Biogeochemistry and microbiology of groundwater during acetate and bicarbonate amendment to an alluvial aquifer

These data are from a field experiment conducted in a shallow alluvial aquifer along the Colorado River in Rifle, Colorado, USA. In this experiment, bicarbonate-promoted uranium desorption and acetate amendment were combined and compared to an acetate amendment-only experiment in the same experimental plot. Data include names and location data for boreholes, geochemical data for all the boreholes between June 1, 2010 and January 1, 2011, microarray data provided as signal to noise ratio (SNR) for individual microarray probes, microarray data provided as signal to noise ratio (SNR) by Genus.

A 1.2-Å snapshot of the final step of bacterial cell wall biosynthesis

The cell wall imparts structural strength and shape to bacteria. It is made up of polymeric glycan chains with peptide branches that are cross-linked to form the cell wall. The cross-linking reaction, catalyzed by transpeptidases, is the last step in cell wall biosynthesis. These enzymes are members of the family of penicillin-binding proteins, the targets of β-lactam antibiotics. We report herein the structure of a penicillin-binding protein complexed with a cephalosporin designed to probe the mechanism of the cross-linking reaction catalyzed by transpeptidases. The 1.2-Å resolution x-ray structure of this cephalosporin bound to the active site of the bifunctional serine type d-alanyl-d-alanine carboxypeptidase/transpeptidase (EC 3.4.16.4) from Streptomyces sp. strain R61 reveals how the two peptide strands from the polymeric substrates are sequestered in the active site of a transpeptidase. The structure of this complex provides a snapshot of the enzyme and the bound cell wall components poised for the final and critical cross-linking step of cell wall biosynthesis.

Expression of the Anabaena hetR gene from a copper-regulated promoter leads to heterocyst differentiation under repressing conditions

Heterocyst differentiation in the filamentous cyanobacterium Anabaena PCC 7120 requires a functional hetR gene. Increased expression of the hetR gene is seen in developing and mature heterocysts in response to fixed nitrogen limitation. We mapped four likely transcriptional start sites for hetR and identified a specific transcript that is positively autoregulated. By using the copper-responsive petE promoter from Anabaena PCC 7120 to drive hetR expression, we show that ectopic expression of hetR increases heterocyst frequency and induces heterocyst differentiation under fully repressing conditions. Coexpression of a reporter gene shows that expression from the petE promoter is smoothly induced depending on the amount of copper supplied. In the heterocyst pattern mutant PatA, where terminally positioned heterocysts are formed almost exclusively, expression of the petE∷hetR fusion does not result in the formation of intercalary heterocysts. These results suggest that although the intracellular concentration of HetR has to be elevated for the differentiation decision, PatA plays a role as well. This role may be in the form of posttranslational modification of HetR, because PatA is a member of the response regulator family of proteins.

Fast Induction of High-Affinity HCO3− Transport in Cyanobacteria1

The induction of a high-affinity state of the CO2-concentration mechanism was investigated in two cyanobacterial species, Synechococcus sp. strain PCC7002 and Synechococcus sp. strain PCC7942. Cells grown at high CO2 concentrations were resuspended in low-CO2 buffer and illuminated in the presence of carbonic anhydrase for 4 to 10 min until the inorganic C compensation point was reached. Thereafter, more than 95% of a high-affinity CO2-concentration mechanism was induced in both species. Mass-spectrometric analysis of CO2 and HCO3− fluxes indicated that only the affinity of HCO3− transport increased during the fast-induction period, whereas maximum transport activities were not affected. The kinetic characteristics of CO2 uptake remained unchanged. Fast induction of high-affinity HCO3− transport was not inhibited by chloramphenicol, cantharidin, or okadaic acid. In contrast, fast induction of high-affinity HCO3− transport did not occur in the presence of K252a, staurosporine, or genistein, which are known inhibitors of protein kinases. These results show that induction of high-affinity HCO3− transport can occur within minutes of exposure to low-inorganic-C conditions and that fast induction may involve posttranslational phosphorylation of existing proteins rather than de novo synthesis of new protein components.

An abundant cell-surface polypeptide is required for swimming by the nonflagellated marine cyanobacterium Synechococcus.

