the parental thermophile.

Obligately anaerobic bacteria in biotechnology

New obligately anaerobic bacteria are being discovered at an accelerating rate and it is becoming very evident that the diversity of anoxic biotransformations has been greatly underestimated. Furthermore, among contemporary anaerobes there are many that thrive in extreme environments including, for example, an impressive array of both archaebacterial and eubacterial hyperthermophiles. Free energy for growth and reproduction may be conserved not only via fermentations but also by anoxygenic photophosphorylation and other modes of creating transmembrane proton potential. Thus forms of anaerobic respiration in which various inorganic oxidants (or indeed carbon dioxide) serve as terminal electron acceptors have greatly extended the natural habitats in which such organisms may predominate. Anaerobic bacteria are, however, often found in nature as members of close microbial communities (consortia) that, although sustained by syntrophic and other relations between component species, are liable to alter their composition and character in response to environmental changes, e.g., availability of terminal oxidants. It follows that the biotechnological exploitation of obligately anaerobic bacteria must be informed by knowledge both of their biochemical capacities and of their normal environmental roles. It is against this background that illustrative examples of the activities of anaerobic bacteria are considered under three heads: 1. Biodegradation/Bioremediation, with special reference to the anaerobic breakdown of aromatic and/or halogenated organic substances; 2. Biosynthesis/Bioproduction, encompassing normal and modified fermentations; and 3. Biotransformations, accomplished by whole or semipermeabilized organisms or by enzymes derived therefrom, with particular interest attaching to the production of chiral compounds by a number of procedures, including electromicrobial reduction.

Purification and properties of a beta-1,4-xylanase from a cellulolytic extreme thermophile expressed in Escherichia coli

1. An endoxylanase (EC 3.2.1.8) was purified from an Escherichia coli strain carrying a xylanase gene from the extreme thermophile "Caldocellum saccharolyticum" strain Tp8T6.3.3.1. It was found to have an M(r) of 42,000 and an isoelectric point of approx. 5.0. 2. The enzyme showed optimum activity at pH 5.0-7.7 and had an activation energy of 44 kJ mol-1. It was stable at room temperature at pH 4.5-11.5 in the presence of 0.5 mg ml-1 bovine serum albumin. The half-life of the enzyme at 75 degrees C was 20 min at pH 6.0 in the presence of 0.5 mg ml-1 bovine serum albumin. 3. The xylanase had highest activity on oat spelts xylan, releasing xylobiose and some xylotriose. The Km for oat spelts xylan was 0.021% (w/v) at pH 6.0. 4. The enzyme had high activity on sugar cane bagasse hemicelluloses A and B, lower activity on larchwood xylan and also hydrolysed carboxymethylcellulose, 4-methylumbelliferyl beta-D-cellobioside and p-nitrophenyl beta-D-cellobioside, but could not hydrolyse xylobiose. 5. It showed transferase activity on p-nitrophenyl beta-D-xylopyranoside. Xylose did not inhibit the enzyme.

Mechanism-based strategies for protein thermostabilization

Strategies for stabilizing enzymes can be derived from a two-step model of irreversible inactivation that involves preliminary reversible unfolding, followed by an irreversible step. Reversible unfolding is best prevented by covalent immobilization, whereas methods such as covalent modification of amino acid residues or 'medium engineering' (by the addition of low-molecular-weight compounds) are effective against irreversible 'incorrect' refolding. Genetic modification of the protein sequence is the most effective approach for preventing chemical deterioration.

Overproduction of an acetylxylan esterase from the extreme thermophile "Caldocellum saccharolyticum" in Escherichia coli

The xynC gene coding for an acetylxylan esterase from the extreme thermophile "Caldocellum saccharolyticum" was overexpressed in Escherichia coli strain RR28 by cloning the gene downstream from the lacZ promoter region of pUC18 (pNZ1447) or downstream from the temperature-inducible lambda pRpL promoters of pJLA602 (pNZ1600). The protein formed high molecular weight aggregates in induced cells of RR28/pNZ1600 but not in RR28/pNZ1447. The enzyme constituted up to 10% of the total cell protein and was located in the cytoplasmic fraction of RR28/pNZ1447. The acetyl esterase was most active at pH 6.0 and 70-75 degrees C with a half-life of 64 h at 70 degrees C and 30 h at 80 degrees C, respectively.

Cloning, sequence analysis, and expression in Escherichia coli of a gene coding for a beta-mannanase from the extremely thermophilic bacterium "Caldocellum saccharolyticum"

A lambda recombinant phage expressing beta-mannanase activity in Escherichia coli has been isolated from a genomic library of the extremely thermophilic anaerobe "Caldocellum saccharolyticum." The gene was cloned into pBR322 on a 5-kb BamHI fragment, and its location was obtained by deletion analysis. The sequence of a 2.1-kb fragment containing the mannanase gene has been determined. One open reading frame was found which could code for a protein of Mr 38,904. The mannanase gene (manA) was overexpressed in E. coli by cloning the gene downstream from the lacZ promoter of pUC18. The enzyme was most active at pH 6 and 80 degrees C and degraded locust bean gum, guar gum, Pinus radiata glucomannan, and konjak glucomannan. The noncoding region downstream from the mannanase gene showed strong homology to celB, a gene coding for a cellulase from the same organism, suggesting that the manA gene might have been inserted into its present position on the "C. saccharolyticum" genome by homologous recombination.

