Extremophiles in a changing world

Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.

Emergency resection surgery for colorectal cancer: Patterns of recurrent disease and survival

AIM

To evaluate prognostic pathological factors associated with early metachronous disease and adverse long-term survival in these patients.

METHODS

Clinical and histological features were analysed retrospectively over an eight-year period for prognostic impact on recurrent disease and overall survival in patients undergoing curative resection of a primary colorectal cancer.

RESULTS

A total of 266 patients underwent curative surgery during the study period. The median age of the study cohort was 68 year (range 26 to 91) with a follow-up of 7.9 years (range 4.6 to 12.6). Resection was undertaken electively in 225 (84.6%) patients and emergency resection in 35 (13.2%). Data on timing of surgery was missing in 6 patients. Recurrence was noted in 67 (25.2%) during the study period and was predominantly early within 3 years (82.1%) and involved hepatic metastasis in 73.1%. Emergency resection (OR = 3.60, P = 0.001), T4 stage (OR = 4.33, P < 0.001) and lymphovascular invasion (LVI) (OR = 2.37, P = 0.032) were associated with higher risk of recurrent disease. Emergency resection, T4 disease and a high lymph node ratio (LNR) were strong independent predictors of adverse long-term survival.

CONCLUSION

Emergency surgery is associated with adverse disease free and long-term survival. T4 disease, LVI and LNR provide strong independent predictive value of long-term outcome and can inform surveillance strategies to improve outcomes.

X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis

BACKGROUND

Pyrrolidone carboxyl peptidases (pcps) are a group of exopeptidases responsible for the hydrolysis of N-terminal pyroglutamate residues from peptides and proteins. The bacterial and archaeal pcps are members of a conserved family of cysteine proteases. The pcp from the hyperthermophilic archaeon Thermococcus litoralis is more thermostable than the bacterial enzymes with which it has up to 40% sequence identity. The pcp activity in archaea and eubacteria is proposed to be involved in detoxification processes and in nutrient metabolism; eukaryotic counterparts of the enzyme are involved in the processing of biologically active peptides.

RESULTS

The crystal structure of pcp has been determined by multiple isomorphous replacement techniques at 1.73 A resolution and refined to an R factor of 18.7% (Rfree = 21.4%). The enzyme is a homotetramer of single open alpha/beta domain subunits, with a prominent hydrophobic core formed from loops coming together from each monomer. The active-site residues have been identified as a Cys143-His167-Glu80 catalytic triad. Structural homology to enzymes of different specificity and mechanism has been identified.

CONCLUSIONS

The Thermococcus pcp has no sequence or structural homology with other members of the cysteine protease family. It does, however, show considerable similarities to other hydrolytic enzymes of widely varying substrate specificity and mechanism, suggesting that they are the products of divergent evolution from a common ancestor. The enhanced thermostability of the T. litoralis pcp may arise from hydrophobic interactions between the subunits and the presence of intersubunit disulphide bridges.

Haloperoxidases and their role in biotransformation reactions

The past year has seen further structural characterisation of both nonmetal and vanadium haloperoxidase enzymes to add to that already known for the haem- and vanadium-containing enzymes. Exploitation of these enzymes for halogenation, sulfoxidation, epoxidation, oxidation of indoles and other biotransformations has increased as more information on their catalytic mechanism has been obtained.

Sequence and structural comparison of thermophilic phosphoglycerate kinases with a mesophilic equivalent

The monomeric glycolytic enzyme phosphoglycerate kinase (PGK) has been used as a model system to study protein thermostability. The primary sequence of this enzyme has been elucidated from 47 species to date. Although only 42 amino acids are totally conserved, most of which line the active site cleft, the protein is structurally conserved. This is achieved by making conservative changes to maintain the same secondary and tertiary folds. The crystal structures of 5 PGK enzymes have been solved by X-ray diffraction methods. This paper seeks to use the available information to understand protein thermostability. Although some general mechanisms to increase stability can be determined, different species have adopted a variety of subtle additive changes to achieve greater protein stability. Comparisons have been directly made between the PGK enzyme from yeast, the moderate thermophilic bacterium Bacillus stearothermophilus, the hyperthermophilic bacteria Thermus thermophilus, Thermotoga maritima, and the hyperthermophilic archaea Sulpholobus solfataricus and Methanothermus fervidus.

