DNA repair mutants of Rhodobacter sphaeroides.

The genome of the photosynthetic eubacterium Rhodobacter sphaeroides 2.4.1 comprises two chromosomes and five endogenous plasmids and has a 65% G+C base composition. Because of these characteristics of genome architecture, as well as the physiological advantages that allow this organism to live in sunlight when in an anaerobic environment, the sensitivity of R. sphaeroides to UV radiation was compared with that of the more extensively studied bacterium Escherichia coli. R. sphaeroides was found to be more resistant, being killed at about 60% of the rate of E. coli. To begin to analyze the basis for this increased resistance, a derivative of R. sphaeroides, strain 2.4.1 delta S, which lacks the 42-kb plasmid, was mutagenized with a derivative of Tn5, and the transposon insertion mutants were screened for increased UV sensitivity (UVs). Eight UVs strains were isolated, and the insertion sites were determined by contour-clamped homogeneous electric field pulsed-field gel electrophoresis. These mapped to at least five different locations in chromosome I. Preliminary analysis suggested that these mutants were deficient in the repair of DNA damage. This was confirmed for three loci by DNA sequence analysis, which showed the insertions to be within genes homologous to uvrA, uvrB, and uvrC, the subunits of the nuclease responsible for excising UV damage.     

Phenotypic and genetic characterization of cytochrome c2 deficient mutants of Rhodobacter sphaeroides

Rhodobacter sphaeroides mutants lacking cytochrome c2 (cyt c2) have been constructed by site-specific recombination between the wild-type genomic cyt c2 structural gene (cycA) and a suicide plasmid containing a defective cyc operon where deletion of cycA sequences was accompanied by insertion of a KnR gene. Southern blot analysis confirmed that the wild-type cyc operon was exchanged for the inactivated cycA gene, presumably by double-reciprocal recombination. Spectroscopic and immunochemical measurements, together with genetic complementation, established that the inability of these mutants to grow under photosynthetic conditions was due to the lack of cyt c2. The cyt c2 deficient strains reduced photooxidized reaction center complexes approximately 4 orders of magnitude more slowly than the parent strain. The phenotype and characteristics of these mutants were restored when a wild-type cyc operon was introduced on a stable low copy number plasmid. These experiments provide the first genetic evidence for the obligatory role of cyt c2 in wild-type cyclic photosynthetic electron transport in R. sphaeroides. We have also observed that the R. sphaeroides cyt c2 deficient strains spontaneously gave rise to photosynthetically competent pseudorevertants at a frequency which suggests that the cyt c2 independent photosynthetic electron transport which suppresses the phenotype of the cyt c2 deficient strains was the result of a single mutation elsewhere in the genome.     

Isolation of the replication region of an indigenous plasmid of Rhodobacter sphaeroides

Abstract The isolation of the replication region of an indigenous plasmid of 42 kb of the phototrophic bacterium Rhodobacter sphaeroides is described. This plasmid was digested with the Bgl II restriction enzyme, ligated to the 2.7 Bgl II fragment of transposon Tn 10 , which contains the tet genes conferring tetracycline resistance, and the mixture was transformed into the Escherichia coli MC1061 strain. One of several chimeric plasmids harboring the replication region of the 42-kb plasmid obtained by this process was named pUA33 and further characterized. Plasmid pUA33 is approx. 8.3 kb. A partial restriction map has been constructed. Plasmid pUA33 is stable in E. coli cells growing under non-selective conditions and is non-self-transmissible. All these data suggest that the pUA33 plasmid may be a very useful tool for gene cloning in R. spheroides .     

Isolation and characterization of transposon Tn5 mutants of Rhodobacter sphaeroides deficient in both nitrate and chlorate reduction.

Abstract The wild-type strain Rhodobacter sphaeroides DSM 158 is a nitrate-reducing bacterium with a periplasmic nitrate reductase. Addition of chlorate to the culture medium causes a stimulation of the phototrophic growth, indicating that this strain is able to use chlorate as an ancillary oxidant. Several mutant strains of R. sphaeroides deficient in nitrate reductase activity were obtained by transposon Tn5 mutagenesis. Mutant strain NR45 exhibited high constitutive nitrate and chlorate reductase activities and phototrophic growth was also increased by the presence of chlorate. In contrast, the stimulation of growth by chlorate was not observed in mutant strains NR8 and NR13, in which transposon Tn5 insertion causes the simultaneous loss of both nitrate and chlorate reductase activities. Tn5 insertion probably does not affect molybdenum metabolism since NR8 and NR13 mutants exhibit both xanthine dehydrogenase and nitrogenase activities. These results that a single enzyme could reduce both nitrate and chlorate in R. sphaeroides DSM 158.     

