Diet is the primary determinant of bacterial community structure in the guts of higher termites

The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically ‘lower termites’ are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this study, we comparatively analysed representatives of different taxonomic lineages and feeding groups of higher termites to identify the major drivers of bacterial community structure in the termite gut, using amplicon libraries of 16S rRNA genes from 18 species of higher termites. In all analyses, the wood‐feeding species were clearly separated from humus and soil feeders, irrespective of their taxonomic affiliation, offering compelling evidence that diet is the primary determinant of bacterial community structure. Within each diet group, however, gut communities of termites from the same subfamily were more similar than those of distantly related species. A highly resolved classification using a curated reference database revealed only few genus‐level taxa whose distribution patterns indicated specificity for certain host lineages, limiting any possible cospeciation between the gut microbiota and host to short evolutionary timescales. Rather, the observed patterns in the host‐specific distribution of the bacterial lineages in termite guts are best explained by diet‐related differences in the availability of microhabitats and functional niches.     

Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues

The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a given protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the Escherichia coli proteome using several proteomic methodologies and globally measured oxidation rates of methionine residues in the presence and absence of tertiary structure, as well as the folding stabilities of methionine-containing domains. These data indicated that buried methionines have a wide range of protection factors against oxidation that correlate strongly with folding stabilities. Consistent with this, we show that in comparison to E. coli, the proteome of the thermophile Thermus thermophilus is significantly more stable and thus more resistant to methionine oxidation. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and propose a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures. Overall, these results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability.     

Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils

Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.     

Protein aggregation as bacterial inclusion bodies is reversible

Inclusion bodies are refractile, intracellular protein aggregates usually observed in bacteria upon targeted gene overexpression. Since their occurrence has a major economical impact in protein production bio-processes, in vitro refolding strategies are under continuous exploration. In this work, we prove spontaneous in vivo release of both beta-galactosidase and P22 tailspike polypeptides from inclusion bodies resulting in their almost complete disintegration and in the concomitant appearance of soluble, properly folded native proteins with full biological activity. Since, in particular, the tailspike protein exhibits an unusually slow and complex folding pathway involving deep interdigitation of beta-sheet structures, its in vivo refolding indicates that bacterial inclusion body proteins are not collapsed into an irreversible unfolded state. Then, inclusion bodies can be observed as transient deposits of folding-prone polypeptides, resulting from an unbalanced equilibrium between in vivo protein precipitation and refolding that can be actively displaced by arresting protein synthesis. The observation that the formation of big inclusion bodies is reversible in vivo can be also relevant in the context of amyloid diseases, in which deposition of important amounts of aggregated protein initiates the pathogenic process.     

PprA: a protein implicated in radioresistance of Deinococcus radiodurans stimulates catalase activity in Escherichia coli

PprA: a pleiotropic protein promoting DNA repair, role in radiation resistance of Deinococcus radiodurans was demonstrated. In this study, the effect of radiation and oxidative stress on transgenic Escherichia coli expressing pprA has been studied. The pprA gene from D. radiodurans KR1 was cloned and expressed in E. coli. Transgenic E. coli cells expressing PprA showed twofold to threefold higher tolerance to hydrogen peroxide as compared to control. The 2.8-fold in vivo stimulation of catalase activity largely contributed by KatE was observed as compared to nonrecombinant control. Furthermore, the purified PprA could stimulate the E. coli catalase activity by 1.7-fold in solution. The effect of PprA on catalase activity observed both in vivo and in vitro was reverted to normal levels in the presence of PprA antibodies. The results suggest that enhanced oxidative stress tolerance in E. coli expressing PprA was due to the PprA stimulation of catalase activity, perhaps through the interaction of these proteins.     

Protein oxidation in plant mitochondria detected as oxidized tryptophan

The formation of N-formylkynurenine by dioxygenation of tryptophan was detected in peptides from rice leaf and potato tuber mitochondria. Proteins in matrix and membrane fractions were separated by two-dimensional gel electrophoresis and identified using a Q-TOF mass spectrometer. N-Formylkynurenine was detected in 29 peptides representing 17 different proteins. With one exception, the oxidation-sensitive aconitase, all of these proteins were either redox active themselves or subunits in redox-active enzyme complexes. The same site was modified in (i) several adjacent spots containing the P protein of the glycine decarboxylase complex, (ii) two different isoforms of the mitochondrial processing peptidase in complex III, and (iii) the same tryptophan residues in Mn-superoxide dismutase in both rice and potato mitochondria. This indicates that Trp oxidation is a selective process.     

Secondary structure as primary determinant of the efficiency of ribosomal binding sites in Escherichia coli.

