Secondary Suppressor Research Articles

Characterization of FtsH Essentiality in Streptococcus mutans via Genetic Suppression.

FtsH belongs to the AAA+ ATP-dependent family of proteases, which participate in diverse cellular processes and are ubiquitous among bacteria, chloroplasts, and mitochondria. FtsH is poorly characterized in most organisms, especially compared to other major housekeeping proteases. In the current study, we examined the source of FtsH essentiality in the human oral microbiome species Streptococcus mutans, one of the primary etiological agents of dental caries. By creating a conditionally lethal ftsH mutant, we were able to identify a secondary suppressor missense mutation in the vicR gene, encoding the response regulator of the essential VicRK two-component system (TCS). Transcriptomic analysis of the vicR (G195R) mutant revealed significantly reduced expression of 46 genes, many of which were located within the genomic island Tnsmu2, which harbors the mutanobactin biosynthetic gene cluster. In agreement with the transcriptomic data, deletion of the mutanobactin biosynthetic gene cluster suppressed ftsH essentiality in S. mutans. We also explored the role of FtsH in S. mutans physiology and demonstrated its critical role in stress tolerance, especially acid stress. The presented results reveal the first insights within S. mutans for the pleiotropic regulatory function of this poorly understood global regulator.

Balancing Positive and Negative Selection: In Vivo Evolution of Candida lusitaniae MRR1.

The evolution of pathogens in response to selective pressures present during chronic infections can influence their persistence and virulence and the outcomes of antimicrobial therapy. Because subpopulations within an infection can be spatially separated and the host environment can fluctuate, an appreciation of the pathways under selection may be most easily revealed through the analysis of numerous isolates from single infections. Here, we continued our analysis of a set of clonally derived Clavispora (Candida) lusitaniae isolates from a single chronic lung infection with a striking enrichment in the number of alleles of MRR1 Genetic and genomic analyses found evidence for repeated acquisition of gain-of-function mutations that conferred constitutive Mrr1 activity. In the same population, there were multiple alleles with both gain-of-function mutations and secondary suppressor mutations that either attenuated or abolished the constitutive activity, suggesting the presence of counteracting selective pressures. Our studies demonstrated trade-offs between high Mrr1 activity, which confers resistance to the antifungal fluconazole, host factors, and bacterial products through its regulation of MDR1, and resistance to hydrogen peroxide, a reactive oxygen species produced in the neutrophilic environment associated with this infection. This inverse correlation between high Mrr1 activity and hydrogen peroxide resistance was observed in multiple Candida species and in serially collected populations from this individual over 3 years. These data lead us to propose that dynamic or variable selective pressures can be reflected in population genomics and that these dynamics can complicate the drug resistance profile of the population.IMPORTANCE Understanding microbial evolution within patients is critical for managing chronic infections and understanding host-pathogen interactions. Here, our analysis of multiple MRR1 alleles in isolates from a single Clavispora (Candida) lusitaniae infection revealed the selection for both high and low Mrr1 activity. Our studies reveal trade-offs between high Mrr1 activity, which confers resistance to the commonly used antifungal fluconazole, host antimicrobial peptides, and bacterial products, and resistance to hydrogen peroxide. This work suggests that spatial or temporal differences within chronic infections can support a large amount of dynamic and parallel evolution and that Mrr1 activity is under both positive and negative selective pressure to balance different traits that are important for microbial survival.

Co-Inactivation of GlnR and CodY Regulators Impacts Pneumococcal Cell Wall Physiology.

