Predation between prokaryotes and the origin of eukaryotes

Accumulating data suggest that the eukaryotic cell originated from a merger of two prokaryotes, an archaeal host and a bacterial endosymbiont. However, since prokaryotes are unable to perform phagocytosis, the means by which the endosymbiont entered its host is an enigma. We suggest that a predatory or parasitic interaction between prokaryotes provides a reasonable explanation for this conundrum. According to the model presented here, the host in this interaction was an anaerobic archaeon with a periplasm‐like space. The predator was a small (facultative) aerobic α‐proteobacterium, which penetrated and replicated within the host periplasm, and later became the mitochondria. Plausible conditions under which this interaction took place and circumstances that may have led to the contemporary complex eukaryotic cell are discussed.     

Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes

The evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes is examined based on protein sequence data. Phylogenies and common signature sequences in some of the most conserved proteins point to a close evolutionary relationship between Archaebacteria and Gram-positive bacteria. The monophyletic nature and distinctness of the Archaebacterial domain is not supported by many of the phylogenies. Within Gram-negative bacteria, cyanobacteria are indicated as the deepest branching lineage, and a clade consisting of Archaebacteria, Gram-positive bacteria and cyanobacteria is supported by signature sequences in many proteins. However, the division within the prokaryotic species viz. Archaebacteria Gram-positive bacteria Cyanobacteria other groups of Gram-negative bacteria, is indicated to be not very rigid but, instead is an evolutionary continuum. It is expected that certain species will be found which represent intermediates in the above transitions. By contrast to the evolutionary relationships within prokaryotes, the eukaryotic species, which are structurally very different, appear to have originated by a very different mechanism. Protein phylogenies and signature sequences provide evidence that the eukaryotic nuclear genome is a chimera which has received major contributions from both an Archaebacterium and a Gram-negative bacterium. To explain these observations, it is suggested that the ancestral eukaryotic cell arose by a symbiotic fusion event between the above parents and that this fusion event led to the origin of both nucleus and endoplasmic reticulum. The monophyletic nature of all extant eukaryotic species further suggests that a 'successful primary fusion' between the prokaryotic species that gave rise to the ancestral eukaryotic cell took place only once in the history of this planet.     

Psychrotolerant <Emphasis Type="Italic">Sphingobacterium kitahiroshimense</Emphasis> LT-2 Isolated from Dhundi Glacier,Himachal Pradesh: Origin Prediction and Future Application

A psychrotolerant bacterium, isolated from Dhundi Glacier, Himachal Pradesh (India) was identified as Sphingobacterium kitahiroshimense LT-2 on the basis of biochemical, molecular and phylogenetic analysis. Sphingobacterium kitahiroshimense was first reported from Japan and was isolated from the city of Kitahiroshima, Hokkaido, Japan. In this report we have discussed about the origin of our strain and predicted that air masses and dust associated microbial cells transportation phenomena may be applicable for the origin of this species in this region. Enzymes and secondary metabolites secreted by the genus Sphingobacterium have enormous potentiality regarding their biotechnological application. Preliminary study of our strain based on metabolic profiling through HPLC showed many new metabolites were secreted by the bacterium when grown in presence of different sugar medium at 28 °C. As far as our knowledge this is the first report about Sphingobacterium species isolated from this region. This preliminary finding will help to draw an idea about the bacterial population in this Himalayan Glaciers (in HP) as well as biotechnological application of this strain can be explored further.     

The Eukaryotic Ribosome: Current Status and Challenges

Despite having been identified first, their greater degree of complexity has resulted in our understanding of eukaryotic ribosomes lagging behind that of their bacterial and archaeal counterparts. A much more complicated biogenesis program results in ribosomes that are structurally, biochemically, and functionally more complex. However, recent advances in molecular genetics and structural biology are helping to reveal the intricacies of the eukaryotic ribosome and to address many longstanding questions regarding its many roles in the regulation of gene expression.Since its initial discovery using differential ultracentrifugation of rat liver homogenates (reviewed in Ref. 1), the ribosome has remained a foundational platform upon which our understanding of the relationship between structure and function at the molecular level has been built. There is a rich history of biochemistry and genetics of eukaryotic ribosomes, including the discovery in the 1950s that they 32 are the site of protein synthesis, the elucidation of the function of the nucleolus, and even the discovery of the first eukaryotic RNA polymerase (reviewed in Ref. 2). Whereas early studies using mammalian ribosomes defined the “integral requirements” for protein synthesis, a switch to bacterial ribosomes in the 1960s facilitated the identification of the “minimal requirements” for the translational machinery, giving rise to a “golden age” of translation. In particular, the greater degree of structural and functional complexity makes eukaryotic ribosomes more challenging to work with than their bacterial and archaeal counterparts. For example, whereas bacterial translation initiation requires only a small set of trans-acting factors and is facilitated by the Shine-Dalgarno sequence, this process in eukaryotes requires a multifactorial complex of trans-acting factors that is almost as massive as the ribosome itself (reviewed in Ref. 3). Here, some of the current topics and challenges in the study of the eukaryotic ribosome are reviewed.     

