The origins of modern proteomes.

Distributions of phylogenetically related protein domains (fold superfamilies), or FSFs, among the three Superkingdoms (trichotomy) are assessed. Very nearly 900 of the 1200 FSFs of the trichotomy are shared by two or three Superkingdoms. Parsimony analysis of FSF distributions suggests that the FSF complement of the last common ancestor to the trichotomy was more like that of modern eukaryotes than that of archaea and bacteria. Studies of length distributions among members of orthologous families of proteins present in all three Superkingdoms reveal that such lengths are significantly longer among eukaryotes than among bacteria and archaea. The data also reveal that proteins lengths of eukaryotes are more broadly distributed than they are within archaeal and bacterial members of the same orthologous families. Accordingly, selective pressure for a minimal size is significantly greater for orthologous protein lengths in archaea and bacteria than in eukaryotes. Alignments of orthologous proteins of archaea, bacteria and eukaryotes are characterized by greater sequence variation at their N-terminal and C-terminal domains, than in their central cores. Length variations tend to be localized in the terminal sequences; the conserved sequences of orthologous families are localized in a central core. These data are consistent with the interpretation that the genomes of the last common ancestor (LUCA) encoded a cohort of FSFs not very different from that of modern eukaryotes. Divergence of bacterial and archaeal genomes from that common ancestor may have been accompanied by more intensive reductive evolution of proteomes than that expressed in eukaryotes. Dollo's Law suggests that the evolution of novel FSFs is a very slow process, while laboratory experiments suggests that novel protein genesis from preexisting FSFs can be relatively rapid. Reassortment of FSFs to create novel proteins may have been mediated by genetic recombination before the advent of more efficient splicing mechanisms.

Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori.

Among the several factors that affect the appearance and spread of acquired antibiotic resistance, the mutation frequency and the biological cost of resistance are of special importance. Measurements of the mutation frequency to rifampicin resistance in Helicobacter pylori strains isolated from dyspeptic patients showed that approximately 1/4 of the isolates had higher mutation frequencies than Enterobacteriaceae mismatch-repair defective mutants. This high mutation frequency could explain why resistance is so frequently acquired during antibiotic treatment of H. pylori infections. Inactivation of the mutS gene had no substantial effect on the mutation frequency, suggesting that MutS-dependent mismatch repair is absent in this bacterium. Furthermore, clarithromycin resistance conferred a biological cost, as measured by a decreased competitive ability of the resistant mutants in mice. In clinical isolates this cost could be reduced, indicating that compensation is a clinically relevant phenomenon that could act to stabilize resistant bacteria in a population.

Comparison of repressor and transcriptional attenuator systems for control of amino acid biosynthetic operons.

In bacteria, expression from amino acid biosynthetic operons is transcriptionally controlled by two main mechanisms with principally different modes of action. When the supply of an amino acid is in excess over demand, its concentration will be high and when the supply is deficient the amino acid concentration will be low. In repressor control, such concentration variations in amino acid pools are used to regulate expression from the corresponding amino acid synthetic operon; a high concentration activates and a low concentration inactivates repressor binding to the operator site on DNA so that initiation of transcription is down or up-regulated, respectively. Excess or deficient supply of an amino acid also speeds or slows, respectively, the rate by which the ribosome translates mRNA base triplets encoding this amino acid. In attenuation of transcription, it is the rate by which the ribosome translates such "own" codons in the leader of an amino acid biosynthetic operon that decides whether the RNA polymerase will continue into the operon, or whether transcription will be aborted (attenuated). If the ribosome rate is fast (excess synthesis of amino acid), transcription will be terminated and if the rate is slow (deficient amino acid supply) transcription will continue and produce more messenger RNAs. Repressor and attenuation control systems have been modelled mathematically so that their behaviour in living cells can be predicted and their system properties compared. It is found that both types of control systems are unexpectedly sensitive when they operate in the cytoplasm of bacteria. In the repressor case, this is because amino acid concentrations are hypersensitive to imbalances between supply and demand. In the attenuation case, the reason is that the rate by which ribosomes translate own codons is hypersensitive to the rate by which the controlled amino acid is synthesised. Both repressor and attenuation mechanisms attain close to Boolean properties in vivo: gene expression is either fully on or fully off except in a small interval around the point where supply and demand of an amino acid are perfectly balanced.Our results suggest that repressors have significantly better intracellular performance than attenuator mechanisms. The reason for this is that repressor, but not attenuator, mechanisms can regulate expression from biosynthetic operons also when transfer RNAs are fully charged with amino acids so that the ribosomes work with maximal speed.

Residual human immunodeficiency virus type 1 infection in lymphoid tissue during highly active antiretroviral therapy: quantitation and virus characterization.

