Ultrastructure of the Acidophilic Aerobic Photosynthetic Bacterium Acidiphilium rubrum

The ultrastructure of cells of Acidiphilium rubrum, which is an acidophilic aerobic photosynthetic bacterium containing zinc-complexed bacteriochlorophyll a, was studied by electron microscopy with the rapid substitution technique. Thin-section electron microscopy indicated that any type of internal photosynthetic membranes was not present in this organism despite a relatively high content of the photopigment. The majority of cells had poly-β-hydroxybutyrate granules and electron-dense spherical bodies identified as being polyphosphate granules. When the organism was grown chemotrophically with 0.1% FeSO₄, it produced another group of electron-dense granules that were associated with the inner part of the cytoplasmic membrane. An energy-dispersive X-ray analysis showed that these membrane-bound, electron-dense granules contained iron. Received: 24 November 1999 / Accepted: 5 January 2000     

Exchange and Complementation of Genes Coding for Photosynthetic Reaction Center Core Subunits among Purple Bacteria

A mutant of the phototrophic species belonging to the β-proteobacteria, Rubrivivax gelatinosus, lacking the photosynthetic growth ability was constructed by the removal of genes coding for the L, M, and cytochrome subunits of the photosynthetic reaction center complex. The L, M, and cytochrome genes derived from five other species of proteobacteria, Acidiphilium rubrum, Allochromatium vinosum, Blastochloris viridis, Pheospirillum molischianum, and Roseateles depolymerans, and the L and M subunits from two other species, Rhodobacter sphaeroides and Rhodopseudomonas palustris, respectively, have been introduced into this mutant. Introduction of the genes from three of these seven species, Rte. depolymerans, Ach. vinosum, and Psp. molischianum, restored the photosynthetic growth ability of the mutant of Rvi. gelatinosus, although the growth rates were 1.5, 9.4, and 10.7 times slower, respectively, than that of the parent strain. Flash-induced kinetic measurements for the intact cells of these three mutants showed that the photo-oxidized cytochrome c bound to the introduced reaction center complex could be rereduced by electron donor proteins of Rvi. gelatinosus with a t_1/2 of less than 10 ms. The reaction center core subunits of photosynthetic proteobacteria appear to be exchangeable if the sequence identities of the LM core subunits between donor and acceptor species are high enough, i.e., 70 % or more.     

异养硝化-好氧反硝化菌脱氮相关酶系及其编码基因的研究进展

水体氮素污染日益严重,如何经济、高效地去除水体氮素已成为研究热点。近年来,研究人员已从不同环境中分离到许多同时具有异养硝化和好氧反硝化功能的菌株,此类菌生长迅速,可在好氧条件下同时实现硝化和反硝化的过程,并可用于脱除有机污染物,是一类应用潜力巨大的脱氮菌。目前,异养硝化-好氧反硝化菌的脱氮途径和机制主要是通过测定氮循环中间产物或终产物、测定相关酶活性、注释部分氮循环相关基因及参考自养硝化菌和缺氧反硝化菌的氮循环途径等进行研究,其完整的氮素转化途径和氮代谢机制还需要进一步明确。总结了目前异养硝化-好养反硝化菌的脱氮相关酶系及其编码基因的研究进展,以期为异养硝化-好氧反硝化菌的理论研究及其在污水脱氮处理上的应用提供参考。     

Photosynthetic Unit Organization in a Red Alga : Relationships between Light-Harvesting Pigments and Reaction Centers

The relative concentration of biliproteins, phycobilisomes, chlorophyll a, and reaction centers I and II are reported for Neoagardhiella bailyei, a macrophytic red alga collected in the field and compared with Anacystis nidulans, a cyanobacterium cultured in the laboratory. The ratios of chlorophyll to reaction center I, of chlorophyll to reaction center II, and the mass of phycobiliprotein per reaction center II are quite similar in Neoagardhiella and Anacystis, supporting the concept that the red algal chloroplast is derived from a cyanobacterial progenitor. The ratios of reaction center I to reaction center II are about 2.3 in both species. The Anacystis phycobilisome has about 40% of the mass of the Neoagardhiella phycobilisome, 4.9 and 14.9 × 10⁶ daltons, respectively. The reaction center II/phycobilisome ratio is about 1.7 in Anacystis and 4.1 in Neoagardhiella. Phycobilisome size and physical restrictions on phycobilisome packing may be a major constraint on the reaction center II-phycobilisome association and the assembly of the photosynthetic membrane in both the red algae and cyanobacteria.     

A Study of Nucleotide Sequences of nifH Genes of Some Methanotrophic Bacteria

Using a previously developed primer system, nifH gene fragments 450 nucleotides long were amplified, cloned, and sequenced for representatives of nitrogen-fixing methanotrophic bacteria of the genera Methylococcus, Methylocystis, and Methylosinus. Fragments of nifH genes were also detected and sequenced in representatives of the genera Methylomonas and Methylobacter, which were not considered diazotrophs until recently. Phylogenetic analysis revealed the remoteness of nifH gene sequences of methanotroph types I and II. At the same time, a close relationship was found between nifH of type I methanotrophs and representatives of -proteobacteria and between nifH genes of type II methanotrophs and representatives of -proteobacteria. The results obtained in this study are in good accordance with the data of phylogenetic analysis based on 16S rRNA sequence comparison with the only exception being Methylococcus capsulatus strains, whose nifH genes proved to be closely related to nifH genes of Methylocystis and Methylosinus representatives. Our findings extend the database of primary sequences of nifH genes and allow the contribution of methanotrophs to the process of nitrogen fixation to be estimated.     