Using a previously described vector (pKL203) we fused several heterologous ribosomal binding sites (RBSs) to the lacZ gene of E. coli and then studied the variation in expression of the fusions. The RBSs originated from bacteriophage Q beta and MS2 genes and the E. coli genes for elongation factor EF-Tu A and B and ribosomal protein L11 (rplK). The synthesis of the lacZ fusion proteins was measured by an immuno precipitation method and found to vary at least 100-fold. Lac-specific mRNA synthesis follows the variation in protein production. It appears that there is a correlation between the efficiency of an RBS to function in the expression of the fused gene and the lack of secondary structure, involving the Shine and Dalgarno nucleotides (SDnts) and/or the initiation codon. This efficiency is context dependent. The sequence of the SD nts and the length and sequence of the spacer region up to the initiation codon alone are not able to explain our results. Deletion mutations, created in the phage Q beta replicase RBS, reveal a complex pattern of control of expression, probably involving the use of a "false" initiation site.     

Protein oxidation in aging: endoplasmic reticulum as a target

Summary. Oxidatively modified proteins have been shown to correlate with the age of an organism or its tissues. An increase in tissue-susceptibility to experimentally induced protein oxidation not only depends on tissue type and age, but also on the maximum lifespan potential of the species. A general, although tissue dependent, decline in anti-oxidative defenses during aging may very well be responsible for this difference in vulnerability. In addition, the level of protein modifications also depends on the nature and the subcellular localization of the proteins involved. Damage to the endoplasmic reticulum (ER), and its subsequent impaired functionality may be involved in the process of aging. This is suggested by; (1) an upregulation of ER stress-response chaperones, (2) a preferential oxidation of ER-resident proteins and, (3) a disturbance of calcium homeostasis. Therefore, this review will focus on the putative involvement of the oxidized endoplasmic reticulum in the process of aging.     

Protein oxidation in plant mitochondria as a stress indicator.

Plant mitochondria produce reactive oxygen species (ROS) as an unavoidable side product of aerobic metabolism, but they have mechanisms for regulating this production such as the alternative oxidase. Once produced, ROS can be removed by several different enzyme systems. Finally, should the first two strategies fail, the ROS produced can act as a signal to the rest of the cell and/or cause damage to DNA, lipids and proteins. Proteins are modified in a variety of ways by ROS, some direct, others indirect e.g. by conjugation with breakdown products of fatty acid peroxidation. Reversible oxidation of cysteine and methionine side chains is an important mechanism for regulating enzyme activity. Mitochondria from both mammalian and plant tissues contain a number of oxidised proteins, but the relative abundance of these post-translationally modified forms is as yet unknown, as are the consequences of the modification for the properties and turnover time of the proteins. Specific proteins appear to be particularly vulnerable to oxidative carbonylation in the matrix of plant mitochondria; these include several enzymes of the Krebs cycle, glycine decarboxylase, superoxide dismutase and heat shock proteins. Plant mitochondria contain a number of different proteases, but their role in removing oxidatively damaged proteins is, as yet, unclear.     

Microalgal-facilitated bacterial oxidation of manganese

In the presence of unicellular microalgae, bacterial manganese oxidation was increased by up to ten times the rate produced by bacterial oxidation alone. Azide-poisoned controls demonstrated that the manganese-oxidizing bacteria were active in the algal-bacterial oxidation of manganese. Scanning electron microscopy showed that oxide formation occurred in a number of structurally different deposits on the surface of the alga. Studies involving algal cell fractionation showed that bacterial manganese oxidation was facilitated by the algal cell wall, possibly via Mn²⁺ adsorption. Variations in growth conditions had an effect on algal-bacterial oxide formation and composition. High nutrient (yeast extract, peptone and/or sucrose) levels favored microbial growth but lowered oxide formation, whereas optimal levels of manganese oxide formation required minimal media. High concentrations of either organic nutrients or mineral salts promoted manganese carbonate precipitation.     

Light-induced Fourier transform infrared (FTIR) spectroscopic investigations of the primary donor oxidation in bacterial photosynthesis

Fourier transform infrared (FTIR) difference spectroscopy of the primary electron donor (P) photo-oxidation has been performed for reaction centers (RCs) and chromatophores of purple photosynthetic bacteria. In the 1800–650 cm⁻¹ spectral region highly reproducible absorbance changes were obtained that can be related to specific changes of individual bond absorption. Several bands in the difference spectra are tentatively assigned to changes of intensity and position of the keto and ester CO vibrations of the P bacteriochlorophylls, and a possible interpretation in terms of changes of their environment or type of bonding to the protein is given. Small difference bands in the amide I and II region allow only minor protein conformational changes.     

Protein oxidation at the air-lung interface

Summary. Whilst performing its normal functions the lung is required to deal with a range of toxic insults. Whether these are infectious agents, allergens or air pollutants they subject the lung to a range of direct and indirect oxidative stresses. In many instances these challenges lead to oxidative alterations of peptides and proteins within the lung. Measurement of protein oxidation products permits the degree of oxidative stress to be assessed and indicates that endogenous antioxidant defences are overwhelmed. The range of protein oxidation products observed is diverse and the nature and extent of specific oxidation products may inform us about the nature of the damaging ROS and NOS. Recently, there has been a significant shift away from the measurement of these oxidation products simply to establish the presence of oxidative stress, to a focus on identifying specific proteins sensitive to oxidation and establishing the functional consequences of these modifications. In addition the identification of specific enzyme systems to repair these oxidative modifications has lead to the belief that protein function may be regulated through these oxidation reactions. In this review we focus primarily on the soluble protein components of within the surface liquid layer in the lung and the consequence of their undue oxidation.     

