Creating auxotrophic mutants in Methylophilus methylotrophus AS1 by combining electroporation and chemical mutagenesis

Stable auxotrophic mutants of the methylotroph Methylophilus methylotrophus AS1 were obtained by a novel mutagenesis technique in which electroporation is used to transport the chemical mutagen N-methyl-N′-nitro-N-nitrosoguanidine (MNNG) across the cell membrane. By combining chemical mutagenesis with electroporation and screening single colonies for auxotrophy in 36 different amino acids and growth factors, 3 auxotrophs per 156 colonies screened were obtained, whereas no auxotrophs were found with chemical mutagenesis alone. MNNG mutagen toxicity was also increased in the methylotroph with this novel mutagenesis technique (death rate 96% compared to 79%). This technique did not increase the mutation rate for strain Escherichia coli BK6 which responds well to simple exposure to the mutagen. Received: 9 December 1996 / Received revision: 31 March 1997 / Accepted: 13 April 1997     

Structure and mechanism of galactose oxidase: catalytic role of tyrosine 495

 The catalytic mechanism of the copper-containing enzyme galactose oxidase involves a protein radical on Tyr272, one of the equatorial copper ligands. The first step in this mechanism has been proposed to be the abstraction of a proton from the alcohol substrate by Tyr495, the axial copper ligand that is weakly co-ordinated to copper. In this study we have generated and studied the properties of a Y495F variant to test this proposal. X-ray crystallography reveals essentially no change from wild-type other than loss of the tyrosyl hydroxyl group. Visible spectroscopy indicates a significant change in the oxidised Y495F compared to wild-type with loss of a broad 810-nm peak, supporting the suggestion that this feature is due to inter-ligand charge transfer via the copper. The presence of a peak at 420 nm indicates that the Y495F variant remains capable of radical formation, a fact supported by EPR measurements. Thus the significantly reduced catalytic efficiency (1100-fold lower k _cat / K _m) observed for this variant is not due to an inability to generate the Tyr272 radical. By studying azide-induced pH changes, it is clear that the reduced catalytic efficiency is due mainly to the inability of Y495F to accept protons. This provides definitive evidence for the key role of Tyr495 in the initial proton abstraction step of the galactose oxidase catalytic mechanism. Received: 17 December 1996 / Accepted: 12 March 1997     

Neighborhood density and reproductive potential in harvester ants

When neighbors compete for resources, the characteristics of a neighborhood may affect fitness. We examined the relationship between reproductive success and the density and size/age characteristics of neighbors in a population of the seed-eating ant, Pogonomyrmex barbatus, in which the ages of all colonies were known. Reproductive success was estimated by trapping and counting the number of alate, reproductive ants emerging from the nest for the annual mating flight. Alate production was negatively related to neighborhood density. Decreased production of alates by more crowded colonies may be due to competition for food with surrounding colonies. Neighbor size/age was unrelated to alate production. If alate production is correlated with lifetime reproductive success, these results suggest that selection favors colonies that monopolize more space, whatever the size of neighboring colonies. Received: 12 February 1996 / Accepted: 6 September 1996     

Response to copper and cadmium stress in wild-type and copper tolerant strains of the lichen alga <Emphasis Type="Italic">Trebouxia erici</Emphasis>: metal accumulation,toxicity and non-protein thiols

Cysteine, glutathione (GSH) and phytochelatins were determined in the cells of both wild and copper tolerant strains of the lichen alga Trebouxia erici following short-term (24 h) exposure to copper and cadmium and long-term (4 weeks) exposure to copper. Both metals caused concentration dependent synthesis of phytochelatins (PC₂–PC₅), but cadmium was a more potent activator of phytochelatin synthesis, even inducing synthesis of PC₅. The copper-tolerant strain did not reveal a higher degree of phytochelatin synthesis than the wild strain, and at 5 μM Cu production of phytochelatins was in fact significantly lower. Lower levels of phytochelatin correlated with significantly decreased intracellular copper content in the copper-tolerant strain. Both strains maintained high GSH levels even at a high copper concentration of 5 μM, and only the highest copper concentration (10 μM) was toxic for both strains, causing a decrease of GSH and PC content in algal cells. Cadmium had less effect on GSH in the cells of both tested strains. In the long term experiments, only relatively small amounts of PC₂ were detected in both strains, but the copper-tolerant strain retained significantly higher levels of reduced glutathione, probably due to the lesser degree of oxidative stress caused by Cu. The significant increase of cysteine synthesis in the copper-tolerant strain found in the present study may be related to copper tolerance in T. erici, while decreased intracellular Cu uptake, detoxification by PCs and increased free proline levels for protection of chloroplast membranes may also be implicated.     