Crystallization and preliminary X-ray studies on Candida cylindracea lipase

As part of the programme to understand the mechanism and specificity of lipase enzymes used in biotransformation reactions, the lipase from Candida cylindracea has been purified and crystallized. This lipase has been widely used by organic chemists for hydrolysis and esterification reactions. Crystals were obtained using polyethylene glycol 6000 as a precipitant and grew to 0.6 mm in the maximum dimension. The enzyme crystallized in the space group P2(1) with unit-cell dimensions a = 94.3, b = 117.0, and c = 114.2 A with beta = 109.2 degrees. Calculations indicate that there are four molecules in the asymmetric unit. The crystals diffract to at least 2.5 A resolution and the structure has been solved by molecular replacement using the lipase from Geotrichum candidum as a search model.

Crystallization and preliminary X-ray crystallographic data withEscherichia colitransketolase

The Escherichia coli enzyme transketolase, a dimeric protein of 2 x 70 kDa (662 amino acids) has been prepared from an overexpression system in E. coli. The purified enzyme has been crystallized from PIPES buffer pH 6.4 and ammonium sulfate. The crystals which grow as large plates diffract to greater than 1.9 A, resolution and are of the space group P2(1)2(1)2(1) with unit-cell dimensions of a = 74.6, b = 125.6 and c = 151.0 A, (Z = 8 with one transketolase dimer in the asymmetric unit). The structure has been solved by molecular replacement using the yeast transketolase enzyme structure as a search model. The enzyme is being used for large-scale biotransformations using various aldehydes and hydroxypyruvate as substrates.

Purification, crystallisation and preliminary X-ray analysis of the vanadium-dependent haloperoxidase from Corallina officinalis

The vanadium-dependent haloperoxidase from the seaweed Corallina officinalis has been purified to homogeneity and crystallised. The protein is reported to be a hexamer of 12 x 64,000 Da, contains no haem, and is dependent on vanadium for activity. The crystals are grown from polyethylene glycol (PEG) 6,000 and 0.4 M potassium chloride. They are stable and diffract to better than 2 A resolution. They are of a cubic space group I23 (or 12(1)3) with cell dimensions a = b = c = 310 A.

The tertiary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by proton magnetic resonance spectroscopy and limited proteolysis experiments

Ribosomal proteins from Escherichia coli have been isolated by a mild purification procedure. Their tertiary structure has been explored by two techniques, proton magnetic resonance and limited proteolysis. A number of proteins when subjected to limited proteolysis produce resistant fragments in good yields. In most cases this does not depend on the specificity of the enzyme used. The proteins S15, S16, S17 and L30 are not degraded at all, whereas a few proteins are very susceptible to proteolysis. 1H-NMR experiments show that the majority of the ribosomal proteins have a uniquely folded tertiary structure. This is particularly pronounced in the four proteins mentioned above which resist proteolysis. In general, a good agreement is observed between the degree of proteolytic resistance and the amount of folding indicated by NMR spectroscopy. Similar studies on a few ribosomal proteins purified under denaturing conditions show that, in contrast, these protein preparations are not structurally homogeneous and that they contain a mixture of denatured and renatured molecules. The results are interpreted in terms of a compactly folded tertiary structure for the four proteinase-resistant proteins while the majority of the other proteins appear to have two domains, one compactly folded and resistant to proteinase and the other flexible and susceptible to proteolysis. A few proteins seem to have a completely flexible structure and can therefore be easily degraded.

Location of protein S4 on the small ribosomal subunit of E. coli and B. stearothermophilus with protein- and hapten-specific antibodies

In spite of considerable effort there is still serious disagreement in the literature about the question of whether epitopes of ribosomal protein S4 are accessible for antibody binding on the intact small ribosomal subunit. We have attempted to resolve this issue using three independent approaches: (i) a re-investigation of the exposure and the location of epitopes of ribosomal protein S4 on the surface of the 30S subunit and 30S core particles of the E. coli ribosome, including rigorous controls of antibody specificity, (ii) a similar investigation of protein S4 from Bacillus stearothermophilus and (iii) the labelling of residue Cys-31 of E. coli S4 with a fluorescein derivative the accessibility of which towards a fluorescein-specific antibody was demonstrated directly by fluorimetry. In each of the three cases the antigen (E. coli S4, B. stearothermophilus S4 or fluorescein) was found to reside on the small lobe.

