Relaxed mutants ofSerratia marcescens SM-6. Biochemical traits and relevance of therel + allele for the formation of exoenzymes

Serratia marcescens SM-6 when starved for a required amino acid stops synthesizing protein and RNA and accumulates two nucleotides which cochromatograph with ppGpp and pppGpp. These features are characteristic of bacterial strains with stringent RNA control (rel ⁺). Two independent mutants were isolated which resemble relaxed (relA) mutants ofEscherichia coli; they continue to synthesize RNA and accumulate neither ppGpp nor pppGpp when deprived of the required amino acid. The extracellular enzyme activities (nuclease, protease, lipase) of the relaxed mutants are about the same as those of the parental stringent strain when studied under standard growth conditions. Exoenzyme-deficient (nuc; prt) and exoenzyme-hyperproducing (nuc ^su) mutants were isolated from both stringent and relaxed strains ofS. marcences SM-6 and no change of the cellular ability to form ppGpp and pppGpp could be observed. From these results it appears that the formation of exoenzymes ofS. marcescens SM-6 is independent of stringent/relaxed RNA control.Abbreviations cpd cyclic nucleotide phosphodiesterase deficient - nuc nuclease deficient - nuc ^su nuclease hyperproducing - prt protease deficient - rel relaxed control - spo ppGpp deficient (spot less) - ppGpp guanosine tetraphosphate - pppGpp guanosine pentaphosphate - TCA trichloroacetic acid - OD optical density - EU enzyme units     

Gene dosage studies with pleiotropic mutants of Serratia marcescens superactive in the synthesis of marcescin A and certain other exocellular proteins

Summary Pleiotropic mutants of Serratia marcescens have been isolated. They synthesize greater quantities of the bacteriocin marcescin A and exocellular lipase and exhibit higher rates of spontaneous induction of prophage than does the wild-type strain. These mutants were found to contain more marcescin A plasmid DNA than the parent strain and, furthermore, this increase in plasmid DNA was observed to be proportional to the increase in synthesis of marcescin A. From these results it is proposed that the mutation functions via a gene-dosage effect (at least in the case of bacteriocin synthesis) and causes an elevated synthesis of bacteriocin plasmid DNA.A preliminary report of this work was presented to the 1972 Summer Meeting of the Gesellschaft für Physiologische Chemie held in Bochum, Germany (Timmis and Winkler, 1972).     

Nonsense mutants of Serratia phage Kappa

Summary Auxotrophs of Serr. marcescens HY, which behaved like nonsense mutants when tested according to Whitfield et al. (1966), were induced to revert to anauxotrophy. Some of the revertants (called su ⁺), together with the parental auxotrophs (called su ^-), allowed to isolate conditional-lethal (sus) mutants of phage Kappa, which produce infectious progeny only in su ⁺ bacteria. All su ⁺ mutants of Serr. marcescens HY were identified as nonsense suppressors using su ⁺ _amber, su ⁺ _ochre, and su ^- strains of Salm. typhimurium as references and the flagella-specific phage Chi as the main tool to connect the Salmonella system with that of Serratia.After treatment of Kappa with three different mutagens 128 sus mutants were isolated which comprise at least 19 complementation groups. 18 sus mutants, representing different cistrons, and the unselective markers c1, c2, and c49 were mapped mainly by two-factor crosses. Reciprocal three-factor crosses of the general type a x bz and az x b (i.e. with outside markers) revealed a circular linkage map of an estimated maximum length of 90 RU (recombination units). Joined rescue of outside markers, e.g. sus ⁺ A94 and e49, from UV-irradiated phage supported the assumption of circular gene linkage. Some data indicate that certain regions of the phage genome might have a higher chance to recombine than others.Abbreviations moi multiplicity of infection - eop efficiency of plating - RU recombination units - MR marker rescue     

Nuclear suppressors of the [poky] cytoplasmic mutant in Neurospora crassa. III. Effects on other cytoplasmic mutants and on mitochondrial ribosome assembly in [poky].