Considerations on bacterial nucleoids

The classic genome organization of the bacterial chromosome is normally envisaged with all its genetic markers linked, thus forming a closed genetic circle of duplex stranded DNA (dsDNA) and several proteins in what it is called as “the bacterial nucleoid.” This structure may be more or less corrugated depending on the physiological state of the bacterium (i.e., resting state or active growth) and is not surrounded by a double membrane as in eukayotic cells. The universality of the closed circle model in bacteria is however slowly changing, as new data emerge in different bacterial groups such as in Planctomycetes and related microorganisms, species of Borrelia, Streptomyces, Agrobacterium, or Phytoplasma. In these and possibly other microorganisms, the existence of complex formations of intracellular membranes or linear chromosomes is typical; all of these situations contributing to weakening the current cellular organization paradigm, i.e., prokaryotic vs eukaryotic cells.     

Aerobic Mineralization of Hexachlorobenzene by Newly Isolated Pentachloronitrobenzene-Degrading Nocardioides sp. Strain PD653

A novel aerobic pentachloronitrobenzene-degrading bacterium, Nocardioides sp. strain PD653, was isolated from an enrichment culture in a soil-charcoal perfusion system. The bacterium also degraded hexachlorobenzene, a highly recalcitrant environmental pollutant, accompanying the generation of chloride ions. Liberation of ¹⁴CO₂ from [U-ring-¹⁴C]hexachlorobenzene was detected in a culture of the bacterium and indicates that strain PD653 is able to mineralize hexachlorobenzene under aerobic conditions. The metabolic pathway of hexachlorobenzene is initiated by oxidative dechlorination to produce pentachlorophenol. As further intermediate metabolites, tetrachlorohydroquinone and 2,6-dichlorohydroquinone have been detected. Strain PD653 is the first naturally occurring aerobic bacteria capable of mineralizing hexachlorobenzene.Hexachlorobenzene (C₆Cl₆; HCB) is one of the most persistent environmental pollutants. Its average half-life in soil is approximately 9 years (2). When HCB is liberated in environment, it is bioaccumulated in plants, zooplankton, and shellfish. Finally, HCB is accumulated in the human body via the food chain, whereupon its possible toxicity adversely affects human health as a result of long-term exposure and accumulation. Therefore, HCB was listed as one of the 12 persistent organic pollutants in the Stockholm Convention.A number of studies have been attempted to develop cleanup technology for environmental pollutants. Microbial degradation is a promising effective way to remediate environmental pollutants, including persistent organic pollutants. However, heavily chlorinated benzenes, especially HCB, are resistant to microbial degradation. Several studies have been reported on the reductive dechlorination of HCB. Reductive dechlorination of HCB to pentachlorobenzene by cytochrome P-450 was found in rat hepatic microsomes (22). Microbial transformation of HCB to trichlorobenzene and dichlorobenzene by reductive dechlorination was observed in anaerobic sewage sludge and a mixed culture (5, 7). Yeh and Pavlostathis maintained such an HCB-dechlorinating mixed culture for more than 1 year by adding surfactants as carbon sources (30). One of the microorganisms that reductively dechlorinates HCB is “Dehalococcoides” sp. strain CBDB1 (12). Dehalococcoides sp. strain CBDB1 dechlorinated HCB and pentachlorobenzene via dehalorespiration and gave a final end product mixture comprised of 1,3,5-trichlorobenzene, 1,3-dichlorobenzene, and 1,4-dichlorobenzene. These reductive dechlorinating processes take a longer time and leave less-chlorinated compounds such as trichlorobenzene and dichlorobenzene as end products.Strictly aerobic, naturally occurring microorganisms that degrade and completely mineralize HCB have not been found. On the other hand, a microorganism capable of mineralizing pentachlorophenol (PCP), Sphingobium chlorophenolicum strain ATCC 39723, was isolated, and its gene organization involved in PCP metabolism was shown (4). Conversion of HCB to PCP was reported by using the genetically engineered mutant of cytochrome P-450_cam (CYP101) (13). Wild-type CYP101 from Pseudomonas putida had low degrading activity for dichlorobenzene and trichlorobenzene but did not decompose more highly chlorinated benzenes. The F87W/Y96F/V247L mutant showed improved di- and trichlorobenzene-degrading activity, but activity toward highly chlorinated benzenes including HCB was still low. The activity upon highly chlorinated benzenes was further improved in the mutant CYP101, F87W/Y96F/L244A/V247L (6). The rate of HCB degradation was increased 200-fold in the mutant. Yan et al. introduced the mutant CYP101 gene into S. chlorophenolicum strain ATCC 39723 by homologous recombination, to produce a complete HCB degrader (28). This genetically engineered bacterium degraded HCB almost completely within 12 h, together with formation of PCP as an intermediate. However, the application of genetically engineered microorganisms in natural areas is strictly restricted in many countries. HCB-degrading aerobes derived from natural sources are still required for remediation of HCB-contaminated areas.We describe here isolation and identification of a novel aerobic soil bacterial species capable of aerobically mineralizing HCB. The characterization of metabolites caused by oxidative removal of the chlorine groups from HCB is also described.     

Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation

Background

The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins.

Methodology/Principal Findings

Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid β-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer.

Conclusions/Significance

Our results support a prokaryotic origin, different from α-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to enter eukaryotes.     

Crenarchaeal CdvA forms double-helical filaments containing DNA and interacts with ESCRT-III-like CdvB

Background

The phylum Crenarchaeota lacks the FtsZ cell division hallmark of bacteria and employs instead Cdv proteins. While CdvB and CdvC are homologues of the eukaryotic ESCRT-III and Vps4 proteins, implicated in membrane fission processes during multivesicular body biogenesis, cytokinesis and budding of some enveloped viruses, little is known about the structure and function of CdvA. Here, we report the biochemical and biophysical characterization of the three Cdv proteins from the hyperthermophilic archaeon Metallospherae sedula.

Methodology/Principal Findings

Using sucrose density gradient ultracentrifugation and negative staining electron microscopy, we evidenced for the first time that CdvA forms polymers in association with DNA, similar to known bacterial DNA partitioning proteins. We also observed that, in contrast to full-lengh CdvB that was purified as a monodisperse protein, the C-terminally deleted CdvB construct forms filamentous polymers, a phenomenon previously observed with eukaryotic ESCRT-III proteins. Based on size exclusion chromatography data combined with detection by multi-angle laser light scattering analysis, we demonstrated that CdvC assembles, in a nucleotide-independent way, as homopolymers resembling dodecamers and endowed with ATPase activity in vitro. The interactions between these putative cell division partners were further explored. Thus, besides confirming the previous observations that CdvB interacts with both CdvA and CdvC, our data demonstrate that CdvA/CdvB and CdvC/CdvB interactions are not mutually exclusive.

Conclusions/Significance

Our data reinforce the concept that Cdv proteins are closely related to the eukaryotic ESCRT-III counterparts and suggest that the organization of the ESCRT-III machinery at the Crenarchaeal cell division septum is organized by CdvA an ancient cytoskeleton protein that might help to coordinate genome segregation.     

