Novel hopanoids from Frankia spp. and related soil bacteria. Squalene cyclization and significance of geological biomarkers revisited

Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents

Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.

Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15)

BACKGROUND

Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in commercial inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biological nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer.

RESULTS

A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the analysis of orthologues helped to predict roles in BNF.

CONCLUSIONS

All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.

Pitfalls of Using Biomarker Maturity Parameters for Organic Matter Maturity Assessment Suggested by Coal Hydrous Pyrolysis

Crude oil maturity assessment is a vital goal for petroleum geochemistry, and equally important is the exploration of maturity indicators of sufficient credibility. While most molecular proxy parameters have been extensively used and have provided some useful insights; the component ratios approach is somewhat limited in validity regarding oil maturity characterization for variable reasons. Novel thermal trends of hopanes and steranes were observed in a series of hydrous pyrolysates of an immature coal (0.49 %Ro) generated at eight target temperatures ranging from 250–375 °C (measured vitrinite reflectance of 0.71–0.91 %Rm), which–further substantiated this idea. Expelled oil and extractable bitumen were combined as the total soluble organic material (tSOM) for each pyrolysis experiment to mitigate the effects of primary expulsion fractionation. While bitumen extracted from the original coal—the 250 °C tSOM—the 275 °C tSOM (0.49–0.73 %Rm) sequence recorded normal increases in C31 αβ-hopane 22S/(22S + 22R) and decreases in C29–C30 βα-moretane/αβ-hopane ratios, low values and continuous decreases in C29 5α-sterane 20S/(20S + 20R) and ββ/(αα + ββ), Ts/(Ts + Tm) and C29Ts/(C29Ts + C29 αβ-hopane) suggested no biomarker thermal isomerization but predominant control from precursor-to-biomarker transformation. Continuous increases in 22S/(22S + 22R) until 1.43 %Rm accorded with thermal isomerization, but a delayed ratio equilibration at 1.43 %Rm again suggested biomarker precursor interference, which also played a role in the reductions in 20S/(20S + 20R) and ββ/(αα + ββ) to 0.9 %Rm, whereas increasing and high values of C29–C30 βα-moretane/αβ-hopane ratios occurring during 0.73–1.43 %Rm. Reversals in 22S/(22S + 22R) and fluctuations in 20S/(20S + 20R) and ββ/(αα + ββ) at elevated maturity levels with minimum yields of biomarker precursors were predominantly controlled by differential isomer degradative rates. These rarely reported thermal distribution patterns of biomarkers illustrated very complicated biomarker generation–destruction processes during maturation and suggested that the release of bond biomarker to the free status may govern the biomarker maturity ratios rather than thermal isomerization. While the rapid heating conditions and high temperatures in pyrolysis differ inevitably from natural evolution under geological conditions, our study unveiled that unusual biomarker ratios in geological samples could be the norm, contradictory to common beliefs. Accordingly, we propose that isomer concentration is an essential tool to validate maturity estimation of organic matter by isomer ratios, especially for highly mature oils and sediment extracts.

Salt Stress Tolerance-Promoting Proteins and Metabolites under Plant-Bacteria-Salt Stress Tripartite Interactions

The rapid increase in soil salinization has impacted agricultural output and poses a threat to food security. There is an urgent need to focus on improving soil fertility and agricultural yield, both of which are severely influenced by abiotic variables such as soil salinity and sodicity. Abiotic forces have rendered one-third of the overall land unproductive. Microbes are the primary answer to the majority of agricultural production’s above- and below-ground problems. In stressful conditions, proper communication between plants and beneficial microbes is critical for avoiding plant cell damage. Many chemical substances such as proteins and metabolites synthesized by bacteria and plants mediate communication and stress reduction. Metabolites such as amino acids, fatty acids, carbohydrates, vitamins, and lipids as well as proteins such as aquaporins and antioxidant enzymes play important roles in plant stress tolerance. Plant beneficial bacteria have an important role in stress reduction through protein and metabolite synthesis under salt stress. Proper genomic, proteomic and metabolomics characterization of proteins and metabolites’ roles in salt stress mitigation aids scientists in discovering a profitable avenue for increasing crop output. This review critically examines recent findings on proteins and metabolites produced during plant-bacteria interaction essential for the development of plant salt stress tolerance.