Summary We have previously isolated six non-allelic, nuclear mutations (su ^I loci) that partially suppress the growth, respiratory and cytochrome abnormalities of the extranuclear [poky] mutant.A comparison of the mitochondrial ribosome profiles of suppressed and unsuppressed [poky] strains revealed that five of the six suppressors alleviate at least partially the deficiency of mitochondrial small ribosomal subunits that is associated with the [poky] genotype.Six independently isolated Group I extranuclear mutants, namely [exn-1], [exn-2], [exn-4], [stp-B ₁], [SG-1] and [SG-3], which have growth and cytochrome phenotypes similar to [poky], also were found to be deficient in small subunits of mitochondrial ribosomes. Using cytochrome aa ₃ and b production as a criterion for mitochondrial protein synthesis, it could be shown that the nuclear su ^I suppressors of [poky] also suppress the other six Group I extranuclear mutants. However, differences in the efficiencies of suppression by su ^I suppressors suggest that at least some of Group I extrachromosomal mutants are not simply re-isolates of [poky], but represent distinct extranuclear mutations.     

Nonsense mutants in the bacteriophage T4D v gene

Ten UV-sensitive mutants of T4D with the v phenotype were isolated. Of these ten mutants, two are amber and two opal. In UV curves and in photoreactivation and multiplicity reactivation (MR) experiments the nonsense mutants show the v phenotype in su⁻ hosts and almost the T4+ phenotype in su⁺ hosts. The mutations are located between rI and e and are alleles of v₁. In crosses with irradiated and non-irradiated phages the recombinant frequency is not reduced by uvs5.Amber uvs5 propagated in CR63 su⁺ is with B su⁻ just as sensitive to UV as uvs5 propagated in B su⁻, which permits the conclusion that the capsid of T4 phage particles does not contain the v gene product.In addition, four mutants with a relative UV sensitivity equal to that of T4x were isolated. These are discussed in the next paper³³.     

Suppression of temperature sensitive mutants of bacteriophage T4 by bacterial opal suppressors

Summary Some of the partial revertants from opal (UGA) mutants of bacteriophage T4 are temperature sensitive in su ^– host cells but are still temperature resistant in su ⁺ cells. Hence these revertants are missense mutants suppressible by bacterial opal suppressors. Such a suppression may be explained in terms of codon-anticodon interactions by the wobble hypothesis.     

Nucleotide alterations in the bacteriophage T4 glutamine transfer RNA that affect ochre suppressor activity

We have determined the nucleotide sequences of the glutamine transfer RNAs that are coded by wild-type and psu₂⁺ ochre-suppressor strains of bacteriophage T4. The two transfer RNAs have the same sequence except for their anticodons, where NUG in the wild-type species is mutated to NUA in the psu₂⁺ species (N is a modified residue of U). This mutation is believed to confer suppressor activity on the psu₂⁺ glutamine tRNA. Three mutants derived from psu₂⁺ by loss of suppressor activity have been characterized with respect to their sequence alterations. Each mutant specifies a transfer RNA differing from the psu₂⁺ species by a nucleotide substitution that occupies a base-paired region in the cloverleaf arrangement of the molecule. The mutants synthesize a reduced amount of tRNA that is defective in nucleotide modifications and processing at the 5′ and 3′ termini.     

Characterization of an amber suppressor in Pneumococcus.

Summary Partial revertant has been isolated, with resistance to aminopretin intermediate between wild type and mutant. This phenotype is the result of a mutation at a gene unlinked to the amiA locus. This suppressor mutation (su⁺) has no phenotypic characteristics by itself except a slow growth. 9 amiA mutants (belonging to 6 sites) are affected by su⁺ out of the 30 investigated mutants (i.e. 22 sites). The efficiency of suppression is site dependent. Two sites out of 14 mutants belonging to the thymidilate synthetase gene are suppressible. Thymidilate synthetase activity is partially restored by su⁺. Optochin mutants can also be suppressed. Thus su⁺ is not gene specific but site specific. Moreover when the str-41 allele conferring resistance to streptomycine is introduced by transformation, the suppression effect is restricted. All these properties are characteristic of an informational suppressor.The t-RNA extracted from the suppressor strain su⁺ but not the wild type restored the synthesis of coat protein coded by RNA from an amber mutant of bacteriophage f2. Attempts to detect ochre suppression activity gave negative results. It is suggested that the su⁺ gene is amber specific.Thus su⁺ can provide insight into the nature of suppressible mutations which should be point mutations. Both low efficiency and high efficiency mutants are affected by su⁺; this is additional evidence that both categories contain point mutations.     