CodY, a nutritional regulator highly conserved in low G+C Gram-positive bacteria, is essential in Streptococcus pneumoniae (the pneumococcus). A published codY mutant possessed suppressing mutations inactivating the fatC and amiC genes, respectively belonging to iron (Fat/Fec) and oligopeptide (Ami) ABC permease operons, which are directly repressed by CodY. Here we analyzed two additional published codY mutants to further explore the essentiality of CodY. We show that one, in which the regulator of glutamine/glutamate metabolism glnR had been inactivated by design, had only a suppressor in fecE (a gene in the fat/fec operon), while the other possessed both fecE and amiC mutations. Independent isolation of three different fat/fec suppressors thus establishes that reduction of iron import is crucial for survival without CodY. We refer to these as primary suppressors, while inactivation of ami, which is not essential for survival of codY mutants and acquired after initial fat/fec inactivation, can be regarded as a secondary suppressor. The availability of codY - ami + cells allowed us to establish that CodY activates competence for genetic transformation indirectly, presumably by repressing ami which is known to antagonize competence. The glnR codY fecE mutant was then found to be only partially viable on solid medium and hypersensitive to peptidoglycan (PG) targeting agents such as the antibiotic cefotaxime and the muramidase lysozyme. While analysis of PG and teichoic acid composition uncovered no alteration in the glnR codY fecE mutant compared to wildtype, electron microscopy revealed altered ultrastructure of the cell wall in the mutant, establishing that co-inactivation of GlnR and CodY regulators impacts pneumococcal cell wall physiology. In light of rising levels of resistance to PG-targeting antibiotics of natural pneumococcal isolates, GlnR and CodY constitute potential alternative therapeutic targets to combat this debilitating pathogen, as co-inactivation of these regulators renders pneumococci sensitive to iron and PG-targeting agents.

Biochemical Activities of Streptococcus pneumoniae Serotype 2 Capsular Glycosyltransferases and Significance of Suppressor Mutations Affecting the Initiating Glycosyltransferase Cps2E

The capsular polysaccharide (CPS) is essential for Streptococcus pneumoniae virulence. Its synthesis requires multiple enzymes, and defects that block completion of the pathway can be lethal in the absence of secondary suppressor mutations. In this study, we examined the functions of three capsular glycosyltransferases (Cps2F, Cps2G, and Cps2I) involved in serotype 2 CPS synthesis, whose deletions select for secondary mutations. We demonstrate that Cps2F is a rhamnosyltransferase that catalyzes addition of the third and fourth sugars in the capsule repeat unit, while Cps2G adds the fifth sugar (glucose). Addition of the terminal residue (glucuronic acid) could not be detected; however, activities of the other glycosyltransferases together with bioinformatic analyses suggest that this step is mediated by Cps2I. Most of the secondary suppressor mutations resulting from loss of these enzymes occur in cps2E, the gene encoding the initiating glycosyltransferase. Examination of the 69 S. pneumoniae serotypes containing Cps2E homologues yielded a consensus amino acid sequence for this protein and demonstrated that there is a highly significant association between the residues that are 100% conserved and those altered by suppressor mutations. Cps2E contains an extracytoplasmic loop whose function is unknown. Among our collection of mutants, six contained missense mutations affecting amino acids in the extracytoplasmic loop. These residues are highly conserved among S. pneumoniae Cps2E homologues, and mutations therein severely reduced CPS synthesis and Cps2E activity. The critical functions of these amino acids suggest a role for the Cps2E extracytoplasmic loop in initiation, and possibly regulation, of capsule synthesis.

Genetic and Biochemical Characterizations of Enzymes Involved in Streptococcus pneumoniae Serotype 2 Capsule Synthesis Demonstrate that Cps2T (WchF) Catalyzes the Committed Step by Addition of β1-4 Rhamnose, the Second Sugar Residue in the Repeat Unit