Enrichment culture and isolation of slow-growing bacteria

 Enrichment containing large numbers of slow-growing bacteria was developed by repeated batch culture under high biomass concentrations (more than 10 000 mg biomass/l). The characteristics of slow-growing bacterial populations were elucidated by application of colony-forming-curve (CFC) analysis. The CFC were obtained by counting the number of visible colonies on agar plates at successive intervals. The enrichment consisted of several groups with different colony-forming rates and the slow-growing bacteria appeared on cell extract/agar plates after 7 days of incubation. It was found that large numbers of slow-growing bacteria survived under starvation conditions. One of the slow colony-forming bacteria, strain TI-X7, was tentatively identified as being of the genus Micrococcus. The enrichment contained a large amount of Micrococcus-like tetrad cells. The dialysate fractions in excess cell extract, permeable through dialysis tubing, were extremely effective for growth of strain TI-X7. Received: 15 December 1995/Accepted: 20 February 1996     

Effect of xylitol and trehalose on dry resistance of yeasts

The effects of dehydration/rehydration on two strains of Saccharomyces cerevisiae: S600, a metabolically engineered xylose-utilising strain, and H158, the non-xylose-utilising host strain; and on the naturally xylose-utilising yeast Pachysolen tannophilus CBS 4044, were compared after glucose and xylose utilisation respectively. The yeast strains differed in their ability to excrete and accumulate intracellular xylitol. A high intracellular xylitol content before and after dehydration coincided with a higher viability after a dehydration/rehydration cycle. The intracellular trehalose content increased during dehydration in all three yeast strains, but this did not correspond to enhanced cell viability after dehydration/rehydration. The results are discussed in relation to the ability of xylitol and trehalose to structure water. Received: 9 July 1996 / Received revision: 29 October 1996 / Accepted: 2 November 1996     

Diet and foraging effort of Adélie penguins in relation to pack-ice conditions in the southern Ross Sea

We investigated the diet and aspects of foraging effort among Adélie penguins (Pygoscelis adeliae) breeding at three colonies on Ross Island, in the southwestern Ross Sea – Capes Royds, Bird and Crozier – during the chick-provisioning period of three austral summers, 1994–1995, 1995–1996 and 1996–1997. During the study period, pack-ice cover differed in waters offshore of these colonies, by colony, seasons and year. Diet differed among colonies only slightly. The fish Pleuragramma antarcticum was the most important prey, especially during years or periods within years when little pack ice was present. With respect to krill, which composed the remainder of diet, juvenile Euphausia crystallorophias were consumed predominantly in a year of heavy pack-ice cover; more adult krill were consumed in 2 years when pack ice was sparse. Foraging trip duration differed by colony, season and year and was related directly to distance from the colony to the nearest pack ice. The amount of food brought to chicks increased as trip duration increased, to a point (2 days), but then decreased as duration increased further (up to 4 days). On the basis of data on mass of parents and of meal sizes to chicks, it appeared that on the longest trips more of the food gathered by parents was used for self maintenance; on the longest trips, parents lost body mass. Successful foraging during chick rearing, the period when adult foraging is most intense, appears to depend on the proximity of pack ice to nesting colonies for this penguin species. Received: 1 October 1997 / Accepted: 25 April 1998     

Construction of L-lysine-overproducing strains of Brevibacterium lactofermentum by targeted disruption of the hom and thrB genes

The mobilization of plasmids from gram-negative Escherichia coli to gram-positive Brevibacterium lactofermentum, mediated by P-type transfer functions, was used to construct disrupted mutants blocked specifically in the homoserine branch of the aspartate pathway. The mutant strain B. lactofermentum R31 showed an efficiency of conjugal transfer two to three orders of magnitude higher than that of the wild-type strain B.␣lactofermentum ATCC 13869. The hom- and thrB- disrupted mutants of B. lactofermentum ATCC 13869 were lysine overproducers. B. lactofermentum R31 mutants do not overproduce lysine because R31 is an alanine-overproducing strain and channels the pyruvate needed for lysine biosynthesis to the production of alanine. Received: 23 January 1996 / Received last revision: 28 July 1996 / Accepted: 5 August 1996     