Certain marine unicellular cyanobacteria of the genus Synechococcus exhibit a unique and mysterious form of motility characterized by the ability to swim in liquid in the absence of flagella. An abundant cell-surface-associated polypeptide that is required for swimming motility by Synechococcus sp. strain WH8102 has been identified, and the gene encoding it, swmA, has been cloned and sequenced. The predicted SwmA protein contains a number of Ca2+-binding motifs as well as several potential N-glycosylation sites. Insertional inactivation of swmA in Synechococcus sp. strain WH8102 results in a loss of the ability to translocate, although the mutant strain, Swm-1, generates torque. This suggests that SwmA functions in the generation of thrust.

Reactions catalyzed by bacterial cytochromes P450

The cytochromes P450 are a large family of oxidative haemoproteins that are responsible for a wide variety of oxidative transformations in a variety of organisms. This review focuses upon the reactions catalyzed specifically by bacterial enzymes, which includes aliphatic hydroxylation, alkene epoxidation, aromatic hydroxylation, oxidative phenolic coupling, heteroatom oxidation and dealkylation, and multiple oxidations including C-C bond cleavage. The potential for the practical application of the oxidizing power of these enzymes is briefly discussed.

Identification, detection, and spatial resolution of Clostridium populations responsible for cellulose degradation in a methanogenic landfill leachate bioreactor

An anaerobic landfill leachate bioreactor was operated with crystalline cellulose and sterile landfill leacbate until a steady state was reached. Cellulose hydrolysis, acidogenesis, and methanogenesis were measured. Microorganisms attached to the cellulose surfaces were hypothesized to be the cellulose hydrolyzers. 16S rRNA gene clone libraries were prepared from this attached fraction and also from the mixed fraction (biomass associated with cellulose particles and in the planktonic phase). Both clone libraries were dominated by Firmicutes phylum sequences (100% of the attached library and 90% of the mixed library), and the majority fell into one of five lineages of the clostridia. Clone group 1 (most closely related to Clostridium stercorarium), clone group 2 (most closely related to Clostridium thermocellum), and clone group 5 (most closely related to Bacteroides cellulosolvens) comprised sequences in Clostridium group III. Clone group 3 sequences were in Clostridium group XIVa (most closely related to Clostridium sp. strain XB90). Clone group 4 sequences were affiliated with a deeply branching clostridial lineage peripherally associated with Clostridium group VI. This monophyletic group comprises a new Clostridium cluster, designated cluster VIa. Specific fluorescence in situ hybridization (FISH) probes for the five groups were designed and synthesized, and it was demonstrated in FISH experiments that bacteria targeted by the probes for clone groups 1, 2, 4, and 5 were very abundant on the surfaces of the cellulose particles and likely the key cellulolytic microorganisms in the landfill bioreactor. The FISH probe for clone group 3 targeted cells in the planktonic phase, and these organisms were hypothesized to be glucose fermenters.

The cellular lipids of Romboutsia.

We have examined the lipids of three isolates, Romboutsia lituseburensis, Romboutsia ilealis, and Romboutsia sp. strain FRIFI, of the newly described genus Romboutsia by two-dimensional thin-layer chromatography (2D-TLC) and by liquid chromatography/mass spectrometry (LC/MS). We have found three phospholipids, phosphatidylglycerol (PG), cardiolipin and phosphatidic acid in all three species. A fourth phospholipid, lysyl-PG, was found in R. lituseburensis and strain FRIFI. Polyprenyl-phosphates were identified in the lipid extracts of all three species. Three glycolipids, mono-, di- and tri-hexosyldiacylglycerol, were common to all three species. An additional glycolipid, tetrahexosyl-diacylglycerol was identified in strain FRIFI. Acylated trihexosyldiacylglycerol and acyl-tetrahexosydiacylglycerol were also found in R. ilealis and strain FRIFI. Remarkably, no alk-1-enyl ether lipids (plasmalogens) were present in Romboutsia as distinct from bacteria of the related genus Clostridium in which these ether lipids are common. We have compared the lipidome of Romboutsia with that recently described for Clostridium difficile, which has plasmalogens, no lysyl-PG, and no tetrahexosyl-diacylglycerol. According to 16S rRNA gene sequencing, Romboutsia spp. and C. difficile are closely related (>95% sequence identity).

