Susan Fishbain

Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes

A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the dsrAB gene homologs of the sulfite reducer Desulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive division) and two members of the genus Thermodesulfobacterium (a separate bacterial division) were monophyletic with delta-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is that dsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the delta-Proteobacteria were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for a dsrAB lateral gene transfer event also was found within the delta-Proteobacteria, affecting Desulfobacula toluolica. The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes in Archaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.

Defining the geometry of the two-component proteasome degron.

The eukaryotic 26S proteasome controls cellular processes by degrading specific regulatory proteins. Most proteins are targeted for degradation by a signal or degron that consists of two parts: a proteasome-binding tag, typically covalently attached polyubiquitin chains, and an unstructured region that serves as the initiation region for proteasomal proteolysis. Here we have characterized how the arrangement of the two degron parts in a protein affects degradation. We found that a substrate is degraded efficiently only when its initiation region is of a certain minimal length and is appropriately separated in space from the proteasome-binding tag. Regions that are located too close or too far from the proteasome-binding tag cannot access the proteasome and induce degradation. These spacing requirements are different for a polyubiquitin chain and a ubiquitin-like (UbL) domain. Thus, arrangement and location of the proteasome initiation region affect a protein’s fate and play a central role in selecting proteins for proteasome-mediated degradation.

Origins and diversification of sulfate-respiring microorganisms

If the diversification of microbial life can be depicted as a single tree, as inferred by comparative sequencing of ribosomal RNAs, this could provide a framework for defining the order of emergence of new metabolic pathways. However, recent recognition that lateral gene transfer has been a significant force in microbial evolution has created uncertainty about the interpretation of taxonomies based on gene sequences. In this context, the origins and evolution of sulfate respiration will be evaluated considering the evolutionary history of a central enzyme in this process, the dissimilatory sulfite reductase. These studies suggest at least two major lateral transfer events during the early diversification of sulfate respiring microorganisms. The high sequence conservation of this enzyme has also provided a mechanism to directly explore the natural diversity of sulfate-respiring organisms using molecular techniques, avoiding the bias of culture-based identification. These studies suggest that the habitat range and evolutionary diversity of this key functional group of organisms is greater than now appreciated.

ATP-dependent Proteases Differ Substantially in Their Ability to Unfold Globular Proteins

ATP-dependent proteases control the concentrations of hundreds of regulatory proteins and remove damaged or misfolded proteins from cells. They select their substrates primarily by recognizing sequence motifs or covalent modifications. Once a substrate is bound to the protease, it has to be unfolded and translocated into the proteolytic chamber to be degraded. Some proteases appear to be promiscuous, degrading substrates with poorly defined targeting signals, which suggests that selectivity may be controlled at additional levels. Here we compare the abilities of representatives from all classes of ATP-dependent proteases to unfold a model substrate protein and find that the unfolding abilities range over more than 2 orders of magnitude. We propose that these differences in unfolding abilities contribute to the fates of substrate proteins and may act as a further layer of selectivity during protein destruction.

Linkage of high rates of sulfate reduction in Yellowstone hot springs to unique sequence types in the dissimilatory sulfate respiration pathway.

ABSTRACT Diversity, habitat range, and activities of sulfate-reducing prokaryotes within hot springs in Yellowstone National Park were characterized using endogenous activity measurements, molecular characterization, and enrichment. Five major phylogenetic groups were identified using PCR amplification of the dissimilatory sulfite reductase genes (dsrAB) from springs demonstrating significant sulfate reduction rates, including a warm, acidic (pH 2.5) stream and several nearly neutral hot springs with temperatures reaching 89°C. Three of these sequence groups were unrelated to named lineages, suggesting that the diversity and habitat range of sulfate-reducing prokaryotes exceeds that now represented in culture.

Rad23 escapes degradation because it lacks a proteasome initiation region

Rad23 is an adaptor protein that binds to both ubiquitinated substrates and to the proteasome. Despite its association with the proteasome, Rad23 escapes degradation. Here we show that Rad23 remains stable because it lacks an effective initiation region where the proteasome can engage the protein and unfold it. Rad23 contains several internal, unstructured loops but these are too short to act as initiation regions. Experiments with model proteins show that internal loops must be surprisingly long to engage the proteasome and support degradation. These length requirements are not specific to Rad23 and reflect a general property of the proteasome.

Natural attenuation of chlorinated solvents at Area 6, Dover Air Force Base: characterization of microbial community structure.