Serine319 and 321 Are Functional in Isocitrate Lyase from Escherichia coli

With site-directed mutagenesis, Ser319 and Ser321 in conserved stretch 3 of tetrameric isocitrate lyase from Escherichia coli were each substituted with alanine, cysteine, asparagine, or threonine in addition to simultaneous alanine/alanine substitutions. Besides their absolute conservation in all aligned isocitrate lyase sequences, the location of these serine residues, which flank a completely conserved proline, had been suggested in the active site in previous research by studies of photoinactivation of the enzyme by vanadate [Ko et al. (1992) J Biol Chem 267:91]. All substitutions for Ser321 and 319 except by threonine appreciably reduced the k_cat of E. coli isocitrate lyase relative to that for wild-type (100) as follows: S319A, 0.4; S319C, 0.05; S319N, 0.01; S319T, 32.3; S321A, 2.9; S321C, 0.3; S321N, 0.1; S321T, 0.3; and S319A/S321A, 0, with little or no effect on the K _m for the substrate Mg²⁺-D_s-isocitrate. The most active variant S319T exhibited threefold less activity than the wild-type enzyme; all variants assembled into tetramers. The S319T mutant isocitrate lyase was 100-fold more active than the S321T variant. This observation suggests that the requirement for a β-hydroxymethyl group of serine in catalysis is less important at position 319 than at position 321. Although most singly substituted variants had very low isocitrate lyase activity, all variants harboring mutant isocitrate lyase of very low activity did grow on acetate as a sole carbon source albeit with longer doubling times and lag phases. Substitution of Pro320 by Ala, Asp, Gly, or His was highly detrimental to activity and increased the K _m for substrate 3.5- to 8-fold; this suggests that Pro fixes the location of adjacent Ser OH groups and facilitates substrate binding and catalysis. From these collective results, it is proposed that Ser319 and Ser321 are involved in E. coli isocitrate lyase catalysis, perhaps by stabilizing the postulated reaction intermediate succinate trianion in the aci-carboxylate form and the related transition state via hydrogen bonding. Received: 3 September 1996 / Accepted: 20 September 1996     

Anaerobic leaching of covellite by Thiobacillus ferrooxidans

Thiobacillus ferrooxidans was able to grow under anaerobic conditions on copper sulphide with ferric ion as the electron acceptor. The dissolution of covellite under these conditions (68% after 35 days) was higher than values observed aerobically in cultures with similar media composition and almost as high as under aerobic conditions without iron. From these results we propose a mechanism for anaerobic bioleaching of covellite in the presence of ferric iron and speculate that it may occur in leach dumps where the oxygen concentration is, as reported elsewhere, very low. Received: 3 September 1996 / Received revision: 13 January 1997 / Accepted: 24 January 1997     

Lack of protection by carotenes against gamma-radiation damage in Phycomyces

Carotenes could protect cells from radiation damage by chemically quenching the free radicals and the activated chemical species originated by the exposure. We tested this hypothesis with strains of the zygomycete Phycomyces blakesleeanus that contained different carotenes (phytoene, lycopene, β-carotene) or different concentrations of β-carotene. Pairs of strains were cultured together, exposed to a maximum of 73 Gy γ-radiation from a ⁶⁰Co source, and allowed to recover and grow further together on limited resources. Irradiation did not affect the relative abundance of each strain in the resulting spore crop. Thus, carotenes did not protect the fungal cells against γ-radiation and did not influence their recovery from damage caused by the exposure. Received: 12 October 1995 / Accepted in revised form: 18 March 1996     

A variant of Saccharomyces cerevisiae pep4 strain with improved oligotrophic proliferation, cell survival and heterologous secretion of α-amylase

A variant of Saccharomyces cerevisiae pep4 strain 20B12, with improved oligotrophic proliferation, cell survival and secretion of heterologous mouse α-amylase, is described. Previously we reported a procedure to enrich NI transformants that are not inhibited by cytotoxic expression of hepatitis B virus surface antigen in the secretion pathway of the protease-A-deficient (pep4) strain. To use the NI cells as a host for heterologous expression, we tried to amend the introduced pYAS/12S vector and obtain a host strain, NI-C, with stable NI phenotype and trp1 marker restored. Southern analysis of genomic DNA of NI-C suggested that the original pYAS/12S was abnormally rearranged and not completely corrected. Further assay showed that the viability and mitotic ability of the NI-C strain were increased. While using the NI-C strain as host for plasmid transformation and heterologous expression of mouse α-amylase, we observed that transformed colonies grew more quickly and secreted more α-amylase than general yeast strains. A further test showed that the NI-C strain was able to use mouse α-amylase as a positive selection marker to form transformed colonies on nitrogen-starved plates that contain starch as the sole carbon source. The results imply that the NI-C variant is an improved pep4 strain that can be used for heterologous expression and for the development of new selective markers in the yeast transformation system. Received: 7 January 1998 / Received last revision: 7 September 1998 / Accepted: 11 October 1998     

Development of a phosphate-removal system using a marine photosynthetic bacterium Chromatium sp.