Genetic evidence for the role of isocytochrome c2 in photosynthetic growth of Rhodobacter sphaeroides Spd mutants.

In Rhodobacter sphaeroides, cytochrome c2 (cyt c2)-deficient mutants are photosynthetically incompetent (PS-). However, mutations which suppress the photosynthetic deficiency (spd mutations) of cyt c2 mutants increase the levels of a cyt c2 isoform, isocyt c2. To determine whether isocyt c2 was required for photosynthetic growth of Spd mutants, we used Tn5 mutagenesis to generate a PS- mutant (TP39) that lacks both cyt c2 and isocyt c2. DNA sequence analysis of wild-type DNA that restores isocyt c2 production and photosynthetic growth to TP39 indicates that it encodes the isocyt c2 structural gene, cycI. The Tn5 insertion in TP39 is approximately 1.5 kb upstream of cycI, and our results show that it is polar onto cycI. The cycI gene has been physically mapped to a region of chromosome I that is approximately 700 kb from the R. sphaeroides photosynthetic gene cluster. Construction of a defined cycI null mutant and complementation of several mutants with the cycI gene under the control of the cyt c2 promoter region indicate that an increase in the levels of isocyt c2 alone is necessary and sufficient for photosynthetic growth in the absence of cyt c2. The data are discussed in terms of the obligate role of isocyt c2 in cyt c2-independent photosynthesis of R. sphaeroides.     

Intracytoplasmic membrane vesiculation in light-harvesting mutants of Rhodobacter sphaeroides and Rhodobacter capsulatus

Abstract In Chlamydomonas reinhardtii there are three glutamate dehydrogenase isozymes which can use both NADH and NADPH as cofactors and respond differently to different nitrogen sources and several stress conditions. From data of induction of isozymes in different metabolic situations, we propose a possible physiological role for each of them in algal carbon and nitrogen metabolism.     

Isolation and characterization of a virulent phage for Rhodobacter sphaeroides

A new virulent bacteriophage, termed øRsV, was isolated from a local sewage plant on the facultative phototrophic bacterium Rhodobacter sphaeroides DSM 159 as the host organism. Electron microscopic studies revealed that in general morphology phage øRsV resembles the T-even Escherichia coli phages. The host range of phage øRsV was restricted to strains of R. sphaeroides. E. coli strains B and K 12 were not infected. The phage genome was characterized on the basis of thermal denaturation profiles and restriction analyses indicating that it consists of about 160 kb of double-stranded DNA lacking cohesive ends. The G+C content was determined to be 46.8 mol%.     

Expression of a cytochrome c2 isozyme restores photosynthetic growth of Rhodobacter sphaeroides mutants lacking the wild-type cytochrome c2 gene

Deletion of the cytochrome c2 gene in the purple bacterium Rhodobacter sphaeroides renders it incapable of phototrophic growth (strain cycA65). However, suppressor mutants which restore the ability to grow phototrophically are obtained at relatively high frequency (1-10 in 10(7)). We examined two such suppressors (strains cycA65R5 and cycA65R7) and found the expected complement of electron transfer proteins minus cytochrome c2: SHP, c', c551.5, and c554. Instead of cytochrome c2 which elutes from DEAE-cellulose between SHP and cytochrome c', at about 50 mM ionic strength in wild-type extracts, we found a new high redox potential cytochrome c in the mutants which elutes with cytochrome c551.5 at about 150 mM ionic strength. The new cytochrome is more acidic than cytochrome c2, but is about the same size or slightly smaller (13,500 Da). The redox potential of the new cytochrome from strain cycA65R7 (294 mV) is about 70 mV lower than that of cytochrome c2. The 280 nm absorbance of the new cytochrome is smaller than that of cytochrome c2, which suggests that there is less tryptophan (the latter has two residues). In vitro kinetics of reduction by lumiflavin and FMN semiquinones show that the reactivity of the new cytochrome is similar to that of cytochrome c2, and that there is a relatively large positive charge (+2.6) at the site of reduction, despite the overall negative charge of the protein. This behavior is characteristic of cytochromes c2 and unlike the majority of bacterial cytochromes examined. Fourteen out of twenty-four of the N-terminal amino acids of the new cytochrome are identical to the sequence of cytochrome c2. The N-termini of the cycA65R5 and cycA65R7 cytochromes were the same. The kinetics and sequence data indicate that the new protein may be a cytochrome c2 isozyme, which is not detectable in wild-type cells under photosynthetic growth conditions. We propose the name iso-2 cytochrome c2 for the new cytochrome produced in the suppressor strains.     