Phosphorylation of deinococcal RecA affects its structural and functional dynamics implicated for its roles in radioresistance of Deinococcus radiodurans

Abstract

Deinococcus RecA (DrRecA) protein is a key repair enzyme and contributes to efficient DNA repair of Deinococcus radiodurans. Phosphorylation of DrRecA at Y77 (tyrosine 77) and T318 (threonine 318) residues modifies the structural and conformational switching that impart the efficiency and activity of DrRecA. Dynamics comparisons of DrRecA with its phosphorylated analogues support the idea that phosphorylation of Y77 and T318 sites could change the dynamics and conformation plasticity of DrRecA. Furthermore, docking studies showed that phosphorylation increases the binding preference of DrRecA towards dATP versus ATP and for double-strand DNA versus single-strand DNA. This work supporting the idea that phosphorylation can modulate the crucial functions of this protein and having good concordance with the experimental data. Abbreviations DrRecA Deinococcus RecA

DSB DNA double-strand breaks

hDNA heteroduplex DNA

STYPK serine/threonine/tyrosine protein kinase

T318 threonine 318

Y77 tyrosine 77

Communicated by Ramaswamy H. Sarma     

The 67kDa laminin receptor as a primary determinant of anti-allergic effects of O-methylated EGCG

Previously we have reported that the O-methylated derivative of (−)-epigallocatechin-3-O-gallate (EGCG), (−)-epigallocatechin-3-O-(3-O-methyl) gallate (EGCG3”Me), possesses anti-allergic activities such as inhibition of histamine release and suppression of the high-affinity IgE receptor (FcεRI) expression. However, the underlying mechanism is still unclear. Recently we have identified the 67 kDa laminin receptor (67LR) as a cell-surface receptor that can mediate biological activities of EGCG. Here we show that the suppression of myosin II regulatory light chain (MRLC) phosphorylation through the cell-surface binding to the 67 LR contributes to the inhibitory effect of EGCG3”Me on the histamine release from the human basophilic KU812 cells. The 67LR also mediated the EGCG3”Me-induced suppression of FcεRI expression by reducing ERK1/2 phosphorylation. These results suggest that anti-allergic effects of EGCG3”Me may be triggered by the inhibition of MRLC or ERK1/2 phosphorylation mediated through the cell-surface 67LR.     

Protein oxidation by the cytochrome P450 mixed-function oxidation system

This mini-review summarizes results of studies on the oxidation of proteins and low-density lipoprotein (LDL) by various mixed-function oxidation (MFO) systems. Oxidation of LDL by the O₂/FeCl₃/H₂O₂/ascorbate MFO system is dependent on all four components and is much greater when reactions are carried out in the presence of a physiological bicarbonate/CO₂ buffer system as compared to phosphate buffer. However, FeCl₃ in this system could be replaced by hemin or the heme-containing protein, hemoglobin, or cytochrome c. Oxidation of LDL by the O₂/cytochrome P450 cytochrome c reductase/NADPH/FeCl₃ MFO system is only slightly higher (25%) in the bicarbonate/CO₂ buffer as compared to phosphate buffer, but is dependent on all components except FeCl₃. Omission of FeCl₃ led to a 60% loss of activity. These results suggest that peroxymonobicarbonate and/or free radical derivatives of bicarbonate ion and/or CO₂ might contribute to LDL oxidation by these MFO systems.     

Observations on the bacterial oxidation of chlorophenoxyacetic acids

Summary Three bacterial strains, one ofF. peregrinum (Stapp and Spicher) and two Achromobacter strains, have been isolated from soil and shown to decompose either 2,4-D, MCPA orp-chlorophenoxyacetic acid. Aerobic conditions are essential for the bacterial decomposition of 2,4-D. Pretreatment of soil with one of the three chlorophenoxyacetic acids accelerated the rate of breakdown of either of the other two. In a liquid medium, growth of theF. peregrinum strain caused breakdown of 2,4-D and liberated 76% of the chlorine in 2,4-D in ionic form. An unknown acidic substance, colourless in acid solution but forming a yellow sodium salt has been detected in cultures ofF. peregrinum or an MCPA-decomposing Achromobacter strain growing inp-chlorophenoxyacetate medium. The bacterial oxidation of chlorophenoxyacetic acid herbicides was attributed to adaptive enzyme formation. Respiration experiments showed that the oxidation of 2,4-D or ofp-chlorophenoxyacetic acid is incomplete. 4-Chloro-2-hydroxyphenoxyacetic acid and 4-chlorocatechol may be metabolic intermediates in the case ofp-chlorophenoxyacetic acid, but no intermediary metabolites have as yet been established for 2,4-D.