A polyphasic approach based on cultivation and direct recovery of 16S rRNA gene sequences was utilized for microbial characterization of an aquifer contaminated with chlorinated ethenes. This work was conducted in order to support the evaluation of natural attenuation of chlorinated ethenes in groundwater at Area 6 at Dover Air Force Base (Dover, DE). Results from these studies demonstrated the aquifer contained relatively low biomass (e.g. direct microscopic counts of < 10(7) bacteria/g of sediment) comprised of a physiologically diverse group of microorganisms including iron reducers, acetogens, sulfate reducers, denitrifiers, aerobic and anaerobic heterotrophs. Laboratory microcosms prepared with authentic sediment and groundwater provided direct microbiological evidence that the mineralization of vinyl chloride and cis-dichloroethene as well as each step in the complete reductive dechlorination of tetracloroethene to ethene can occur in the Area 6 aquifer. Enrichment cultures capable of the oxidative degradation of cis-1,2-dichloroethene (cis-DCE) and vinyl chloride (VC) were obtained from groundwater across the aquifer demonstrating the possible importance of direct, non-cometabolic oxidation of cis-DCE and VC in natural attenuation. Culture-independent analyses based upon recovery of 16S rRNA gene sequences revealed the presence of anaerobic organisms distributed primarily between two major bacterial divisions: the delta subdivision of the Proteobacteria and low-G + C gram positive. Recovery of sequences affiliated with phylogenetic groups containing known anaerobic-halorespiring organisms such as Desulfitobacterium, Dehalobacter, and certain groups of iron reducers provided qualitative support for a role of reductive dechlorination processes in the aquifer. This molecular data is suggestive of a functional linkage between the microbiology of the site and the apparent natural attenuation process. The presence and distribution of microorganisms were found to be consistent with a microbially driven attenuation of chlorinated ethenes within the aquifer and in accord with a conceptual model of aquifer geochemistry which suggest that both reductive and oxidative mechanisms are involved in heterogeneous, spatially distributed processes across the aquifer.

Sequence composition of disordered regions fine-tunes protein half-life

The proteasome controls the concentrations of most proteins in eukaryotic cells. It recognizes its protein substrates through ubiquitin tags and initiates degradation at disordered regions within the substrate. Here we show that the proteasome has pronounced preferences for the amino acid sequence of the regions at which it initiates degradation. Specifically, proteins in which the initiation regions have biased amino acid compositions show longer half-lives in yeast than proteins with unbiased sequences in the regions. The relationship is also observed on a genomic scale in mouse cells. These preferences affect the degradation rates of proteins in vitro, can explain the unexpected stability of natural proteins in yeast and may affect the accumulation of toxic proteins in disease. We propose that the proteasomes sequence preferences provide a second component to the degradation code and may fine-tune protein half-life in cells.

High Rates of Sulfate Reduction in a Low-Sulfate Hot Spring Microbial Mat Are Driven by a Low Level of Diversity of Sulfate-Respiring Microorganisms

ABSTRACT The importance of sulfate respiration in the microbial mat found in the low-sulfate thermal outflow of Mushroom Spring in Yellowstone National Park was evaluated using a combination of molecular, microelectrode, and radiotracer studies. Despite very low sulfate concentrations, this mat community was shown to sustain a highly active sulfur cycle. The highest rates of sulfate respiration were measured close to the surface of the mat late in the day when photosynthetic oxygen production ceased and were associated with a Thermodesulfovibrio-like population. Reduced activity at greater depths was correlated with novel populations of sulfate-reducing microorganisms, unrelated to characterized species, and most likely due to both sulfate and carbon limitation.

Phylogenetic and narG Analysis of a Hyphomicrobium Isolate

Abstract. An obligately methylotrophic organism was isolated from a water well that manifested symptoms of biofouling. The isolate was appendaged and utilized methylamine, dimethylamine, trimethylamine, or methanol as the sole carbon and energy source. The isolate exhibited hydroxypyruvate reductase activity, suggesting C1-assimilation via the serine pathway. Fatty acid profiling indicated the predominance of 18:1 cis-fatty acids. The isolate did not grow anaerobically with nitrate as the final electron acceptor. Genomic DNA from the isolate did not hybridize against the narG gene, which encodes the alpha subunit of dissimilatory nitrate reductase in Escherichia coli. The phenotypic data suggested the assignment of the isolate to the genus Hyphomicrobium. The identification was supported by phylogenetic characterization based on 16S rRNA sequence comparisons of the isolate.