The marine photosynthetic bacterium Chromatium sp. successfully removed orthophosphate when grown phototrophically. The phosphate-uptake rate was almost constant at more than 5.0 mg- PO₄ ³⁻/l in synthetic medium. Addition of seawater causes flocculation of this strain. The successful use of seawater as an inexpensive source of magnesium could prove to be effective in the removal of photosynthetic bacterial cells from a medium. A semicontinuous culture system was used for the removal of low concentrations of phosphate and the phosphate-uptake activity of Chromatium sp. was maintained under 0.1 day⁻¹ dilution rate. This strain was also able to remove high concentrations of phosphate from domestic sewage. Received 24 May 1996 / Received revision: 5 August 1996 / Accepted: 6 September 1996     

A deletion in the sapA homologue cluster is responsible for the loss of the S-layer in Campylobacter fetus strain TK

The surface array protein (SAP) of Campylobacter fetus strain TK is encoded by seven homologous sapA genes clustered on the chromosomal DNA. The spontaneously arising variant strain TK(SAP^–) produces no SAP and carries an approximately 10-kb chromosomal deletion. To elucidate the mechanism underlying the loss of SAP synthesis, we analyzed the region containing the sapA homologues and the deletion. We constructed a physical map of the sapA cluster region by aligning the clones that contain sapA homologues. These analyses demonstrated that all sapA homologues were located within a limited region of about 50 kb of chromosomal DNA of strain TK. The TK(SAP^–) deletion was located within this cluster and was 13.3 kb in size. The deletion occurred between two sapA homologues and resulted in the formation of a chimeric sapA homologue in the variant strain. Sequence analysis of the upstream regions and the conserved regions of all sapA homologues revealed a high degree of similarity. However, only one sapA homologue contained a putative promoter sequence. This promoter sequence was located in the deleted region. Thus, the deletion of the promoter appears to be responsible for the loss of SAP expression in TK(SAP^–). Received: 17 May 1996 / Accepted: 6 December 1996     

Bioreduction of Cu(II) by Cell-Free Copper Reductase from a Copper Resistant <Emphasis Type="Italic">Pseudomonas</Emphasis> sp. NA

Environmental copper contamination is a serious human health problem. Copper reductase is produced by microorganisms to facilitate copper uptake by ATPases into the cells increasing copper biosorption. This study assessed the reduction of Cu(II) by cell-free extracts of a highly copper-resistant bacterium, Pseudomonas sp. strain NA, isolated from vineyard soil contaminated with copper. Both intact cells and cell-free extract of Pseudomonas sp. strain NA displayed substantial reduction of Cu(II). Intact cells reduced more then 80 mg L⁻¹ of Cu(II) from medium amended with 200 mg L⁻¹ of copper after 24 h of incubation. Cell-free extract of the isolate reduced more than 65% of the Cu(II) at initial copper concentration of 200 mg L⁻¹ after 24 h. Soluble protein production was high at 72 h of incubation at 100 mg L⁻¹ of copper, with more then 60 μg L⁻¹ of total soluble protein in cell-free extract recorded. Cu(II) reduction by isolate NA was increased when copper concentration increased for both intact cells and cell-free extract. Results indicate that Pseudomonas sp. strain NA produces copper reductase enzyme as the key mechanism of copper biotransformation.     