Untersuchungen zur Funktion multipler DnaJ-Proteine in dem Cyanobakterium Synechocystis sp. PCC 6803

Sowohl in Synechocystis sp. PCC 6803 als auch in anderen Cyanobakterien konnten multiple DnaJ-Proteine nachgewiesen werden, deren Funktion jedoch noch weitestgehend unverstanden ist. Im Rahmen dieser Arbeit wurden die Funktionen der multiplen DnaJ-Proteine von Synechocystis sp. charakterisiert. Das DnaJ-Protein, Sll0897 gehört aufgrund seiner Domänenstruktur zu den Typ I-Proteinen, Slr0093 und Sll1933 zu den Typ II-Proteinen und Sll0909, Sll1011, Sll1384 und Sll1666 zu den Typ III DnaJ-Proteinen. Durch Komplementationsstudien des E. coli ΔdnaJ-Stammes OD259 konnte eine Komplementation des Wachstumsdefekts bei höheren Temperaturen durch die Proteine Slr0093 und Sll0897 gezeigt werden. In Synechocystis war eine komplette Disruption von sll1933 nicht möglich, weshalb das Protein Sll1933 unter normalen Wachstumsbedingungen essentiell ist. Doppelte Insertionmutationen waren lediglich bei der Kombination der Gene sll0909 und sll1384 möglich. Untersuchungen des Wachstumsverhaltens der dnaJ-Disruptions-stämme unter Hitze- und Kältestressbedingungen zeigten, dass das Protein Sll0897 eine wichtige Funktion bei der Stressantwort in Synechocystis besitzt und unter Hitzestressbedingungen essentiell ist. Eine vollständige Deletion des Gens sll0897 war Synechocystis sp. bereits unter normalen Wachstumsbedingungen nicht möglich. Bei den für ein Wachstum mindestens notwendigen Domänen des Sll0897 handelt es sich um die charakteristische J-Domäne und die Glycin-Phenylalanin-reiche Domäne. Unter Hitzestressbedingungen ist das Volllängen-Protein Sll0897 für ein Wachstum essentiell. rnNeben den in vivo Wachstumsexperimenten wurde eine Methode zur heterologen Expression der sieben DnaJ-Proteine in E. coli und einer nativen Reinigung von Slr0093, Sll0897, Sll0909 und Sll1666 etabliert. Untersuchungen zur Thermostabilität der gereinigten Proteine zeigten für das Slr0093 und Sll1666 einen reversiblen Prozess, wodurch sie auch nach dem Hitzestress noch als Faltungshelfer fungieren können. Bei den Proteinen Sll0897 und Sll0909 ist der Prozess jedoch nicht reversibel, so dass sie nach Hitzestresseinwirkung neu synthetisiert oder durch Chaperoneinwirkung korrekt gefaltet werden müssen. Die Affinitäts-„Pull-Down“ Analysen lieferten keine klaren Hinweise auf die DnaK-Interaktionspartner der Proteine Slr0093, Sll0897, Sll0909 und Sll1666, weshalb weitere Untersuchungen notwendig sind. Mit Hilfe der Gelfiltrationsanalysen konnten die errechneten molaren Massen der Proteine Slr0093 und Sll1666 bestätigt und beide Proteine in einer monomeren Form nachgewiesen werden. Die DnaJ-Proteine Sll0897 und Sll0909 konnten in zwei oligomeren Zuständen detektiert werden. Analysen der ATPase-Aktivität des DnaK2-Proteins alleine und des DnaK2-Proteins zusammen mit den DnaJ-Proteinen Slr0093, Sll0897, Sll0909 und Sll1666 zeigten eine Steigerung der ATP-Hydrolyserate bei der Interaktion von DnaK und DnaJ, wobei Sll0897 die größte Steigerung der ATPase-Aktivität des DnaK2 induzierte.

Some observations on the growth and cyst production characteristics of the brine shrimp Artemia sp. (Gujarat strain) in pond culture and its potential for import substitution

Experimental culture of the brine shrimp Artemia sp. (Gujarat strain) and production of cyst is discussed. The qualitative and quantitative aspects of the cyst and its economic potential for import substitution are highlighted.

Thylakoid terminal oxidases are essential for the cyanobacterium Synechocystis sp. PCC 6803 to survive rapidly changing light intensities.