Mechanism of suppression inDrosophila: Regulation of tryptophan oxygenase by thesu(s) + allele

The suppressor gene,su(s)², inDrosophila melanogaster restores the production of red and brown eye pigments for some purple and vermilion mutant alleles, respectively. We showed previously that the product of thesu(s)⁺ allele caused inhibition of the sepiapterin synthase A produced by the purple mutant but did not affect the wild-type enzyme. Suppression was accomplished by removingsu(s)⁺ from the genome. We now report that the tryptophan oxygenase, produced by suppressible vermilion alleles, is also inhibited by extracts fromsu(s)⁺ flies. The inhibition of the vermilion enzyme can be reduced or eliminated, respectively, by prior storage of the extract at 4 or –20°C or by boiling, whereas the wild-type enzyme is not affected by extracts ofsu(s)⁺ flies. Also, when the suppressible vermilion strain is raised on certain diets, brown eye pigment production occurs. This epigenetic suppression was reduced by the presence of an extra copy ofsu(s)⁺ in the genome. These data support a posttranslational mechanism for regulation of enzyme activity in which the activity of the mutant enzyme is reduced by the product of thesu(s)⁺ allele. How thesu(s)⁺ gene product can distinguish between the normal and the mutant forms of these two enzymes is discussed, along with other mechanisms for suppression that are currently under investigation.This work was supported in part by a grant from the KOSEF, Korea Science and Engineering Foundation, and the National Science Foundation under the U.S.-East Asia Cooperative Science Program as well as the Office of Health and Environmental Research, U.S. Department of Energy, under Contract DE-AC05-840R21400 with the Martin Marietta Energy Systems, Inc.     

The staphylococcal nuclease prevents biofilm formation in <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> and other biofilm-forming bacteria

The staphylococcal nuclease, encoded by the nuc1 gene, is an important virulence factor of Staphylococcus aureus. However, the physiological role of the nuclease has not been fully characterized. The current study observed that biofilm development could be prevented in staphylococcal nuclease-producing strains of S. aureus; however, when the nuc1 gene was knocked out, the ability to form a biofilm significantly increased. Scanning electron and confocal scanning laser microscopy were used to evaluate the role of the nuc1 gene in biofilm formation. Moreover, the nuc1 gene product, staphylococcal nuclease, and recombinant NUC1 protein were found to have a visible effect on other biofilm-forming bacteria, such as Pseudomonas aeruginosa, Actinobacillus pleuropneumoniae, and Haemophilus parasuis. The current study showed a direct relationship between staphylococcal nuclease production and the prevention of biofilm development. The findings from this study underscore the important role of staphylococcal nuclease activity to prevent biofilm formation in S. aureus. They also provided evidence for the biological role of staphylococcal nucleases in other organisms.     

Rescue of First-Step-Transfer Amber Mutants by “Second-Step-Transfer-Blocked” Bacteriophage T5 on an su− Strain

T5 st0 phages irreversibly blocked in the injection of their second-step-transfer DNA can produce active A1 and A2 proteins which complement first-step-transfer amber mutants infecting an su⁻ strain.     

Synthesis of Analogs of Pestalotin

Starch-utilizing mutants of Escherichia coli which can grow well on starch or amylose as the sole carbon source were isolated. The maximal viable cell number of the starch-utilizing mutants on the polysaccharide media reached the same level (4 × 10⁹ cells/ml) as that with glucose medium after incubation for 24 hours at 37°C. The isolated mutants could produce more intracellular α-amylase than the wild-type strain, and the enzyme activity was detected in the extracellular fluid. Polyacrylamide gel electrophoresis showed that the intracellular and extracellular enzymes had similar electrophoretic mobilities. These observations suggested that the ability of growth on the polysaccharide media was due to the excreted α-amylase, which appeared to be identical with the intracellular enzyme.     