Accumulation of Fe, Cr and Ni Metals inside Cells of Acidophilic Bacterium Acidiphilium rubrum that Produces Zn-Containing Bacteriochlorophyll a

The accumulations of metals were studied in cells of aerobicacidophilic proteobacterium Acidiphilium rubrum; this spicesuses Zn, instead of Mg as the central atom of bacteriochlorophyllin its photosynthetic apparatus. Energy dispersive X-ray analysis(EDX) of the cell surfaces gave peaks of P, S, Si and Mg. Transmissionelectron micrograph images showed a high density globule of0.11µm in diameter in each 1.1 x 0.3µm cell. AnEDX analysis of the black precipitate that was collected afterthe centrifuga-tion of disrupted cells showed high amounts ofthe heavy metals Fe, Cr, Ni and traces of K, Ca, P, Si and Alin the order of atomic content. An X-ray powder diffractionanalysis indicated that Fe, Cr and Ni exist as alloys. The metalaccumulations interpret the high tolerance of this bacteriumto the toxic heavy metals abundant in acidic growth medium.Zn seems to specifically exist as Zn-bacteriochlo-rophyll ain this organism, because no significant accumulation of Znwas detected on the cell surface, black precipitate, or cytoplasmicmembranes. (Received December 26, 1997; Accepted April 21, 1998)     

浑球红细菌谷氨酰胺合成酶基因(glnA)及PⅡ蛋白基因(glnB)的序列分析

测定了浑球红细菌的glnA和／glnB基因DNA序列,共2707nt。其中glnA基因编码区为1401nt,编码467个氨基酸;glnB基因编码区为336nt,编码112个氨基醚。DNA序列的G＋C百分含量为65％,它们的密码子第三位GC利用率高达89．1％。在氨基酸序列上,GS酶和PⅡ蛋白与其它不同属的细菌间有较好的同源性,尤其是固氮类细菌间同源性较高。     

Chlorophyll Chemistry Before and After Crystals of Photosynthetic Reaction Centers

The experimental, theoretical and structural research leading to the identification and characterization of the (bacterio) chlorophyll species that mediate the primary events of solar energy transduction and dynamics is reviewed and examined from the author's perspective.     

NMR of Redox Proteins of Plants, Yeasts and Photosynthetic Bacteria

NMR spectroscopy has evolved dramatically over the past 15 years, establishing a new, reliable methodology for studying biomacromolecules at atomic resolution. The three-dimensional structure and dynamics of a biomolecule or a biomolecular complex is only one of the main types of information available using NMR. The spectral assignment to the specific nuclei of a biostructure is a very precise reflection of their electronic environment. Any change in this environment due to a structural change, the binding of a ligand or the redox state of a redox cofactor, will be very sensitively reported by changes in the different NMR parameters. The capabilities of the NMR method are currently expanding dramatically and it is turning into a powerful means to study biosystems dynamically in exchange between different conformations, exchanging ligands, transient complexes, or the activation/inhibition of regulated enzymes. We review here several NMR studies that have appeared during the past 5 or 6 years in the field of redox proteins of plants, yeasts and photosynthetic bacteria. These new results illustrate the recent biomolecular NMR evolution and provide new physiological models for understanding the different types of electron transfer, including glutaredoxins, thioredoxins and their dependent enzymes, the ferredoxin-NADP oxidoreductase complex, flavodoxins, the plastocyanin-cytochrome f complex, and cytochromes c.     

Using Triplet Periodicity of Nucleotide Sequences for Finding Potential Reading Frame Shifts in Genes

We introduce a novel approach for the detection of possible mutations leading to a reading frame (RF) shift in a gene. Deletions and insertions of DNA coding regions are considerable events for genes because an RF shift results in modifications of the extensive region of amino acid sequence coded by a gene. The suggested method is based on the phenomenon of triplet periodicity (TP) in coding regions of genes and its relative resistance to substitutions in DNA sequence. We attempted to extend 326 933 regions of continuous TP found in genes from the KEGG databank by considering possible insertions and deletions. We revealed totally 824 genes where such extension was possible and statistically significant. Then we generated amino acid sequences according to active (KEGG''s) and hypothetically ancient RFs in order to find confirmation of a shift at a protein level. Consequently, 64 sequences have protein similarities only for ancient RF, 176 only for active RF, 3 for both and 581 have no protein similarity at all. We aimed to have revealed lower bound for the number of genes in which a shift between RF and TP is possible. Further ways to increase the number of revealed RF shifts are discussed.     

Nucleotide Sequences of Genes Encoding Allosamidin-sensitive and -insensitive Chitinases Produced by Allosamidin-producing Streptomyces

Allosamidin is a strong inhibitor of family 18 chitinases. We previously reported the presence of allosamidin-sensitive and -insensitive chitinases (chitinase S and IS) in the culture filtrate of the allosamidin-producing strain, Streptomyces sp. AJ9463. In this study, we cloned and sequenced the genes encoding the two chitinases, which clarified that chitinase S and IS belong to the family 18 and 19 chitinase, respectively.     

Amino Acid Composition and Terminal Sequences of Ferredoxins from Two Photosynthetic Green Bacteria

The amino acid composition of ferredoxins from Chlorobium thiosulfatophilum 8327 and Chloropseudomonas ethylicum, like C. thiosulfatophilum Tassajara, resembled ferredoxins from nonphotosynthetic anaerobes rather than Chromatium; the terminal sequences, however, more closely resembled Chromatium ferredoxin.     

Rapid Evolution of the Sequences and Gene Repertoires of Secreted Proteins in Bacteria

Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.     

The Construction,Cloning, and Expression of Synthetic Genes Coding for Totally Artificial Proteins

Abstract

A series of genes was generated from three interchangeable cassettes, each coding for a specific set of amino acids. The genes were inserted into two different fusion expression vectors and two direct expression vectors. The expression studies demonstrated that proteolytic stability of the proteins is affected by the N-terminal region of the protein.