Bacterial Responses to a Simulated Colon Tumor Microenvironment

One of the few bacteria that have been consistently linked to colorectal cancer (CRC) is the opportunistic pathogen Streptococcus gallolyticus. Infections with this bacterium are generally regarded as an indicator for colonic malignancy, while the carriage rate of this bacterium in the healthy large intestine is relatively low. We speculated that the physiological changes accompanying the development of CRC might favor the colonization of this bacterium. To investigate whether colon tumor cells can support the survival of S. gallolyticus, this bacterium was grown in spent medium of malignant colonocytes to simulate the altered metabolic conditions in the CRC microenvironment. These in vitro simulations indicated that S. gallolyticus had a significant growth advantage in these spent media, which was not observed for other intestinal bacteria. Under these conditions, bacterial responses were profiled by proteome analysis and metabolic shifts were analyzed by ¹H-NMR-spectroscopy. In silico pathway analysis of the differentially expressed proteins and metabolite analysis indicated that this advantage resulted from the increased utilization of glucose, glucose derivates, and alanine. Together, these data suggest that tumor cell metabolites facilitate the survival of S. gallolyticus, favoring its local outgrowth and providing a possible explanation for the specific association of S. gallolyticus with colonic malignancy.The human intestine is the habitat for several hundred different bacterial species with an increasing bacterial concentration and variability toward the distal colon (1). The resident gut microbiota is essential for human health by making dietary nutrients available to the host and preventing the invasion of pathogens by competitive colonization and nutrient competition (2, 3). Strikingly, the part of the intestine with the highest bacterial colonization, the colon, is also most affected by cancer, with 146,970 annual cases in the United States of America (4). In a healthy colonic environment, the host has several defense mechanisms to shield itself from bacterial infection, such as the viscous mucus layer overlaying the epithelium. However, the progression of CRC¹ is accompanied by changes in the integrity of the colon, including reduced mucus production (5) and increased epithelial permeability (6). These physiological changes can drive the intestinal ecosystem, which is relatively stable during adult life, into dysbiosis (7, 8). As a consequence, the host may become more susceptible to opportunistic bacterial infections (9–11).One of the few bacteria that have been consistently linked to CRC is the opportunistic pathogen Streptococcus gallolyticus (previously known as Streptococcus bovis biotype I). In CRC patients the fecal carriage rate of this bacterium is increased from 10% to about 50% (12), which suggests that this disease facilitates the colonic survival of S. gallolyticus. Importantly, ∼60% of patients that present with S. gallolyticus endocarditis have concomitant CRC (both adenomas and carcinomas) (13, 14), which largely exceeds the rates reported in the general population (∼25%) (15). These patients had no gastro-intestinal signs or clinical symptoms of malignancy and CRC was only detected because this bacterial infection guided the physician to perform a colonoscopy.Several mechanisms for this apparent association between S. gallolyticus and CRC can be envisaged. Recently, we postulated a model in which the collagen binding ability of S. gallolyticus contributes to the specific colonization of malignant colonic sites (16). However, the altered microenvironment of the tumor may also provide conditions that favor survival and outgrowth of S. gallolyticus in this newly formed intestinal niche. For example, Hirayama et al. have shown that glucose-1-phosphate and fructose-1-phophate levels as well as amino acid concentrations were significantly higher in tumor tissue than in normal tissue (17). To investigate if this altered nutritional status of the CRC microenvironment could facilitate the foraging of S. gallolyticus, we simulated the influence of colon tumor cell metabolites on S. gallolyticus growth by incubating this bacterium in spent medium of malignant cells. Subsequently, the bacterial responses were profiled by two-dimensional proteome analysis, and metabolic shifts in the culture medium were assessed by ¹H-NMR-spectroscopy. In silico pathway analysis and further in vitro simulations showed that, unlike other intestinal bacteria, S. gallolyticus had a growth advantage under these conditions, which could mainly be attributed to increased glycolysis. These results provide the first molecular support that tumor metabolites may facilitate the local outgrowth of tumor-foraging bacteria, such as S. gallolyticus.     

Metabolism of Pentose Sugars in the Hyperthermophilic Archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius

We have previously shown that the hyperthermophilic archaeon, Sulfolobus solfataricus, catabolizes d-glucose and d-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the Entner-Doudoroff pathway. At each step, one enzyme is active with both C6 epimers, leading to a metabolically promiscuous pathway. On further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the C5 sugars, d-xylose and l-arabinose. In the current paper we establish that this promiscuity for C6 and C5 metabolites is also exhibited by the third enzyme in the pathway, 2-keto-3-deoxygluconate aldolase, but that the second step requires a specific C5-dehydratase, the gluconate dehydratase being active only with C6 metabolites. The products of this pathway for the catabolism of d-xylose and l-arabinose are pyruvate and glycolaldehyde, pyruvate entering the citric acid cycle after oxidative decarboxylation to acetyl-coenzyme A. We have identified and characterized the enzymes, both native and recombinant, that catalyze the conversion of glycolaldehyde to glycolate and then to glyoxylate, which can enter the citric acid cycle via the action of malate synthase. Evidence is also presented that similar enzymes for this pentose sugar pathway are present in Sulfolobus acidocaldarius, and metabolic tracer studies in this archaeon demonstrate its in vivo operation in parallel with a route involving no aldol cleavage of the 2-keto-3-deoxy-pentanoates but direct conversion to the citric acid cycle C5-metabolite, 2-oxoglutarate.     