Isolation and characterization of DNA repair deficient mutants from Penicillium chrysogenum

Summary Mutants sensitive to far ultraviolet light (UV) and 4-nitroquinoline-1-oxide (4NQO) have been isolated from Penicillium chrysogenum NRRL 1951. Two strains HP500 and HP508 are examined in detail. Their cross sensitivity to and altered mutation by UV and 4NQO suggests that damage caused by both agents is repaired through similar pathways in Penicillium chrysogenum. Strain HP500 is refractive to UV and 4NQO mutagenesis and is likely to be defective in an error-prone mechanism of repair. Mutation by N-methyl-N-nitro-N-nitrosoguanidine (MNNG) in HP500 is also reduced, indicating involvement of an error-prone UV repair process in MNNG mutagenesis in Penicillium chrysogenum. Strain HP508 shows an increase of forward mutation rate up to 4.5 times over that of the wild-type, when compared at similar surviving fractions and is also hypermutable by 4NQO. The repair defect present in strain HP508 has been demonstrated by its inability to remove DNA sites sensitive to single strand specific nuclease during post-irradiation incubation of protoplasts.     

Photolithoautotrophic growth and control of CO2 fixation in Rhodobacter sphaeroides and Rhodospirillum rubrum in the absence of ribulose bisphosphate carboxylase-oxygenase.

Rhodospirillum rubrum and Rhodobacter sphaeroides were shown to be capable of photolithoautotrophic growth in the absence of the reductive pentose phosphate (Calvin) cycle. Ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) deletion strains were incapable of photolithoautotrophic growth using hydrogen as an electron donor but were able to grow in the absence of organic carbon using less reduced inorganic electron donors, i.e., thiosulfate or sulfide. Wild-type R. rubrum grown in the presence of thiosulfate contained RubisCO levels that were 50-fold lower compared with those in cells growth with hydrogen as an electron donor without substantially influencing rates of photolithoautotrophic growth. These results suggest there are two independent CO2 fixation pathways that support photolithoautotrophic growth in purple nonsulfur photosynthetic bacteria, indicating that these organisms have developed sophisticated control mechanisms to regulate the flow of carbon from CO2 through these separate pathways.     

Differential expression of the CO2 fixation operons of Rhodobacter sphaeroides by the Prr/Reg two-component system during chemoautotrophic growth

In Rhodobacter sphaeroides, the two cbb operons encoding duplicated Calvin-Benson Bassham (CBB) CO2 fixation reductive pentose phosphate cycle structural genes are differentially controlled. In attempts to define the molecular basis for the differential regulation, the effects of mutations in genes encoding a subunit of Cbb3 cytochrome oxidase, ccoP, and a global response regulator, prrA (regA), were characterized with respect to CO2 fixation (cbb) gene expression by using translational lac fusions to the R. sphaeroides cbb(I) and cbb(II) promoters. Inactivation of the ccoP gene resulted in derepression of both promoters during chemoheterotophic growth, where cbb expression is normally repressed; expression was also enhanced over normal levels during phototrophic growth. The prrA mutation effected reduced expression of cbb(I) and cbb(II) promoters during chemoheterotrophic growth, whereas intermediate levels of expression were observed in a double ccoP prrA mutant. PrrA and ccoP1 prrA strains cannot grow phototrophically, so it is impossible to examine cbb expression in these backgrounds under this growth mode. In this study, however, we found that PrrA mutants of R. sphaeroides were capable of chemoautotrophic growth, allowing, for the first time, an opportunity to directly examine the requirement of PrrA for cbb gene expression in vivo under growth conditions where the CBB cycle and CO2 fixation are required. Expression from the cbb(II) promoter was severely reduced in the PrrA mutants during chemoautotrophic growth, whereas cbb(I) expression was either unaffected or enhanced. Mutations in ccoQ had no effect on expression from either promoter. These observations suggest that the Prr signal transduction pathway is not always directly linked to Cbb3 cytochrome oxidase activity, at least with respect to cbb gene expression. In addition, lac fusions containing various lengths of the cbb(I) promoter demonstrated distinct sequences involved in positive regulation during photoautotrophic versus chemoautotrophic growth, suggesting that different regulatory proteins may be involved. In Rhodobacter capsulatus, ribulose 1,5-bisphosphate carboxylase-oxygenase (RubisCO) expression was not affected by cco mutations during photoheterotrophic growth, suggesting that differences exist in signal transduction pathways regulating cbb genes in the related organisms.     