Sediment retention in encrusting Palythoa spp.—a biological twist to a geological process

 Carpet sea anemones of the genus Palythoa are common inhabitants of reef crest environments in the Florida Keys reef tract. Through a unique assimilation mechanism, Palythoa spp. entomb carbonate sediment within their tissues. The amount of sediment assimilated is significant, averaging almost 45% of wet tissue weight. Palythoa spp. assimilate all available minerals on the reef. Aragonite, magnesium calcite, calcite and minor quantities of siliciclastic components are all assimilated in proportions comparable to their content in adjacent sediment sinks. There is also no preference in terms of skeletal composition; coral grit, coralline red algae, Halimeda and other allochems are all equally assimilated into Palythoa spp. tissue. The only preference is particle size. Sediment extracted from tissue samples is generally ?125 μm in size, far finer than ambient sediment found adjacent to Palythoa spp. colonies (predominantly >500 μm). Much of the finest sediment extracted from Palythoa spp. tissue is composed of elongated crystal aggregates of aragonite. These particles appear to have been produced in situ through biologically influenced mineralization. Aggregates nucleated on exogenous sediment and attained their elongated form as assimilation proceeded. When Palythoa spp. colonies die, the assimilated sediment and the crystal aggregates are released back into the reef environment. The eventual fate of this material has yet to be determined. Accepted: 5 July 1996     

Production of exopolysaccharide by Pseudomonas sp. ATCC 31461 (Pseudomonas elodea ) using whey as fermentation substrate

An improved strain of Pseudomonas sp. ATCC 31461 (Pseudomonas elodea), capable of producing broth viscosities of 11 000 and 4700 mPa s (cP) when grown in enriched whey permeate and enriched sweet whey broths respectively, was isolated. The isolation was by serial transfers of the parent on lactose-rich and sweet whey broths. Maximum viscosities and biopolymer production were observed in 25% (v/v) whey concentration. In whey concentrations of 50% (v/v) or greater, residual glucose was detected in the broth and biopolymer production was low. This strain is capable of totally utilising the lactose in up to 50% (v/v) whey in 64 h. Enzyme activities suggest that the transport of lactose in P. elodea is by the permease system as opposed to the phosphotransferase system. The location of β-galactosidase is mainly intracellular. The improved strain is able to utilise lactose better than the parent and produce 1.6 times more intracellular β-galactosidase activity compared to the parent. Received: 3 May 1996 / Received revision: 8 August 1996 / Accepted: 10 August 1996     

Major differences between the rrnA operons of two strains of Agrobacterium vitis

The sequence of the rrnA operon and its flanking regions was determined for the Agrobacterium vitis type strain NCPPB3554. Compared to the earlier obtained rrnA sequence of A. vitis strain S4, several important differences were noted: the sequences diverged at the 5′-flanking region, within the 16S–23S intergenic region, and within the 23S rRNA sequence. The B8 stem-loop structure at the 5′-end of the 23S rRNA of strain NCPPB3554 was 142 nt shorter than that of strain S4. These findings have important consequences for the use of ribosomal RNA gene sequences in phylogenetic comparisons. Received: 16 February 1996 / Accepted: 26 April 1996     

Copper Resistance and Accumulation in the Zygomycete Mucor rouxii

Two copper-resistant (Cop^r) mutants, strains P1 and P3, were obtained from the dimorphic fungus Mucor rouxii. They were characterized as to their ability to take up copper in a growth medium supplemented with this metal ion. Detection of copper by linear sweep striping voltammetry in cell walls and in the cell wall-free fraction of disrupted cells revealed a higher content of the metal in both mutant fractions, as compared with those of the copper-sensitive (Cop^s) parental strain. Copper binding by M. rouxii growing cells was also studied through the use of a cytochemical method based on the compounds neocuproine (NCP) and sodium diethyldithiocarbamate (DTC). This method indicated that the P1 Cop^r strain accumulated more metal than the parental Cop^s strain, both on the cellular surface and in the intracellular milieu. Received: 30 January 1996 / Accepted: 7 March 1996     

Production of methoxyphenol-type natural aroma chemicals by biotransformation of eugenol with a new Pseudomonas sp.

In our screening program for microorganisms that are able to metabolize eugenol, the main component of the essential oil of the clove tree Syzigium aromaticum (sy. Eugenia cariophyllus), we found a new Pseudomonas sp. that produces several substituted methoxyphenols when eugenol is fed to the culture. A taxonomic characterization of this new organism has been performed. Examples of the biotransformation products, produced in high amounts, were vanillic acid with 3.25 g/l within 99 h, ferulic acid with 5.8 g/l within 75 h and coniferyl alcohol with 3.22 g/l within 47.5 h. By changing the culture conditions the ratio of the different metabolites could be varied. Based on these results a scheme for the degradation of eugenol by this strain has been established. Received: 1 April 1996 / Received revision: 24 June 1996 / Accepted: 1 July 1996