Metabolic profiling by <Superscript>1</Superscript>H NMR spectroscopy of saliva shows clear distinction between control and diseased case of periodontitis

Introduction

Periodontitis is a chronic, non-reversible inflammatory disease of the oral cavity leading to destruction of periodontal tissues. Thus, the estimation of bacterial metabolite, tissue damage and secretory metabolites of the triggered inflammatory cells likely to yield results. It may be of value for understanding the pathophysiology of the disease by metabolic profiling of saliva samples using high-resolution NMR spectroscopy.

Objective

The study will evaluate the difference in salivary metabolites in healthy and periodontal condition along with fetching of possible biomarkers in case of chronic periodontitis.

Methods

¹H- NMR spectroscopy has been employed in 114 saliva samples in search of distinctive differences and spectral data were further subjected to multivariate analysis.

Result

One-hundred metabolites were characterised and assigned in the ¹H NMR spectra of saliva. The statistical analysis of control (Healthy subjects) and diseased (Periodontal subjects) using PLS-DA model resulted in R² of 0.84 and Q² of 0.79. There was an elevation in the concentration of statistically discriminant metabolites. The twenty newly identified metabolites in saliva indicates bacterial population shift along with change in homeostasis. These disturbs the biofilm, a real protector against any possible bio-damage on tooth surface. These newly identified metabolites could define better geographically diversified periodontal condition.

Conclusion

Analysis clearly differentiates healthy subjects from the diseased ones. Few newly identified metabolites along with the pool of metabolites may serve as biomarkers for distinguishing the severity and complexity of periodontitis.

     

Variation of secondary metabolite levels in maize seedling roots induced by inoculation with Azospirillum, Pseudomonas and Glomus consortium under field conditions

Background and aims

Many plant-beneficial microorganisms can influence secondary plant metabolism, but whether these effects add up when plants are co-inoculated is unclear. This issue was assessed, under field conditions, by comparing the early impacts of seed inoculation on secondary metabolite profiles of maize at current or reduced mineral fertilization levels.

Methods

Maize seeds were inoculated singly with selected strains from bacterial genera Pseudomonas and Azospirillum or mycorrhizal genus Glomus, or with these strains combined two by two or all three together. At 16?days, maize root methanolic extracts were analyzed by RP-HPLC and secondary metabolites (phenolics, flavonoids, xanthones, benzoxazionoids, etc.) identified by LC/MS.

Results

Inoculation did not impact on plant biomass but resulted in enhanced total root surface, total root volume and/or root number in certain inoculated treatments, at reduced fertilization. Inoculation led to qualitative and quantitative modifications of root secondary metabolites, particularly benzoxazinoids and diethylphthalate. These modifications depended on fertilization level and microorganism(s) inoculated. The three selected strains gave distinct results when used alone, but unexpectedly all microbial consortia gave somewhat similar results.

Conclusions

The early effects on maize secondary metabolism were not additive, as combining strains gave effects similar to those of Glomus alone. This is the first study demonstrating and analyzing inoculation effects on crop secondary metabolites in the field.     

Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes

Background

In eukaryotes, PPP (p rotein p hosphatase P) family is one of the two known protein phosphatase families specific for Ser and Thr. The role of PPP phosphatases in multiple signaling pathways in eukaryotic cell has been extensively studied. Unlike eukaryotic PPP phosphatases, bacterial members of the family have broad substrate specificity or may even be Tyr-specific. Moreover, one group of bacterial PPPs are diadenosine tetraphosphatases, indicating that bacterial PPP phosphatases may not necessarily function as protein phosphatases.