Five genes (cps2E, cps2T, cps2F, cps2G, and cps2I) are predicted to encode the glycosyltransferases responsible for synthesis of the Streptococcus pneumoniae serotype 2 capsule repeat unit, which is polymerized to yield a branched surface structure containing glucose-glucuronic acid linked to a glucose-rhamnose-rhamnose-rhamnose backbone. Cps2E is the initiating glycosyltransferase, but experimental evidence supporting the functions of the remaining glycosyltransferases is lacking. To biochemically characterize the glycosyltransferases, the donor substrate dTDP-rhamnose was first synthesized using recombinant S. pneumoniae enzymes Cps2L, Cps2M, Cps2N, and Cps2O. In in vitro assays with each of the glycosyltransferases, only reaction mixtures containing recombinant Cps2T, dTDP-rhamnose, and the Cps2E product (undecaprenyl pyrophosphate glucose) generated a new product, which was consistent with lipid-linked glucose-rhamnose. cps2T, cps2F, and cps2I deletion mutants produced no detectable capsule, but trace amounts of capsule were detectable in Δcps2G mutants, suggesting that Cps2G adds a nonbackbone sugar. All Δcps2F, Δcps2G, and Δcps2I mutants contained different secondary suppressor mutations in cps2E, indicating that the initial mutations were lethal in the absence of reduced repeat unit synthesis. Δcps2T mutants did not contain secondary mutations affecting capsule synthesis. The requirement for secondary mutations in mutants lacking Cps2F, Cps2G, and Cps2I indicates that these activities occur downstream of the committed step in capsule synthesis and reveal that Cps2T catalyzes this step. Therefore, Cps2T is the β1-4 rhamnosyltransferase that adds the second sugar to the repeat unit and, as the committed step in type 2 repeat unit synthesis, is predicted to be an important point of capsule regulation.

The Campylobacter jejuni stringent response controls specific stress survival and virulence‐associated phenotypes

Campylobacter jejuni is a highly prevalent food-borne pathogen that causes diarrhoeal disease in humans. A natural zoonotic, it must overcome significant stresses both in vivo and during transmission despite the absence of several traditional stress response genes. Although relatively little is understood about its mechanisms of pathogenesis, its ability to interact with and invade human intestinal epithelial cells closely correlates with virulence. A C. jejuni microarray-based screen revealed that several known virulence genes and several uncharacterized genes, including spoT, were rapidly upregulated during infection of human epithelial cells. spoT and its homologue relA have been shown in other bacteria to regulate the stringent response, an important stress response that to date had not been demonstrated for C. jejuni or any other epsilon-proteobacteria. We have found that C. jejuni mounts a stringent response that is regulated by spoT. Detailed analyses of a C. jejuni delta spoT mutant revealed that the stringent response is required for several specific stress, transmission and antibiotic resistance-related phenotypes. These include stationary phase survival, growth and survival under low CO2/high O2 conditions, and rifampicin resistance. A secondary suppressor strain that specifically rescues the low CO2 growth defect of the delta spoT mutant was also isolated. The stringent response additionally proved to be required for the virulence-related phenotypes of adherence, invasion, and intracellular survival in two human epithelial cell culture models of infection; spoT is the first C. jejuni gene shown to participate in longer term survival in epithelial cells. Microarray analyses comparing wild-type to the delta spoT mutant also revealed a strong correlation between gene expression profiles and phenotype differences observed. Together, these data demonstrate a critical role for the C. jejuni stringent response in multiple aspects of C. jejuni biology and pathogenesis and, further, may lend novel insight into unexplored features of the stringent response in other prokaryotic organisms.

The Bacillus subtilis catabolite control protein CcpA exerts all its regulatory functions by DNA-binding.

In Bacillus subtilis, carbon catabolite control is mediated by the regulatory protein CcpA. In addition to loss of catabolite repression, ccpA mutants exhibit a severe growth defect. They are not able to grow with glucose and ammonium as single sources of carbon and nitrogen, respectively. Only ccpA mutant strains carrying either secondary suppressor mutations or that are affected in specific amino acids in the DNA-binding domain of CcpA grow on minimal media. We addressed the importance of DNA-binding by CcpA for both carbon catabolite repression and growth of a mutant strain. A strain specifically deleted for the N-terminal DNA-binding domain of CcpA was constructed. This deletion resulted in complete loss of catabolite repression of beta-xylosidase synthesis and prevented bacteria from growing on minimal media, suggesting that DNA-binding by CcpA is required for both carbon catabolite repression and efficient growth on minimal media.