Cyanobacteria perform photosynthesis and respiration in the thylakoid membrane, suggesting that the two processes are interlinked. However, the role of the respiratory electron transfer chain under natural environmental conditions has not been established. Through targeted gene disruption, mutants of Synechocystis sp. PCC 6803 were generated that lacked combinations of the three terminal oxidases: the thylakoid membrane-localized cytochrome c oxidase (COX) and quinol oxidase (Cyd) and the cytoplasmic membrane-localized alternative respiratory terminal oxidase. All strains demonstrated similar growth under continuous moderate or high light or 12-h moderate-light/dark square-wave cycles. However, under 12-h high-light/dark square-wave cycles, the COX/Cyd mutant displayed impaired growth and was completely photobleached after approximately 2 d. In contrast, use of sinusoidal light/dark cycles to simulate natural diurnal conditions resulted in little photobleaching, although growth was slower. Under high-light/dark square-wave cycles, the COX/Cyd mutant suffered a significant loss of photosynthetic efficiency during dark periods, a greater level of oxidative stress, and reduced glycogen degradation compared with the wild type. The mutant was susceptible to photoinhibition under pulsing but not constant light. These findings confirm a role for thylakoid-localized terminal oxidases in efficient dark respiration, reduction of oxidative stress, and accommodation of sudden light changes, demonstrating the strong selective pressure to maintain linked photosynthetic and respiratory electron chains within the thylakoid membrane. To our knowledge, this study is the first to report a phenotypic difference in growth between terminal oxidase mutants and wild-type cells and highlights the need to examine mutant phenotypes under a range of conditions.

固氮蓝藻Anabaena sp.7120的叶绿素蛋白复合体的分离和光谱特性的研究

用光合膜片增溶和SDS-聚丙烯酰胺凝胶电泳方法,从固氮蓝藻Anabaena sp.7120分离到7条色素带。迁移率较慢的五条叶绿素蛋白复合体带,具有相同的吸收光谱和室温荧光光谱特性。它们的红区最大吸收峰在676nm;蓝区最大吸收峰在438nm。它们的室温荧光发射最高峰在672—673nm;在710,732和740nm都有小峰。这些是CPⅠ叶绿素所特有的。我们认为这5条带都是属于光系统Ⅰ的叶绿素蛋白复合体。另一条迁移率稍快的叶绿素蛋白复合体带为CPⅡ。它的红区最大吸收峰在672nm;蓝区最大吸收峰在436n

DnaJ-like protein gene sll1384 is involved in phototaxis in Synechocystis sp PCC 6803

In Synechocystis sp. PCC 6803, gene sll1384 encodes a protein with a DnaJ domain at its N-terminal portion and a TPR domain at the C-terminal portion. An sll1384 mutant shows no difference from the wild type in adaptation to different temperatures, but almost completely loses its capability of phototactic movement. After complementation with sll1384, the mutant regains the phototaxis. As shown with electron microscopy, on the cell surface, mutant cells have pili that appear to be the same as that of the wild type. Also, the transformation efficiency remains unchanged in the mutant. It is postulated that Sll1384 regulates phototaxis of Synechocystis through protein-protein interaction. It is the first DnaJ-like protein gene identified in a cyanobacterium for a role in phototaxis.

ApcD is necessary for efficient energy transfer from phycobilisomes to photosystem I and helps to prevent photoinhibition in the cyanobacterium Synechococcus sp PCC 7002

Phyrobilisomes (PBS) are the major light-harvesting, protein-pigment complexes in cyanobacteria and red algae. PBS absorb and transfer light energy to photosystem (PS) II as well as PS I, and the distribution of light energy from PBS to the two photosystems is regulated by light conditions through a mechanism known as state transitions. In this study the quantum efficiency of excitation energy transfer from PBS to PS I in the cyanobacterium Synechococcus sp. PCC 7002 was determined, and the results showed that energy transfer from PBS to PS I is extremely efficient. The results further demonstrated that energy transfer from PBS to PS I occurred directly and that efficient energy transfer was dependent upon the allophycocyanin-B alpha subunit, ApcD. In the absence of ApcD, cells were unable to perform state transitions and were trapped in state 1. Action spectra showed that light energy transfer from PBS to PS I was severely impaired in the absence of ApcD. An apcD mutant grew more slowly than the wild type in light preferentially absorbed by phyrobiliproteins and was more sensitive to high light intensity. On the other hand, a mutant lacking ApcF, which is required for efficient energy transfer from PBS to PS II, showed greater resistance to high light treatment. Therefore, state transitions in cyanobacteria have two roles: (1) they regulate light energy distribution between the two photosystems; and (2) they help to protect cells from the effects of light energy excess at high light intensities. (C) 2009 Elsevier B.V. All rights reserved.