Results

We describe the presence in eukaryotes of three groups of expressed genes encoding "non-conventional" phosphatases of the PPP family. These enzymes are more closely related to bacterial PPP phosphatases than to the known eukaryotic members of the family. One group, found exclusively in land plants, is most closely related to PPP phosphatases from some α-Proteobacteria, including Rhizobiales, Rhodobacterales and Rhodospirillaceae. This group is therefore termed Rhi zobiales / Rh odobacterales / Rh odospirillaceae-l ike ph osphatases, or Rhilphs. Phosphatases of the other group are found in Viridiplantae, Rhodophyta, Trypanosomatidae, Plasmodium and some fungi. They are structurally related to phosphatases from psychrophilic bacteria Shewanella and Colwellia, and are termed She wanella-l ike ph osphatases, or Shelphs. Phosphatases of the third group are distantly related to ApaH, bacterial diadenosine tetraphosphatases, and are termed A paH-l ike ph osphatases, or Alphs. Patchy distribution of Alphs in animals, plants, fungi, diatoms and kinetoplasts suggests that these phosphatases were present in the common ancestor of eukaryotes but were independently lost in many lineages. Rhilphs, Shelphs and Alphs form PPP clades, as divergent from "conventional" eukaryotic PPP phosphatases as they are from each other and from major bacterial clades. In addition, comparison of primary structures revealed a previously unrecognised (I/L/V)D(S/T)G motif, conserved in all bacterial and "bacterial-like" eukaryotic PPPs, but not in "conventional" eukaryotic and archaeal PPPs.

Conclusions

Our findings demonstrate that many eukaryotes possess diverse "bacterial-like" PPP phosphatases, the enzymatic characteristics, physiological roles and precise evolutionary history of which have yet to be determined.

     

Distinctive features of the microbial diversity and the polyketide synthase genes spectrum in the community of the endemic Baikal sponge <Emphasis Type="Italic">Swartschewskia papyracea</Emphasis>

The diversity of the symbiotic community of the endemic Baikal sponge Swartschewskia papyracea was studied, and an analysis of the polyketide synthases genes spectrum in sponge-associated microorganisms was carried out. Six bacterial phyla were detected in the S. papyracea microbiome: Verrucomicrobia, Cyanobacteria, Actinobacteria, Bacteroidetes, Proteobacteria, and Planctomycetes. Unlike the microbial associations of other freshwater sponges, the community under study was dominated by the phylaVerrucomicrobia (42.1%) and Cyanobacteria (17.5%), while the proportion of the Proteobacteria was unusually low (9.7%). In the S. papyracea community metagenome, there were identified 18 polyketide synthases genes fragments, the closest homologues of which included the polyketide synthases of the microorganisms belonging to the bacterial phyla Cyanobacteria, Proteobacteria (classes Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), and Acidobacteria as well as the eukaryotic algae of the phylum Heterokonta (class Eustigmatophyceae). Polyketide synthase sequences from S. papyracea formed three groups on the phylogenetic tree: a group of hybrid NRPS/PKS complexes, a group of cyanobacterial polyketide synthases, and a group of homologues of the eukaryotic alga Nannochloropsis gaditana. Notably, the identified polyketide synthase genes fragments showed only a 57–88% similarity to the sequences from the databases, which implies the presence of genes controlling the synthesis of the novel, still unstudied, polyketide compounds in the S. papyracea community. It was proposed that the habitat conditions of S. papyracea affect the taxonomic composition of the microorganisms associated with the sponge, including the diversity of the producers of secondary metabolites.     

Evolution of peroxisomes illustrates symbiogenesis

Recently, the group of McBride reported a stunning observation regarding peroxisome biogenesis: newly born peroxisomes are hybrids of mitochondrial and ER‐derived pre‐peroxisomes. What was stunning? Studies performed with the yeast Saccharomyces cerevisiae had convincingly shown that peroxisomes are ER‐derived, without indications for mitochondrial involvement. However, the recent finding using fibroblasts dovetails nicely with a mechanism inferred to be driving the eukaryotic invention of peroxisomes: reduction of mitochondrial reactive oxygen species (ROS) generation associated with fatty acid (FA) oxidation. This not only explains the mitochondrial involvement, but also its apparent absence in yeast. The latest results allow a reconstruction of the evolution of the yeast's highly derived metabolism and its limitations as a model organism in this instance. As I review here, peroxisomes are eukaryotic inventions reflecting mutual host endosymbiont adaptations: this is predicted by symbiogenetic theory, which states that the defining eukaryotic characteristics evolved as a result of mutual adaptations of two merging prokaryotes. See also the video abstract here: https://youtu.be/HtyKhQ3DSxg