The Bacillus subtilis catabolite control protein CcpA exerts all its regulatory functions by DNA-binding

In Bacillus subtilis, carbon catabolite control is mediated by the regulatory protein CcpA. In addition to loss of catabolite repression, ccpA mutants exhibit a severe growth defect. They are not able to grow with glucose and ammonium as single sources of carbon and nitrogen, respectively. Only ccpA mutant strains carrying either secondary suppressor mutations or that are affected in specific amino acids in the DNA-binding domain of CcpA grow on minimal media. We addressed the importance of DNA-binding by CcpA for both carbon catabolite repression and growth of a mutant strain. A strain specifically deleted for the N-terminal DNA-binding domain of CcpA was constructed. This deletion resulted in complete loss of catabolite repression of β-xylosidase synthesis and prevented bacteria from growing on minimal media, suggesting that DNA-binding by CcpA is required for both carbon catabolite repression and efficient growth on minimal media.

Mutant strains of Saccharomyces cerevisiae lacking sphingolipids synthesize novel inositol glycerophospholipids that mimic sphingolipid structures.

Mutant strains of Saccharomyces cerevisiae, termed SLC, make no detectable sphingolipids when cultured without a sphingolipid long chain base such as phytosphingosine (Dickson, R.C., Wells, G.B., Schmidt, A., and Lester, R.L. (1990) Mol. Cell. Biol. 10, 2176-2181). When grown with phytosphingosine they make sphingolipids in normal amounts. SLC strains carry a secondary suppressor mutation that bypasses the need to synthesize a long chain base. Hypothetically, the suppressor mutation could function by mutating a gene whose protein product required a sphingolipid for function, by increasing the level of one or more endogenous lipids, or by making new lipid(s). Here we demonstrate that SLC strains make novel inositol glycerophospholipids when cultured without a long chain base. The novel lipids are phosphatidylinositol (PI), mannosyl-PI, and inositol-P-(mannosyl-PI), containing 1 mol of C26 fatty acid, ordinarily found in yeast sphingolipids but not usually found in glycerophospholipids; the C26 fatty acid appears to be located at the SN-2 position of the glycerol. In addition, mono-fattyacyl versions of these three compounds were also identified. The polar head groups and hydrophobic portions of these novel lipids are strikingly similar to S. cerevisiae sphingolipids found in wild-type cells. We speculate that the novel lipids structurally mimic sphingolipids and thereby compensate for some sphingolipid function(s) necessary for growth.

The exoR gene of Rhizobium meliloti affects RNA levels of other exo genes but lacks homology to known transcriptional regulators

Rhizobium meliloti strains mutant in the exoR gene overproduce an exopolysaccharide called succinoglycan or EPS I. Protein fusions to several different exo genes required for EPS I biosynthesis are expressed at a higher level in an exoR strain than in a wild-type strain, showing that the overproduction of EPS I in exoR strains results at least in part from increased gene expression. This regulation is important to nodulation, since exoR mutants fail to invade alfalfa nodules unless secondary suppressor mutations that cause a decrease in EPS I production occur. Here, we show that an exoR strain contains higher levels of mRNA for other exo genes than does the wild-type parental strain. ExoR therefore most probably exerts its regulatory effect at the level of transcription. In addition, we have localized, subcloned, and sequenced the exoR gene. A newly constructed insertion allele of exoR has the same phenotype as the original mutant. The deduced sequence of ExoR is 268 amino acids long but does not show homology to other sequenced genes.

Lysis of Escherichia coli by the bacteriophage phi X174 E protein: inhibition of lysis by heat shock proteins

