Kenji V. P. Nagashima

HORIZONTAL TRANSFER OF GENES CODING FOR THE PHOTOSYNTHETIC REACTION CENTERS OF PURPLE BACTERIA

Phylogenetic trees were drawn and analyzed based on the nucleotide sequences of the 1.5-kb gene fragment coding for the L and M subunits of the photochemical reaction center of various purple photo-synthetic bacteria. These trees are mostly consistent with phylogenetic trees based on 16S rRNA and soluble cy-tochrome c, but differ in some significant details. This inconsistency implies horizontal transfer of the genes that code for the photosynthetic apparatus in purple bacteria. Possibilities of similar transfers of photosynthesis genes during the evolution of photosynthesis are discussed especially for the establishment of oxygenic photosynthesis.

Horizontal Transfer of the Photosynthesis Gene Cluster and Operon Rearrangement in Purple Bacteria

Abstract. A 37-kb photosynthesis gene cluster was sequenced in a photosynthetic bacterium belonging to the β subclass of purple bacteria (Proteobacteria), Rubrivivax gelatinosus. The cluster contained 12 bacteriochlorophyll biosynthesis genes (bch), 7 carotenoid biosynthesis genes (crt), structural genes for photosynthetic apparatuses (puf and puh), and some other related genes. The gene arrangement was markedly different from those of other purple photosynthetic bacteria, while two superoperonal structures, crtEF–bchCXYZ–puf and bchFNBHLM–lhaA–puhA, were conserved. Molecular phylogenetic analyses of these photosynthesis genes showed that the photosynthesis gene cluster of Rvi. gelatinosus was originated from those of the species belonging to the α subclass of purple bacteria. It was concluded that a horizontal transfer of the photosynthesis gene cluster from an ancestral species belonging to the α subclass to that of the β subclass of purple bacteria had occurred and was followed by rearrangements of the operons in this cluster.

Phylogeny and photosynthetic features of Thiobacillus acidophilus and related acidophilic bacteria : its transfer to the genus Acidiphilium as Acidiphilium acidophilum comb. nov

Phylogenetic analyses based on 16S rDNA sequences and genomic DNA-DNA relatedness showed that the sulphur-oxidizing facultative chemolithotroph Thiobacillus acidophilus was closely related to members of the genus Acidiphilium, which is a group of strictly aerobic, heterotrophic acidophiles now categorized into aerobic photosynthetic bacteria. Lipophilic pigment analyses revealed that zinc-chelated bacteriochlorophyll a and carotenoids occurred in appreciable amounts in T. acidophilus and all established species of the genus Acidiphilium. PCR experiments showed that T. acidophilus as well as Acidiphilium species contained puf genes, encoding the photosynthetic reaction centre proteins and the core light-harvesting complex of the purple bacteria. There were high similarities between T. acidophilus and Acidiphilium species in the primary structure of their reaction centre proteins deduced from the nucleotide sequence data. The phylogenetic tree of the reaction centre proteins was in agreement with the 16S rDNA sequence-based phylogenetic tree in the relationship between T. acidophilus and Acidiphilium species and between the Acidiphilium cluster and other purple photosynthetic bacteria. Based on these results, together with previous phylogenetic and phenotypic information, it is proposed to reclassify T. acidophilus (Guay and Silver) Harrison 1983 as Acidiphilium acidophilum comb. nov. The type strain is ATCC 27807T (= DSM 700T).

Porphyrobacter tepidarius sp. nov., a moderately thermophilic aerobic photosynthetic bacterium isolated from a hot spring.

A new thermophilic bacterium, strain OT3T (T = type strain), was isolated from a brackish hot spring. Strain OT3T is an obligate aerobe that synthesizes bacteriochlorophyll a and has a photosynthetic apparatus. This isolate is a thermophilic bacterium with an optimal growth temperature of 40 to 48 degrees C. The cells are nonmotile, ovoid to short rods. An analysis of 16S rRNA sequences revealed that the new strain forms a coherent cluster with members of the alpha-4 group of the alpha subclass of the Proteobacteria, which contains the genera Erythrobacter, Erythromicrobium, and Porphyrobacter. The closest relative is Porphyrobacter neustonensis, with a 16S rRNA sequence similarity of 96.8%. The in vivo absorption spectrum has maxima at 460, 494, 596, 800, and 870 nm. The main carotenoids are OH-beta-carotene sulfate derivatives, nostoxanthin, and bacteriorubixanthinal. Growth occurs with glucose, acetate, glutamate, butyrate, Casamino Acids, and yeast extract as sole energy sources. The pigment composition and nutritional profile of the new isolate are similar to the pigment composition and nutritional profile of P. neustonensis. Although there are marked differences in cell morphology between the new isolate and the budding bacterium P. neustonensis, the results of phenotypic and genetic comparisons suggest that the new isolate is closely related to P. neustonensis. Consequently, we assign the new isolate to the genus Porphyrobacter and propose the name Porphyrobacter tepidarius sp. nov. for it; the type strain of P. tepidarius is strain OT3 (= DSM 10595).

Photocurrent and electronic activities of oriented-His-tagged photosynthetic light-harvesting/reaction center core complexes assembled onto a gold electrode.

