J. Thomas Beatty

The purple phototrophic bacteria

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Gene transfer agents: phage-like elements of genetic exchange.

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The Complete Genome Sequence of Roseobacter denitrificans Reveals a Mixotrophic Rather than Photosynthetic Metabolism

Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cells genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.

Long-Chain Acyl-Homoserine Lactone Quorum-Sensing Regulation of Rhodobacter capsulatus Gene Transfer Agent Production

Purple aerobic anoxygenic phototrophs (AAPs) are the only organisms known to capture light energy to enhance growth only in the presence of oxygen but do not produce oxygen. The highly adaptive AAPs compose more than 10% of the microbial community in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas CO2. We present the complete genomic sequence and feature analysis of the AAP Roseobacter denitrificans, which reveal clues to its physiology. The genome lacks genes that code for known photosynthetic carbon fixation pathways, and most notably missing are genes for the Calvin cycle enzymes ribulose bisphosphate carboxylase (RuBisCO) and phosphoribulokinase. Phylogenetic evidence implies that this absence could be due to a gene loss from a RuBisCO-containing alpha-proteobacterial ancestor. We describe the potential importance of mixotrophic rather than autotrophic CO2 fixation pathways in these organisms and suggest that these pathways function to fix CO2 for the formation of cellular components but do not permit autotrophic growth. While some genes that code for the redox-dependent regulation of photosynthetic machinery are present, many light sensors and transcriptional regulatory motifs found in purple photosynthetic bacteria are absent.

Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments

Many proteobacteria use acyl-homoserine lactones as quorum-sensing signals. Traditionally, biological detection systems have been used to identify bacteria that produce acyl-homoserine lactones, although the specificities of these detection systems can limit discovery. We used a sensitive approach that did not require a bioassay to detect production of long-acyl-chain homoserine lactone production by Rhodobacter capsulatus and Paracoccus denitrificans. These long-chain acyl-homoserine lactones are not readily detected by standard bioassays. The most abundant acyl-homoserine lactone was N-hexadecanoyl-homoserine lactone. The long-chain acyl-homoserine lactones were concentrated in cells but were also found in the culture fluid. An R. capsulatus gene responsible for long-chain acyl-homoserine lactone synthesis was identified. A mutation in this gene, which we named gtaI, resulted in decreased production of the R. capsulatus gene transfer agent, and gene transfer agent production was restored by exogenous addition of N-hexadecanoyl-homoserine lactone. Thus, long-chain acyl-homoserine lactones serve as quorum-sensing signals to enhance genetic exchange in R. capsulatus.

Generation of succinyl-coenzyme A in photosynthetic bacteria

The bacterial genus Rhodopseudomonas is comprised of photosynthetic bacteria found widely distributed in aquatic sediments. Members of the genus catalyze hydrogen gas production, carbon dioxide sequestration, and biomass turnover. The genome sequence of Rhodopseudomonas palustris CGA009 revealed a surprising richness of metabolic versatility that would seem to explain its ability to live in a heterogeneous environment like sediment. However, there is considerable genotypic diversity among Rhodopseudomonas isolates. Here we report the complete genome sequences of four additional members of the genus isolated from a restricted geographical area. The sequences confirm that the isolates belong to a coherent taxonomic unit, but they also have significant differences. Whole genome alignments show that the circular chromosomes of the isolates consist of a collinear backbone with a moderate number of genomic rearrangements that impact local gene order and orientation. There are 3,319 genes, 70% of the genes in each genome, shared by four or more strains. Between 10% and 18% of the genes in each genome are strain specific. Some of these genes suggest specialized physiological traits, which we verified experimentally, that include expanded light harvesting, oxygen respiration, and nitrogen fixation capabilities, as well as anaerobic fermentation. Strain-specific adaptations include traits that may be useful in bioenergy applications. This work suggests that against a backdrop of metabolic versatility that is a defining characteristic of Rhodopseudomonas, different ecotypes have evolved to take advantage of physical and chemical conditions in sediment microenvironments that are too small for human observation.