Lysis of Escherichia coli by the cloned E protein of bacteriophage phi X174 was more rapid than expected when bacteria were shifted from 30 to 42 degrees C at the time of E induction. Since such treatment also induces the heat shock response, we investigated the effect of heat shock proteins on lysis. An rpoH mutant was more sensitive to lysis by E, but a secondary suppressor mutation restored lysis resistance to parental levels, which suggests that the sigma 32 subunit itself did not directly increase lysis resistance. At 30 degrees C, mutants in five heat shock genes (dnaK, dnaJ, groEL, groES, and grpE) were more sensitive to lysis than were their wild-type parents. The magnitude of lysis sensitivity varied with mutation and strain background, with dnaK, dnaJ, and groES mutants consistently exhibiting the greatest sensitivities. Extended protection against lysis occurred when overproduction of heat shock proteins was induced artificially in cells that contained a plasmid with the rpoH+ gene under control of the tac promoter. This protective effect was completely abolished by mutations in dnaK, dnaJ, or groES but not by grpE or groEL mutations. Altered membrane behavior probably explains the contradiction whereby an actual temperature shift sensitized cells to lysis, but production of heat shock proteins exhibited protective effects. The results demonstrate that E-induced lysis can be divided into two distinct operations which may now be studied separately. They also emphasize a role for heat shock proteins under non-heat-shock conditions and suggest cautious interpretation of lysis phenomena in systems where E protein production is under control of a temperature-sensitive repressor.

Lack of secondary suppressor response in enhanced allografted rats with endogenous suppressor activity in spleen and diminished cytotoxic T cell response.

In order to better understand the mechanisms of alloimmunization occurring in transplantation, we studied the immune response of an inbred rat strain (WF) to varied presentation of alloantigens (LEW). Hyperimmunized rats acutely reject transplanted allografts and demonstrate direct cytotoxic activity, as well as an expanded potential to generate cytotoxic and suppressor cell activity. In contrast, passively and actively enhanced animals, which exhibit allograft tolerance, demonstrate endogenous suppressor cell activity and significantly reduced potential to generate cytotoxic and suppressor cell activity. Thus, the method of immunization of the same responder strain animals with identical alloantigens will determine whether rejection or tolerance is evidenced following transplantation. The suppressor T cell activity demonstrated in the enhanced animals appears to regulate the immune response by reducing cell proliferation when challenged with alloantigen. However, when restimulated in vitro with donor cells, splenic suppressor activity declines--i.e., there is not a secondary suppressor response.

The distribution of the Qa-2 alloantigen on functional T lymphocytes.

The expression of Qa-2 on functional lymphocytes was investigated in vitro and in vivo by using a monoclonal anti-Qa-2 antibody. In vitro treatment of T cells with antibody and complement demonstrated that T cells mediating help or delayed-type hypersensitivity for anti-SRBC responses were Qa-2+. In addition, cytotoxic T cells and either their precursors or cells involved in their generation were Qa-2+, as were anti-HGG suppressor T cells. Panning techniques were also used to show that secondary suppressor T cells were Qa-2+ and that there may be heterogeneity in suppressor T cells defined by Qa-2 expression. In vivo treatment of mice with anti-Qa-2 resulted in decrease in immune responsiveness seen by i) prolongation of skin grafts with either H-2D or I-A differences, ii) suppression of delayed-type hypersensitivity, and iii) inhibition of T cell-mediated suppression. Finally, IgG, but not IgM, anti-body-forming cells were Qa-2+.

Cyclophosphamide-sensitive contrasuppression in TNP-anterior chamber associated immune deviation (TNP-ACAID).

Injection of trinitrophenyl (TNP)-modified splenocytes (TNP-Sp) into the anterior chamber of the eye results in systemic tolerance to TNP, a phenomenon termed anterior chamber associated immune deviation (TNP-ACAID). Two distinct suppressor pathways develop after the induction of TNP-ACAID. The primary suppressor pathway (I) is antigen-specific, is mediated by a cyclophosphamide (Cy)-sensitive suppressor T cell (Ts-I), and requires a Cy-sensitive auxillary cell. The secondary suppressor pathway (II) is antigen nonspecific, is mediated by a Cy-resistant suppressor T cell (Ts-II), and requires a TNP-pulsed accessory macrophage. Suppression via pathway II is demonstrable only when Ts-I cells are functionally inactivated by Cy. Furthermore, the addition of T cells from Sp containing active Ts-I inhibits Ts-II. This suppression of a suppressor cell (i.e., contrasuppression) is mediated by either Ts-I or a third T cell population, which is also Cy sensitive.