A polyhistidine (His) tag was fused to the C- or N-terminus of the light-harvesting (LH1)-α chain of the photosynthetic antenna core complex (LH1-RC) from Rhodobacter sphaeroides to allow immobilization of the complex on a solid substrate with defined orientation. His-tagged LH1-RCs were adsorbed onto a gold electrode modified with Ni-NTA. The LH1-RC with the C-terminal His-tag (C-His LH1-RC) on the modified electrode produced a photovoltaic response upon illumination. Electron transfer is unidirectional within the RC and starts when the bacteriochlorophyll a dimer in the RC is activated by light absorbed by LH1. The LH1-RC with the N-terminal His-tag (N-His LH1-RC) produced very little or no photocurrent upon illumination at any wavelength. The conductivity of the His-tagged LH1-RC was measured with point-contact current imaging atomic force microscopy, indicating that 60% of the C-His LH1-RC are correctly oriented (N-His 63%). The oriented C-His LH1-RC or N-His LH1-RC showed semiconductive behavior, that is, had the opposite orientation. These results indicate that the His-tag successfully controlled the orientation of the RC on the solid substrate, and that the RC produced photocurrent depending upon the orientation on the electrode.

Photosynthetic Apparatus in Roseateles depolymerans 61A Is Transcriptionally Induced by Carbon Limitation

ABSTRACT Production of a photosynthetic apparatus in Roseateles depolymerans 61A, a recently discovered freshwater β-Proteobacterium showing characteristics of aerobic phototrophic bacteria, was observed when the cells were subjected to a sudden decrease in carbon sources (e.g., when cells grown with 0.1 to 0.4% Casamino Acids were diluted or transferred into medium containing ≤0.04% Casamino Acids). Accumulation of bacteriochlorophyll (BChl) a was observed in the presence of oxygen and was enhanced under semiaerobic conditions (2% oxygen) but was reduced in the presence of light. Similarly to what has been reported regarding some aerobic phototrophic bacteria belonging to the α subclass of the Proteobacteria, viability of the cells in the carbon source-free medium was prolonged under aerobic-light (10 W m−2) conditions, possibly due to photosynthetic energy conversion, but was not prolonged under aerobic-dark conditions. The puf operon, which encodes most of the apoproteins of light-harvesting and reaction center complexes, was sequenced, and the effect of changes in Casamino Acids concentrations, oxygen, and light on its expression was estimated by the accumulation of its mRNA. The expression of the puf operon was induced by the decrease in carbon sources, similarly to what was observed for the accumulation of BChl a under aerobic and semiaerobic conditions (≥0.2% O2), and was reduced in the presence of light. Transcription of the R. depolymerans puf operon is considered to be controlled by changes in carbon nutrients in addition to oxygen tension and light intensity.

Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs.

Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.

A New Cytochrome Subunit Bound to the Photosynthetic Reaction Center in the Purple Bacterium, Rhodovulum sulfidophilum

The nucleotide sequence of the pufoperon, which contains the genes encoding the B870 light-harvesting protein and the reaction center complex of the purple photosynthetic bacterium, Rhodovulum sulfidophilum, was determined. The operon, which consisted of six genes, pufQ,pufB, pufA, pufL, pufM, and pufC, is a new variety in photosynthetic bacteria in the sense thatpufQ and pufC coexist. The amino acid sequence of the cytochrome subunit of the reaction center deduced from thepufC sequence revealed that this cytochrome contains only three possible heme-binding motifs; the heme-1-binding motif of the corresponding tetraheme cytochrome subunits was not present. This is the first exception of the “tetraheme” cytochrome family in purple bacteria and green filamentous bacteria. The pufC sequence also revealed that the sixth axial ligands to heme-1 and heme-2 irons were not present in the cytochrome either. This cytochrome was actually detected in membrane preparation as a 43-kDa protein and shown to associate functionally with the photosynthetic reaction center as the immediate electron donor to the photo-oxidized special pair of bacteriochlorophyll. This new cytochrome should be useful for studies on the role of each heme in the cytochrome subunit of the bacterial reaction center and the evolution of proteins in photosynthetic electron transfer systems.

Complete Genome Sequence of Phototrophic Betaproteobacterium Rubrivivax gelatinosus IL144

Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in freshwater ponds, sewage ditches, activated sludge, and food processing wastewater. There have not been many studies on photosynthetic betaproteobacteria. Here we announce the complete genome sequence of the best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC 100245).

Phylogenetic analysis of photosynthetic genes of Rhodocyclus gelatinosus: Possibility of horizontal gene transfer in purple bacteria.

Nucleotide sequences of the genes coding for the M and cytochrome subunits of the photosynthetic reaction center of Rhodocyclus gelatinosus, a purple bacterium in the β subdivision, were determined. The deduced amino acid sequences of these proteins were compared with those of other photosynthetic bacteria. Based on the homology of these two photosynthetic proteins, Rc. gelatinosus was placed in the α subdivision of purple bacteria, which disagrees with the phylogenetic trees based on 16S rRNA and soluble cytochrome c2. Horizontal transfer of the genes which code for the photosynthetic apparatus in purple bacteria can be postulated if the phylogenetic trees based on 16S rRNA and soluble cytochrome c2 reflect the real history of purple bacteria.