Origin and Geochemical Implications of Hopanoids in Saline Lacustrine Crude Oils from Huanghekou East Sag and Laizhouwan Northeastern Sag, Bohai Bay Basin

A suite of low-mature crude oils (five high-sulfur oils and six low-sulfur oils) from the Huanghekou and the Laizhouwan Sags, Bohai Bay Basin, are analyzed to investigate the fate of the hopanoids. Abundant hopanes, such as secohopanes, 25-norhopanes, benzohopanes, aromatized secohopanes, and sulfide hopanes, are identified, and their carbon isotope compositions are determined. Varying ¹³C isotope values of C₃₁ hopane (-38.7-34.0‰) and C_29-30 hopanes (-38.5-31.5‰) suggest different bacterial sources of these compounds. The presence of 25-norhopanes with enriched heavy carbon isotopes in severely biodegraded oils suggests that they are microbially mediated products. The detection of the isotopically depleted C₂₉ and C₃₀ D-ring-8,14-secohopanes (-45.6-41.2‰) indicates that secohopanes are from methane-oxidizing bacteria (methanotrophs). The presence of isorenieratane, lower aryl isoprenoid ratios, and a good correlation between the sulfur content and the gammacerane index indicate the presence of green sulfur bacteria (Chlorobiaceae) under photic zone euxinic conditions. Water column stratification results in good preservation of the organic matter, and it is in favor of diversity of aquatic microorganisms. The ratios of C₃₅/C₃₄ sulfide hopane, C₃₅ sulfide hopane-2/C₃₅ sulfide hopane-1, and C₃₅/C₃₄ benzohopane are influenced by the reducing environments in this region. In addition, the D-ring monoaromatized 8,14-secohopanoid/(D-ring monoaromatized 8,14-secohopanoid + benzohopanes) and C₃₁-C₃₅ secomoretanes/secohopanes are affected by the maturity. We hypothesize that the reducing environments and thermal effects are important markers for the hopanoid transformation, including the incorporation of inorganic sulfur in substituting functional groups, cyclizing, aromatizing, and opening ring C of the hopanoids.

Bacterial terpenome

Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.

Environmental controls on bacteriohopanepolyol profiles of benthic microbial mats from Lake Fryxell, Antarctica

Bacteriohopanepolyols (BHPs) are pentacyclic triterpenoid lipids that contribute to the structural integrity and physiology of some bacteria. Because some BHPs originate from specific classes of bacteria, BHPs have potential as taxonomically and environmentally diagnostic biomarkers. For example, a stereoisomer of bacteriohopanetetrol (informally BHT II) has been associated with anaerobic ammonium oxidation (anammox) bacteria and suboxic to anoxic marine environments where anammox is active. As a result, the detection of BHT II in the sedimentary record and fluctuations in the relative abundance of BHT II may inform reconstructions of nitrogen cycling and ocean redox changes through the geological record. However, there are uncertainties concerning the sources of BHT II and whether or not BHT II is produced in abundance in non-marine environments, both of which are pertinent to interpretations of BHT II signatures in sediments. To address these questions, we investigate the BHP composition of benthic microbial mats from Lake Fryxell, Antarctica. Lake Fryxell is a perennially ice-covered lake with a sharp oxycline in a density-stabilized water column. We describe the diversity and abundance of BHPs in benthic microbial mats across a transect from oxic to anoxic conditions. Generally, BHP abundances and diversity vary with the morphologies of microbial mats, which were previously shown to reflect local environmental conditions, such as irradiance and oxygen and sulfide concentrations. BHT II was identified in mats that exist within oxic to anoxic portions of the lake. However, anammox bacteria have yet to be identified in Lake Fryxell. We examine our results in the context of BHPs as biomarkers in modern and ancient environments.