REGULATION OF DELAYED-TYPE HYPERSENSITIVITY

Mice develop highly significant levels of delayed-type hypersensitivity (DTH) to major and minor histocompatibility antigens when injected s.c. with lymphoid cells from X-irradiated allogeneic donors. However, when mice are inoculated i.v. with a high dose of X-irradiated allogeneic lymphoid cells, they not only fail to develop DTH to the allogeneic cells, but their ability to respond to an immunogenic challenge of the alloantigens is also significantly depressed. This suppression is adoptively transferable by antigen-specific suppressor T cells and not by immune serum. Cell surface phenotypic analysis shows that the primary suppressor cells for alloantigens are Thy-1+, Lyt-1+2-, and Ia-, whereas the secondary suppressor cells appearing after boosting injection are Thy-1+, Lyt-1+2+, and Ia-. These suppressor T (Ts) cells localize in the lymphoid organs shortly after their induction and are largely absent from the spleen or lymph node 1 month later. However, "suppressor memory" can be recalled by an immunogenic dose of alloantigens which would normally induce DTH effector cells rather than suppressor cells in naive mice. When the suppressor cells were cultured in vitro for 48 hr, the supernatant contained suppressive activity. It appears likely that the manifestation of the suppressor cells is via soluble, antigen-specific suppressor factor(s), the production of which is dependent on viable T cells.

Glycine transfer RNA of Escherichia coli: II. Impaired GGA-recognition in strains containing a genetically altered transfer RNA; Reversal by a secondary suppressor mutation

The glycine-specific tRNA from Escherichia coli is separable into three components (tRNA I Gly, tRNA II Gly and tRNA III Gly) by chromatography over BD-ellulose. ‡ ‡ Abbreviations used: BD-cellulose, benzoylated DEAE-cellulose; genetic symbols are explained in the legend of Table 1. Triplet binding studies reveal that tRNA I Gly recognizes predominantly GpGpG, tRNA II Gly recognizes both GpGpG and GpGpA, and tRNA III Gly recognizes GpGpU and GpGpC. Strains carrying a suppressor ( glyTsu) of the trpA36 mutation (Gly → Arg, GGA → AGA) lack a functional tRNA II Gly and, as a result, exhibit severe pleiotropic effects. As expected, the binding of [ 14C]glycyl-tRNA from glyTsu strains to ribosomes is only weakly stimulated by GpGpA (8% of the control), while binding in the presence of GpGpG, GpGpU and GpGpC is relatively normal. On the other hand, suppressed strains ( glyUsu) lacking a functional tRNA I Gly do not show these adverse effects, and tRNA from these strains displays a nearly normal codon recognition pattern. The pleiotropic effects seen in glyTsu strains lacking a normal tRNA II Gly are reversed either by (a) the presence of a normal glyT + gene in the same organism, or (b) by secondary mutations ( ins) unlinked to the glyT region. The GpGpA-stimulated binding of glyTsu ins tRNA to ribosomes is partially restored to normal. Transfer RNA from ins strains contains a new tRNA Gly species (tRNA III Gly), easily detectable by BD-cellulose chromatography. This new tRNA III Gly, binds to ribosomes in the presence of GpGpA or GpGpG, but not GpGpU or GpGpC. The results indicate that tRNA III Gly is formed by a genetically induced alteration of a portion of tRNA III Gly. It seems likely that the ins mutation results in a GGU/C → GGA/G change in a redundant tRNA III Gly species, thus relieving the pleiotropy induced by the loss of a normal tRNA II Gly.

A Low Pressure Ionization Gauge

An ionization gauge is described which uses an ion gun designed for end extraction. An out-of-sight ion collector is used to extend the x-ray limit normally present in simpler structures. The gauge head has a sensitivity of 60 Torr−1 without a secondary suppressor electrode or 20 Torr−1 with a secondary suppressor. The gauge head is not difficult to make, uses a simple power supply, and does not require any focusing adjustment. Ion trajectories, plotted by a digital computer, are used to give an insight into the efficient operation of the structure.