The RecB Nuclease Domain Binds to RecA-DNA Filaments: Implications for Filament Loading

The E. coli RecBCD enzyme facilitates the loading of RecA onto single-stranded DNA produced by the combined helicase/nuclease activity of RecBCD. The nuclease domain of RecB protein, RecB^nuc, has been previously shown to bind RecA. Surprisingly, RecB^nuc also binds to phage and eukaryotic homologs of RecA, leading to the suggestion that RecB^nuc interacts with the polymerization motif that is present in all three proteins. This mode of interaction could only be with monomeric RecA, as this motif would be buried in filaments. We show that RecB^nuc binds extensively to the outside of RecA-DNA filaments. Three-dimensional reconstructions suggest that RecB^nuc binds to the ATP-binding core of RecA, with a displacement of the C-terminal domain of RecA. Solution experiments confirm that the interaction of RecB^nuc is only with the RecA core. Since the RecA C-terminal domain has been shown to be regulatory, the interaction observed may be part of the loading mechanism where RecB displaces the RecA C-terminal domain and activates a RecA monomer for polymerization.     

Characterization of the thylakoid membranes of the tobacco aurea mutant Su/su and of three green revertant plants

Phenotypic characterizations of the semidominant aurea tobacco (Nicotiana tabacum L.) mutant Su/su, the homozygous mutant Su/Su and three green revertants (R1, R2, and R3) are presented. The leaf color of Su/su plants varies from yellow to light-green when grown under high and low energy fluence rates (33.0 and 3.3 W m^–2), respectively. The change in visual phenotype under high-light conditions is correlated with decreased content of chlorophyll per leaf area, agranal chloroplast ultrastructure, changes in the number of chlorophyll-protein complexes, and absence of two or more of the light harvesting chlorophyll-polypeptides of 25,000–29,000 dalton. The homozygous mutant grown under low light was shown to be completely lacking in grana stacks and to be deficient in chlorophyll-protein complexes. Revertant R1 was found to be identical to wild-type plants in all parameters examined (leaf color, chloroplast ultrastructure, chlorophyll-protein complexes, chlorophyll-protein complex polypeptides) except in chlorophyll content. It did not show an increased chlorophyll and carotenoid content as did the wild-type plants when exposed to high light. Revertants R2 and R3 were similar to the heterozygous mutant Su/su in most of the parameters examined. They yellowed because of a loss of chlorophyll and an increase in the amount of carotenoids, had agranal chloroplasts, and had variant chlorophyll-protein complexes when grown under high light intensities. However, each appeared to contain some of the light-harvesting pigment-protein complex polypeptides found to be absent in Su/su when grown under high-light conditions.Abbreviations HL high light - LL low light - SDS sodium dodecyl sulfate This paper is part of a Ph.D. thesis by P.J.K. in the Program in Genetics, Michigan State University     

Isolation of an Escherichia coli strain restricting bacteriophage suppressor

Summary A bacterial mutant is described which restricts bacteriophage amber suppressor psu ⁺. Restriction, probably, operates at a translational level. The new strain provides the system of identification of bacteriophage amber mutants suppressed by psu ⁺ using suppressornegative (su ^-) bacterial strains.     

Genes required for both gliding motility and development in Myxococcus xanthus

Myxococous xanthus cells can glide both as individual cells, dependent on A dventurous motility (A motility), and as groups of cells, dependent upon S ocial motility (S motility), Tn5-lac mutagenesis was used to generate 16 new A^- and nine new S^- mutations. In contrast with previous results, we find that subsets of A^- mutants are defective in fruiting body morphogenesis and/or myxospore differentiation. All S^- mutants are defective in fruiting body morphogenesis, consistent with previous results. Whereas some S^- mutants produce a wild-type complement of spores, others are defective in the differentiation of myxospores. Therefore, a subset of the A genes and all of the S genes are critical for fruiting body morphogenesis. Subsets of both A and S genes are essential for sporulation. Three S::Tn5–lac insertions result in surprising phenotypes. Colonies of two S^- mutants glide on ‘swim’ (0.35% agar) plates to form fractal patterns. These S^- mutants are the first examples of a bacterium in which mutations result in fractal patterns of colonial spreading. An otherwise wild-type strain with one S^- insertion resembles the frz^- sglA1^- mutants upon development, suggesting that this S^- gene defines a new chemotaxis component in M. xanthus.     