浑球红细菌（Rhodobacter sphaeroides）中氢化酶正调节基因hupR的克隆及功能分析

从光合细菌Rhodobacter sphaeroides基因文库中分离出含有氢化酶基因簇（hup）的粘粒cosmid 1后,亚克隆了R.sphaeroides的氢化酶调节基因hupR,测定了hupR的核苷酸序列,并完成了氢化酶基因簇的部分物理图谱。实验结果表明,hupR基因全长1476bp,编码的HupR基因分子量约为54.031kD(EMBL接受号：A243734)。与R.capsulatus中HupR相比,同源性高达73％。同源性比较结果表明,它属于双组分调节系统中受体蛋白。hupR基因在E.coli中进行了体外表达,纯化后测定得到的HupR蛋白 分子量大小与hupR基因推测的分子量大小一致。通过双交换,将卡那霉素抗性基因插入hupR基因,获得丧失氢化酶活性的hupR^-的突变株,KR5和KR7。hupS∷lacZ融合基因在野生型中的转录表达量是在该突变株中的7－9倍。将hupR基因置于弱启动子pfru下游,构建了质粒pNRC3,并将其导入hupR^-的突变株,可使突变株重新获得氢化酶活性。以上结果说明,HupR蛋白对氢化酶的转录表达起着正调节作用。在HupR蛋白的磷酸化区域进行定点和缺失突变。不影响HupR激活氢化酶基因的表达,推测HupR蛋白是在非磷酸化的状态下起调节作用的。     

Replication of plasmid R6K in DNA polymerase deficient mutants of Escherichia coli.

The plasmid R6K has been introduced into a number of Escherichia coli polymerase deficient (pol) mutants. In polCts mutants transferred to the nonpermissive temperature to inactivate polymerase III, R6K replicates but the replication products have a density in dye-CsCl gradients intermediate between supercoiled and linear forms. This aberrant replication requires normal cellular levels of polymerase I since it does not occur in polA polCts mutants. Normal R6K replication and maintenance occur in a polA polB polC+ host, however, we cannot tell from our experiments wheather polymerase I or III replicates R6K in polA+ polC+ host. Polymerase II, the polB gene product, has no detectable role in R6K replication.     

Inhibited growth of Clostridium butyricum in efficient H2-producing co-culture with Rhodobacter sphaeroides

Applied Microbiology and Biotechnology - Cell number of Clostridium butyricum and Rhodobacter sphaeroides in co-culture was measured using q-PCR approach. During efficient H2 photoproduction from...     

DNA sequence analysis of the photosynthesis region of Rhodobacter sphaeroides 2.4.1

This paper describes the DNA sequence of the photosynthesis region of Rhodobacter sphaeroides 2.4.1^T. The photosynthesis gene cluster is located within a ~73 kb AseI genomic DNA fragment containing the puf, puhA, cycA and puc operons. A total of 65 open reading frames (ORFs) have been identified, of which 61 showed significant similarity to genes/proteins of other organisms while only four did not reveal any significant sequence similarity to any gene/protein sequences in the database. The data were compared with the corresponding genes/ORFs from a different strain of R.sphaeroides and Rhodobacter capsulatus, a close relative of R.sphaeroides. A detailed analysis of the gene organization in the photosynthesis region revealed a similar gene order in both species with some notable differences located to the pucBAC=cycA region. In addition, photosynthesis gene regulatory protein (PpsR, FNR, IHF) binding motifs in upstream sequences of a number of photosynthesis genes have been identified and shown to differ between these two species. The difference in gene organization relative to pucBAC and cycA suggests that this region originated independently of the photosynthesis gene cluster of R.sphaeroides.     

Isolation of low-copy-number sequences that neighbor satellite DNA in mammals

To investigate the role of satellite DNA in eukaryotic genomes, we isolated from an African green monkey (Cercopithecus aethiops) genomic library cloned segments containing the previously described deca-satellite linked to low-copy-number genomic sequences. Three such clones were obtained. The low-copy-number sequences in the three clones do not cross-hybridize suggesting that they derive from different genomic loci. The structure of one of the clones, λAMkA, is described in detail. Subcloned segments containing the low-copy-number sequences from λAMkA anneal to monkey, human and mouse genomic DNA. The subcloned probes were used to select clones containing homologous sequences from a second, independent monkey library as well as from human and mouse genomic libraries. Several of the newly isolated monkey clones hybridized to probes containing the species-specific deca- and -satellites, confirming the genomic association of the low-copy-number sequence in λAMkA with satellite DNA. Moreover, several of the human and mouse clones hybridized to species-specific human and mouse satellite DNAs, respectively. These experiments indicate that the low-copy-number sequence in λMkA and its association with satellite DNA is conserved in primates and rodents.