Pleiotropic effects of pufX gene deletion on the structure and function of the photosynthetic apparatus of Rhodobacter capsulatus

Pathways of succinyl-Coenzyme A (succinyl-CoA) formation in various photosynthetic bacteria were investigated through several approaches, including determination of activity levels of relevant enzymes. Extracts of photosynthetically grown cells of representative Rhodospirillaceae and Chromatium vinosum showed α-ketoglutarate dehydrogenase (KGD) activities sufficient to account for generation of the succinyl-CoA required for biosynthetic metabolism. Except as noted below, the observed ratios of fumarate reductase/succinate dehydrogenase activities were low, consistent with the conclusion that these organisms produce succinyl-CoA oxidatively from α-ketoglutarate (KG), rather than by reductive metabolism of fumarate. On the other hand, the green bacterium Chlorobium limicola appears to produce succinyl-CoA by the reductive pathway; in this organism, KGD activity could not be detected, and a high fumarate reductase/succinate dehydrogenase ratio was observed. Results obtained with Rhodopseudomonas gelatinosa suggest that this otherwise typical member of the Rhodospirillaceae may be able to generate succinyl-CoA via both “arms” of the citric acid cycle, that is, oxidatively from KG, and reductively from fumarate. To further explore the several physiological roles of the conversion: KG→succinyl-CoA in Rhodopseudomonas capsulata, a mutant (strain KGD 11) almost completely blocked in KGD activity was isolated and studied in detail. Under anaerobic photosynthetic conditions, KGD 11 grows readily on succinate as the sole carbon source; in contrast to the wild type parent, however, it cannot grow with l-glutamate as the source of carbon. The R. capsulata parental strain can grow in darkness as an aerobic heterotroph on various carbon/energy sources including pyruvate, D,L-malate, or succinate. Mutant KGD 11, however, is unable to grow aerobically on the substrates noted. These results indicate that the energy for aerobic dark growth of R. capsulata is provided by ”respiratory phosphorylation” fueled by citric acid cycle function, and that this requires a substantial level of KGD activity. The present findings also indicate that citric acid cycle sequences in most of the Rhodospirillaceae prominently used in current research are geared to operate in the oxidative direction, as in nonphotosynthetic aerobic heterotrophs.

Isolation of Tellurite- and Selenite-Resistant Bacteria from Hydrothermal Vents of the Juan de Fuca Ridge in the Pacific Ocean

By deletion of the pufX gene of Rhodobacter capsulatus from a plasmid carrying the puf operon and complementation of a chromosomal puf operon deletion, we created pufX mutants and used them to characterize possible functions of the pufX gene product. The pufX mutants were incapable of photosynthetic growth in a minimal medium, or in a rich medium at low light intensities, although second-site mutations suppressed this phenotype. Measurements made in vitro with intact and solubilized chromatophore preparations indicated that the individual complexes of the photosynthetic unit seemed to function normally, but electron transfer from the reaction center to the cytochrome b/c1 complex was impaired. The structures of the photosynthetic apparatus of pseudo-wild type and mutant strains were evaluated using absorption spectroscopy and electron microscopy. The pufX mutants had intracytoplasmic membrane invaginations about 50% larger in diameter than those of the pseudo-wild type and higher levels of B870 light-harvesting complex. It is concluded that the PufX protein plays an important role in the structure of the functional photosynthetic unit, and its absence results in loss of efficient electron transfer from the QB site of the reaction center to the Qz site of the cytochrome b/c1 complex.

On the natural selection and evolution of the aerobic phototrophic bacteria

ABSTRACT Deep-ocean hydrothermal-vent environments are rich in heavy metals and metalloids and present excellent sites for the isolation of metal-resistant microorganisms. Both metalloid-oxide-resistant and metalloid-oxide-reducing bacteria were found. Tellurite- and selenite-reducing strains were isolated in high numbers from ocean water near hydrothermal vents, bacterial films, and sulfide-rich rocks. Growth of these isolates in media containing K2TeO3 or Na2SeO3 resulted in the accumulation of metallic tellurium or selenium. The MIC of K2TeO3 ranged from 1,500 to greater than 2,500 μg/ml, and the MIC of Na2SeO3 ranged from 6,000 to greater than 7,000 μg/ml for 10 strains. Phylogenetic analysis of 4 of these 10 strains revealed that they form a branch closely related to members of the genus Pseudoalteromonas, within the γ-3 subclass of the Proteobacteria. All 10 strains were found to be salt tolerant, pH tolerant, and thermotolerant. The metalloid resistance and morphological, physiological, and phylogenetic characteristics of newly isolated strains are described.

The gene transfer agent of Rhodobacter capsulatus and "constitutive transduction" in prokaryotes.

This contribution gives a brief survey of the short history since the discovery of the aerobic phototrophic bacteria to focus on a general evolutionary scenario. Most of the citations are of reviews that have covered the earlier literature and to which the reader is directed at appropriate places in the following text. The data summarized in these reviews are supplemented with information from recent or otherwise key primary publications in order to support a synthesis that addresses vexing questions about bacteria containing photosynthetic pigment-protein complexes, but which are incapable of growth with light as the sole, or even the major source of energy.