Magnetic resonance studies of the binding of oligonucleotide substrates to mutants of staphylococcal nuclease

By a combination of NMR docking and model building, the substrate binding site on staphylococcal nuclease was found to accommodate a trinucleotide and to consist of three subsites, each interacting with a single nucleotidyl unit of DNA. Binding of the essential Ca²⁺ activator and substrate cleavage occur between subsites 1 and 2. Hence, catalytically productive binding would span subsites 1 and 2 while nonproductive binding would span subsites 2 and 3. Lys-49 is near subsite 1, and Lys-84 and Tyr-115 interact with substrates at sub site 3 [Weber, D. J., Gittis, A. G., Mullen, G. P., Abeygunawardana, C., Lattman, E. E., Mildvan, A. S. Proteins 13:275–287, 1992]. The proposed locations of these subsites were independently tested by the effects of the K49A, K84A, and Y115A mutations of staphylococcal nuclease on the binding of Mn²⁺, Ca²⁺, and the dinucleotide and trinucleotide substrates, 5′-pdTdA, dTdA, and dTdAdG. These three mutants have previously been shown to be fully active and to have CD and 2D NMR spectra very similar to those of the wild-type enzyme (Chuang, W.-J., Weber, D. J., Gittis, A. G., Mildvan, A. S. Proteins 17:36–48, 1993). All three mutant enzymes and their pdTdA and dTdA complexes (but not their dTdAdG complex) bind Mn²⁺ and Ca²⁺ more weakly than the wild-type enzyme by factors ranging from 2 to 11. The presence of a terminal phosphate as in 5′-pdTdA raises the affinity of the substrate for staphylococcal nuclease and its three mutants by two orders of magnitude and for the corresponding enzyme–metal complexes by three to four orders of magnitude, suggesting that the terminal phosphate is coordinated by the enzyme-bound divalent cation. Such complexation would result in the nonproductive binding of 5′-pdTdA at subsites 2 and 3. Accordingly, the K84A and Y115A mutations significantly weaken the binding of 5′-pdTdA and its metal to staphylococcal nuclease by factors of 2.2 to 37.8, while the K49A mutation has much smaller or no effect. Such nonproductive binding explains the low activity of staphylococcal nuclease with small substrates, especially those With a terminal phosphate. Similarly, the K84A and Y115A mutations weaken the binding of dTdA and its metal complexes to the enzyme by factors of 3.4 to 13.1 while the K49A mutation has smaller effects indicating significant nonproductive binding of dTdA. The trinucleotide dTdAdG binds more tightly to wild-type and mutant staphylococcal nuclease and to its metal complexes than does the dinucleotide dTdA by factors of 2.4 to 12.2, reflecting the occupancy of an additional subsite. Predominantly productive binding of dTdAdG is indicated by the 1.7? to 8.3?fold lower affinities of the K49A, K84A, and Y115A mutants for the trinucleotide and its metal complexes. The largest effects on dTdAdG binding are seen with the Y115A mutation presumably reflecting the dual role of Tyr-115 both in donating a hydrogen bond to a phosphodiester oxygen between subsites 2 and 3 and in stacking onto the guanine base at subsite 3. © 1994 John Wiley & Sons, Inc.     

Characterization of revertants of stmF mutants of Dictyostelium discoideum: Evidence that stmF is the structural gene of the cgmp-specific phosphodiesterase

stmF mutants of Dictyostelium discoideum produce long, banded aggregation streams on growth plates and exhibit altered cGMP metabolism. To learn more about the role of cGMP in chemotaxis and the nature of the defect in these mutants, 15 nonstreaming (Stm⁺) revertants of two stmF mutants were isolated and characterized. Fourteen of the revertants continued to show the elevated cAMP-induced cGMP response and very low cGMP-specific phosphodiesterase (cGPD) activity characteristic of their stmF parents. Parasexual genetic analysis revealed that many of these Stm⁺ revertants carried phenotypic suppressors unlinked to stmF. One Stm⁺ revertant, strain HC344, exhibited a low, prolonged cGMP response and relatively high cGPD activity throughout development. To determine whether the elevated cGPD activity in this revertant resulted from increased enzyme production or enhanced enzyme activity, cGPDs were partially purified from the wild-type strain, the stmF parent and revertant HC344, and properties of the enzymes were compared. cGPDs from the stmF mutant and the revertant showed similar differences from the wild-type enzyme in kinetic properties, thermal stability, and sensitivity to certain inhibitors. These results suggest that stmF is the structural gene of the cGPD. In addition, the unusual cGMP response in revertant HC344 appeared to be due to increased production of an altered cGPD.