Hopanoid lipids: from membranes to plant-bacteria interactions

Lipid research represents a frontier for microbiology, as showcased by hopanoid lipids. Hopanoids, which resemble sterols and are found in the membranes of diverse bacteria, have left an extensive molecular fossil record. They were first discovered by petroleum geologists. Today, hopanoid-producing bacteria remain abundant in various ecosystems, such as the rhizosphere. Recently, great progress has been made in our understanding of hopanoid biosynthesis, facilitated in part by technical advances in lipid identification and quantification. A variety of genetically tractable, hopanoid-producing bacteria have been cultured, and tools to manipulate hopanoid biosynthesis and detect hopanoids are improving. However, we still have much to learn regarding how hopanoid production is regulated, how hopanoids act biophysically and biochemically, and how their production affects bacterial interactions with other organisms, such as plants. The study of hopanoids thus offers rich opportunities for discovery.

Temperature and pH control on lipid composition of silica sinters from diverse hot springs in the Taupo Volcanic Zone, New Zealand

Microbial adaptations to environmental extremes, including high temperature and low pH conditions typical of geothermal settings, are of interest in astrobiology and origin of life investigations. The lipid biomarkers preserved in silica deposits associated with six geothermal areas in the Taupo Volcanic Zone were investigated and variations in lipid composition as a function of temperature and pH were assessed. Lipid analyses reveal highly variable abundances and distributions, reflecting community composition as well as adaptations to extremes of pH and temperature. Biomarker profiles reveal three distinct microbial assemblages across the sites: the first in Champagne Pool and Loop Road, the second in Orakei Korako, Opaheke and Ngatamariki, and the third in Rotokawa. Similar lipid distributions are observed in sinters from physicochemically similar springs. Furthermore, correlation between lipid distributions and geothermal conditions is observed. The ratio of archaeol to bacterial diether abundance, bacterial diether average chain length, degree of GDGT cyclisation and C₃₁ and C₃₂ hopanoic acid indices typically increase with temperature. At lower pH, the ratio of archaeol to bacterial diethers, degree of GDGT cyclisation and C₃₁ and C₃₂ hopanoic acid indices are typically higher. No trends in fatty acid distributions with temperature or pH are evident, likely reflecting overprinting due to population influences.

Significant natural product biosynthetic potential of actinorhizal symbionts of the genus frankia, as revealed by comparative genomic and proteomic analyses

Bacteria of the genus Frankia are mycelium-forming actinomycetes that are found as nitrogen-fixing facultative symbionts of actinorhizal plants. Although soil-dwelling actinomycetes are well-known producers of bioactive compounds, the genus Frankia has largely gone uninvestigated for this potential. Bioinformatic analysis of the genome sequences of Frankia strains ACN14a, CcI3, and EAN1pec revealed an unexpected number of secondary metabolic biosynthesis gene clusters. Our analysis led to the identification of at least 65 biosynthetic gene clusters, the vast majority of which appear to be unique and for which products have not been observed or characterized. More than 25 secondary metabolite structures or structure fragments were predicted, and these are expected to include cyclic peptides, siderophores, pigments, signaling molecules, and specialized lipids. Outside the hopanoid gene locus, no cluster could be convincingly demonstrated to be responsible for the few secondary metabolites previously isolated from other Frankia strains. Few clusters were shared among the three species, demonstrating species-specific biosynthetic diversity. Proteomic analysis of Frankia sp. strains CcI3 and EAN1pec showed that significant and diverse secondary metabolic activity was expressed in laboratory cultures. In addition, several prominent signals in the mass range of peptide natural products were observed in Frankia sp. CcI3 by intact-cell matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). This work supports the value of bioinformatic investigation in natural products biosynthesis using genomic information and presents a clear roadmap for natural products discovery in the Frankia genus.