Structural and functional studies on protein S20 from the 30-S subunit of the Escherichia coli ribosome

Fragments resistant to proteolysis have been obtained from the ribosomal protein S20. They provide evidence for a structural domain stretching from the middle of the protein to its C terminus. With the exception of a large fragment of this protein lacking only 14 residues at the N terminus, all fragments had lost their ability to bind to 16-S rRNA. The protein in the S20 . 16-S-RNA complex was highly protected against enzymic digestion, indicating that the entire protein is involved in interaction with the nucleic acid. Circular dichroism showed a high alpha helix content (36%) for the intact protein and a low alpha helix content (2%) for the large fragment. Intrinsic fluorescence studies demonstrated that the single tyrosine residue in protein S20 is exposed to the solvent in the intact protein and is not exposed in the S20 . 16-S-RNA complex. Irreversible thermal denaturation of the protein was followed by fluorescence of the tyrosine and was found between 50 degrees C and 70 degrees C.

Distance measurement by energy transfer: the 3' end of 16-S RNA and proteins S4 and S17 of the ribosome of Escherichia coli

Escherichia coli ribosomal proteins S4 and S17 were specifically labelled at their thiol groups with the acetylaminoethyl-dansyl and/or bimane fluorophores. Each formed a complex with 16-S RNA and, when the other 30-S ribosomal proteins were added, a complete 30-S subunit with at least partial activity. If the 3' end of the RNA was also labelled (with fluorescein) then the distance between the two fluorophores could be measured by Förster-type energy transfer. The result for S4 was 6.0 nm (60 A) in the ribonucleoprotein complex and 5.6 nm (56 A) in the 30-S subunit, and for S17 6.3 nm (63 A) in the complex and 6.2 nm (62 A) in the subunit. There is no evidence for a major change in the relative disposition of the 3' and 5' ends of the 16-S RNA during formation of the 30-S subunit. Sources of error are discussed, including the question of multiple labelling. In order to measure more accurately the extent of energy transfer a procedure based upon enzymic digestion was developed and is detailed in this paper.

Structural domains of ribosomal protein S8 and their relationship to ribosomal RNA binding

Escherichia coli ribosomal protein S8 has been subjected to mild proteolytic digestion in order to search for structural domains within the protein [1]. A characteristic fragment produced in high yield after chymotrypsin treatment has been located with the protein sequence. Circular dichroism has shown this domain to be rich in alpha helix. However, the fragment loses its ability to bind to 16S rRNA as does a similar fragment produced by trypsin cleavage. The intact protein is required for rRNA binding and is highly protected against proteolytic digestion when bound to the RNA.

Ribosomal protein S20 purified under mild conditions almost completely inhibits its own translation

The efficiency of ribosomal protein S20 to act as repressor of its own synthesis in an in vitro system was found to depend greatly on the procedures employed to purify this protein. Whilst conventionally purified r-protein S20 inhibited its own synthesis by some 30%, up to 90% inhibition was observed if "milder" purification conditions were used. Evidence is presented that the latter preparation shows also a higher binding affinity to 16S rRNA.

Small-angle X-ray titration of the complex formed between the ribosomal protein S4 and its 16S binding site, S4-RNA: a central core in the 30S subunit

X-ray scattering titrations at 21 degree C and in ribosomal reconstitution buffer indicate that the S4-RNA and the protein S4 from a 1:1 complex with a stability constant, log K approximately 6.5. When the complex forms, there is only a limited change in the scattering curve indicating that S4-RNA essentially retains its conformation during the complex formation. The increase in the gyration radius as a result of the complex formation, delta R = 4 +/- 3 A, as well as the experimental scattering curve of the complex can be explained by models where the protein S4 is supposed to interact with the periphery of the S4-RNA.