     

Aerobic carbon monoxide oxidation in the course of growth of a hyperthermophilic archaeon, <Emphasis Type="Italic">Sulfolobus</Emphasis> sp. ETSY

An aerobic hyperthermophilic CO-oxidizing archaeon, Sulfolobus sp. strain ETSY, was isolated and characterized. Presently, it is the only known representative of both hyperthermophiles and Archaea that is capable of aerobic oxidation of CO, a gas of global importance for atmospheric chemistry and of local importance as one of the substrates for the microbial communities of hydrothermal vents. In the genome of Sulfolobus sp. ETSY we found genetic determinants of aerobic CO oxidation: a coxFMSLDE gene cluster and two separately located coxG genes. We also found such gene clusters in the genomes of certain strains of Sulfolobus islandicus and Sulfolobus solfataricus. On the phylogenetic tree of large subunits of aerobic CO-dehydrogenases (CoxLs), these proteins of Sulfolobus representatives formed a compact cluster within one of the branches formed by bacterial form I CoxLs. Thus we argue that the ability to oxidize CO aerobically was acquired by Sulfolobus ancestor from Bacteria relatively late in the evolution, presumably after the formation of the atmosphere with a high oxygen content.     

Biodegradation of a high molecular weight aliphatic ether – indications of an unusual biodegradation pathway

An aliphatic ether (1-phytanyl-1-octadecanyl-ether) of high molecular weight was used as a sole carbon source in degradation experiments with different aerobic bacteria. The enriched culture B5, obtained from fuel contaminated soils, was able to degrade the substance for more than 90%. A culture of Rhodococcus ruber was similarly effective. Detailed investigation of the metabolites allowed us to characterize an unusual degradation pathway via a mid-chain oxidation mechanism (`internal oxidative pathway'). Obviously, formation of intermediate alkenes mainly at the unbranched side chain was a prerequisite for bacterial degradation of the added substrate. Degradation proceeded – in spite of the usually preferred terminal oxidation – via oxidation of the internal double bond and was followed by an ester cleavage. In turn, a series of alcohols was formed which were subsequently oxidized to the respective carboxylic acids and were further metabolized via the normal -oxidation pathway.     

Lysis of Antarctic algal strains by bacterial pathogen

The present paper describes the isolation, physiological and genetic characteristic of a bacterial agent which inhibits the growth of algae and causes death of laboratory cultures of Antarctic microalgal strains: prokaryotic cyanobacteria Synechocystis salina and green eukaryotic microalga Choricistis minor. The bacterial strain LB1 was isolated from algal damaged laboratory cultures of S. salina. It was established that this bacterium is obligate aerobic, Gram-positive, non-spore-forming, immotile, irregular rods with dimensions 0.3–2 μm. Our results showed that LB1 has algicidal effect to S. salina as well as to C. minor. Transmission electron microscopy observations confirmed the destruction of S. salina by the bacterium. Biochemical analysis of LB1 revealed positive reaction to d-glucose, catalase, hydrolysis of gelatin, acid production from: lactose, l-arabinose, l-ramnose, esculin and β-galactosidase. The partial sequence (1,404 bp) of the 16S rRNA gene of LB1 showed 99 % similarity with type strains of the genus Microbacterium. The results of the biochemical, antimicrobial and of 16S rRNA analysis of LB1 allowed us to identify LB1 as Microbacterium sp. Studying expression of pathogenicity of the bacteria to algal cultures will help to solve the problem of algal production for biotechnological purposes.     

Biotransformation of the neonicotinoid insecticides imidacloprid and thiamethoxam by Pseudomonas sp. 1G

We report the isolation of a Pseudomonas sp. which is able to transform imidacloprid and thiamethoxam under microaerophilic conditions in the presence of an alternate carbon source. This bacterium, Pseudomonas sp. 1G, was isolated from soil with a history of repeated exposure to imidacloprid. Both insecticides were transformed to nitrosoguanidine (NNO), desnitro (NH), and urea (O) metabolites and a transformation pathway is proposed. This is the first conclusive report of bacterial transformation of the ‘magic nitro’ group which is responsible for the insect selectivity of neonicotinoid insecticides.