Purification and properties of an aryl beta-xylosidase from a cellulolytic extreme thermophile expressed in Escherichia coli

An aryl beta-xylosidase was purified to homogeneity from an Escherichia coli strain containing a recombinant plasmid carrying a beta-xylosidase (EC 3.2.1.37) gene from the extremely thermophilic anaerobic bacterium isolate Tp8T6.3.3.1 ('Caldocellum saccharolyticum'). It has a pI of 4.3 and shows optimal activity at pH 5.7. The enzyme is highly specific, acting on o- and p-nitrophenyl beta-D-xylopyranosides and minimally on p-nitrophenyl alpha-L-arabinopyranoside. It does not act on xylobiose. The Km for p-nitrophenyl beta-D-xylopyranoside at the optimum pH for activity is 10 mM, and at pH 7.0 is 6.7 mM. Xylose is a competitive inhibitor with Ki 40 mM. Thermal inactivation follows first-order kinetics at 65 and 70 degrees C with t1/2 values of 4.85 h and 40 min respectively. The t1/2 at 70 degrees C is increased 3-fold and 4-fold by the addition of 0.5 mg of BSA/ml and 2 mM-dithiothreitol respectively.

Xylanase from the extremely thermophilic bacterium "Caldocellum saccharolyticum": overexpression of the gene in Escherichia coli and characterization of the gene product

A xylanase encoded by the xynA gene of the extreme thermophile "Caldocellum saccharolyticum" was overexpressed in Escherichia coli by cloning the gene downstream from the temperature-inducible lambda pR and pL promoters of the expression vector pJLA602. Induction of up to 55 times was obtained by growing the cells at 42 degrees C, and the xylanase made up to 20% of the whole-cell protein content. The enzyme was located in the cytoplasmic fraction in E. coli. The temperature and pH optima were determined to be 70 degrees C and pH 5.5 to 6, respectively. The xylanase was stable for at least 72 h if incubated at 60 degrees C, with half-lives of 8 to 9 h at 70 degrees C and 2 to 3 min at 80 degrees C. The enzyme had high activity on xylan and ortho-nitrophenyl beta-D-xylopyranoside and some activity on carboxymethyl cellulose and para-nitrophenyl beta-D-cellobioside. The gene was probably expressed from its own promoter in E. coli. Translation of the xylanase overproduced in E. coli seemed to initiate at a GTG codon and not at an ATG codon as previously determined.

Cloning, sequence analysis, and expression of genes encoding xylan-degrading enzymes from the thermophile "Caldocellum saccharolyticum"

A lambda recombinant bacteriophage coding for xylanase and beta-xylosidase activity has been isolated from a genomic library of the extremely thermophilic anaerobe "Caldocellum saccharolyticum." Partial Sau3AI fragments of the lambda recombinant DNA were ligated into pBR322. A recombinant plasmid with an insertion of ca. 7 kilobases of thermophilic DNA expressing both enzymatic activities was isolated. The location of the genes has been established by analyzing deletion derivatives, and the DNA sequence of 6.067 kilobases of the insert has been determined. Five open reading frames (ORFs) were found, one of which (ORF1; Mr 40,455) appears to code for a xylanase (XynA) which also acts on o-nitrophenyl-beta-D-xylopyranoside. Another, ORF5 (Mr 56,365), codes for a beta-xylosidase (XynB). The xynA gene product shows significant homology with the xylanases from the alkalophilic Bacillus sp. strain C125 and Clostridium thermocellum.

Isolation of phenol-degrading Bacillus stearothermophilus and partial characterization of the phenol hydroxylase

Bacillus stearothermophilus BR219, isolated from river sediment, degraded phenol at levels to 15 mM at a rate of 0.85 mumol/h (4 x 10(6) cells). The solubilized phenol hydroxylase was NADH dependent, exhibited a 55 degrees C temperature optimum for activity, and was not inhibited by 0.5 mM phenol.

Sequence structure and expression of a cloned beta-glucosidase gene from an extreme thermophile

The gene for a beta-glucosidase from the extremely thermophilic bacterium Caldocellum saccharolyticum has been isolated from a genomic library and sequenced. An open reading frame identified by computer analysis of the sequence could encode a protein of Mr 54,400, which is close to the size of the polypeptide experimentally determined using maxicells. Analysis of the amino-terminal residues of the protein produced in Escherichia coli suggests that it is processed by a methionine aminopeptidase. A sequence within C. saccharolyticum DNA upstream of the beta-glucosidase gene was found to act as a promoter for expression of the thermophile gene in E. coli. The protein has been overproduced in E. coli and Bacillus subtilis where it retains its enzymatic activity and heat stability. There appears to be a single copy of the gene in Caldocellum DNA.