A hypersaline microbial mat from the Pacific Atoll Kiritimati: insights into composition and carbon fixation using biomarker analyses and a 13C-labeling approach

Modern microbial mats are widely recognized as useful analogs for the study of biogeochemical processes relevant to paleoenvironmental reconstruction in the Precambrian. We combined microscopic observations and investigations of biomarker composition to investigate community structure and function in the upper layers of a thick phototrophic microbial mat system from a hypersaline lake on Kiritimati (Christmas Island) in the Northern Line Islands, Republic of Kiribati. In particular, an exploratory incubation experiment with (13)C-labeled bicarbonate was conducted to pinpoint biomarkers from organisms actively fixing carbon. A high relative abundance of the cyanobacterial taxa Aphanocapsa and Aphanothece was revealed by microscopic observation, and cyanobacterial fatty acids and hydrocarbons showed (13)C-uptake in the labeling experiment. Microscopic observations also revealed purple sulfur bacteria (PSB) in the deeper layers. A cyclic C(19:0) fatty acid and farnesol were attributed to this group that was also actively fixing carbon. Background isotopic values indicate Calvin-Benson cycle-based autotrophy for cycC(19:0) and farnesol-producing PSBs. Biomarkers from sulfate-reducing bacteria (SRB) in the top layer of the mat and their (13)C-uptake patterns indicated a close coupling between SRBs and cyanobacteria. Archaeol, possibly from methanogens, was detected in all layers and was especially abundant near the surface where it contained substantial amounts of (13)C-label. Intact glycosidic tetraether lipids detected in the deepest layer indicated other archaea. Large amounts of ornithine and betaine bearing intact polar lipids could be an indicator of a phosphate-limited ecosystem, where organisms that are able to substitute these for phospholipids may have a competitive advantage.

Biosynthesis of hopanoids by sulfate-reducing bacteria (genus Desulfovibrio)

Sulfate reduction accounts for about a half of the remineralization of organic carbon in anoxic marine shelf regions. Moreover, it was already a major microbial process in the very early ocean at least 2.4 billion years before the present. Here we demonstrate for the first time the capability of sulfate-reducing bacteria (SRB) to biosynthesize hopanoids, compounds that are quantitatively important and widely distributed biomarkers in recent and fossil sediments dating back to the late Archean. We found high concentrations (9.8-12.3 mg per gram of dry cells) of non-extended and extended bacteriohopanoids (bacteriohopanetetrol, aminobacteriohopanetriol, aminobacteriohopanetetrol) in pure cultures of SRB belonging to the widely distributed genus Desulfovibrio. Biohopanoids were found--considered as membrane rigidifiers--in more than 50% of bacterial species analysed so far. However, their biosynthesis appeared to be restricted to aerobes or facultative anaerobes with a very few recently described exceptions. Consequently, findings of sedimentary hopanoids are often used as indication for oxygenated settings. Nevertheless, our findings shed new light on the presence of hopanoids in specific anoxic settings and suggests that SRB are substantial sources of this quantitatively important lipid class in recent but also past anoxic environments.

Structure and reactivity of the dammarenyl cation: configurational transmission in triterpene synthesis

[reaction: see text] The dammarenyl cation (13) is the last common intermediate in the cyclization of oxidosqualene to a diverse array of secondary triterpene metabolites in plants. We studied the structure and reactivity of 13 to understand the factors governing the regio- and stereospecificity of triterpene synthesis. First, we demonstrated that 13 has a 17beta side chain in Arabidopsis thaliana lupeol synthase (LUP1) by incubating the substrate analogue (18E)-22,23-dihydro-20-oxaoxidosqualene (21) with LUP1 from a recombinant yeast strain devoid of other cyclases and showing that the sole product of 21 was 3beta-hydroxy-22,23,24,25,26,27-hexanor-17beta-dammaran-20-one. Quantum mechanical calculations were carried out on gas-phase models to show that the 20-oxa substitution has negligible effect on substrate binding and on the activation energies of reactions leading to either C17 epimer of 13. Further molecular modeling indicated that, because of limited rotational freedom in the cyclase active site cavity, the C17 configuration of the tetracyclic intermediate 13 can be deduced from the angular methyl configuration of the pentacyclic or 6-6-6-6 tetracyclic product. This rule of configurational transmission aided in elucidating the mechanistic pathway accessed by individual cyclases. Grouping of cyclases according to mechanistic and taxonomic criteria suggested that the transition between pathways involving 17alpha and 17beta intermediates occurred rarely in evolutionary history. Two other mechanistic changes were also rare, whereas variations on cation rearrangements evolved readily. This perspective furnished insights into the phylogenetic relationships of triterpene synthases.