HIV-1 can persist in infected patients despite undetectable plasma viremia. To characterize the residual viral load, repetitive blood and tonsillar samples were collected from 11 HIV-1-positive individuals before and during 96 weeks of therapy with zidovudine, lamivudine, and indinavir. HIV-1 RNA in tonsils was quantified by RT-PCR and infectious HIV-1 provirus by the limiting dilution assay. Genotypic resistance analyses and biological characterization were performed on plasma virus, blood, and tonsillar isolates. Tonsillar infectious HIV-1 provirus and HIV-1 RNA declined by 2 and 3 log(10), respectively, but 10(3)-10(4) cells, less than 0.5% of the total body CD4(+) T cell population carrying infectious HIV-1 provirus, remained involved in active viral replication of drug-sensitive R5 viruses. Thus, the dominant HIV-1 residual infection consists of < or = 10(6) latently infected CD4(+) cells. Plasma HIV-1 RNA decline of > 1.5 log(10) during the first 2 weeks of therapy may indicate low levels of this latent reservoir. Whereas the reservoir of latently infected cells remains stable, actively replicating HIV-1 continuously declines during prolonged antiretroviral therapy. Thus, although viral eradication seems unlikely, antiretroviral therapy may induce an extended period of virologic latency in HIV-1-positive individuals.

Fluctuations in repressor control: thermodynamic constraints on stochastic focusing.

The influence of fluctuations in molecule numbers on genetic control circuits has received considerable attention. The consensus has been that such fluctuations will make regulation less precise. In contrast, it has more recently been shown that signal fluctuations can sharpen the response in a regulated process by the principle of stochastic focusing (SF) (, Proc. Natl. Acad. Sci. USA. 97:7148-7153). In many cases, the larger the fluctuations are, the sharper is the response. Here we investigate how fluctuations in repressor or corepressor numbers can improve the control of gene expression. Because SF is found to be constrained by detailed balance, this requires that the control loops contain driven processes out of equilibrium. Some simple and realistic out-of-equilibrium steps that will break detailed balance and make room for SF in such systems are discussed. We conclude that when the active repressors are controlled by corepressor molecules that display large ("coherent") number fluctuations or when corepressors can be irreversibly removed directly from promoter-bound repressors, the response in gene activity can become significantly sharper than without intrinsic noise. A simple experimental design to establish the possibility of SF for repressor control is suggested.

Structural basis of the anionic interface preference and kcat* activation of pancreatic phospholipase A2.

Pancreatic phospholipase A(2) (PLA2) shows a strong preference for the binding to the anionic interface and a consequent allosteric activation. In this paper, we show that virtually all the preference is mediated through 3 (Lys-53, -56, and -120) of the 12 cationic residues of bovine pancreatic PLA2. The lysine-to-methionine substitution enhances the binding of the enzyme to the zwitterionic interface, and for the K53,56,120M triple mutant at the zwitterionic interface is comparable to that for the wild type (WT) at the anionic interface. In the isomorphous crystal structure, the backbone folding of K53,56M K120,121A and WT are virtually identical, yet a significant change in the side chains of certain residues, away from the site of substitution, mostly at the putative contact site with the interface (i-face), is discernible. Such reciprocity, also supported by the spectroscopic results for the free and bound forms of the enzyme, is expected because a distal structural change that perturbs the interfacial binding could also affect the i-face. The results show that lysine-to-methionine substitution induces a structural change that promotes the binding of PLA2 to the interface as well as the substrate binding to the enzyme at the interface. The kinetic results are consistent with a model in which the interfacial Michaelis complex exists in two forms, and the complex that undergoes the chemical step is formed by the charge compensation of Lys-53 and -56. Analysis of the incremental changes in the kinetic parameters shows that the charge compensation of Lys-53 and -56 contributes to the activation and that of Lys-120 contributes only to the structural change that promotes the stability of the Michaelis complex at the interface. The charge compensation effects on these three residues also account for the differences in the anionic interface preference of the evolutionarily divergent secreted PLA2.

Gradients in nucleotide and codon usage along Escherichia coli genes.

The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.

Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated.

Living cells differ from most other chemical systems in that they involve regulation pathways that depend very nonlinearly on chemical species that are present in low copy numbers per cell. This leads to a variety of intracellular kinetic phenomena that elude macroscopic modeling, which implicitly assumes that cells are infinitely large and fluctuations negligible. It is of particular importance to assess how fluctuations affect regulation in cases where precision and reliability are required. Here, taking finite cell size and stochastic aspects into account, we reinvestigate theoretically the mechanism of zero-order ultrasensitivity for covalent modification of target enzymes ( Proc. Natl. Acad. Sci. USA. 78:6840-6844). Macroscopically, this mechanism can produce a very sharp transition in target concentrations for very small changes in the activity of the converter enzymes. This study shows that the transition is much more gradual in a finite cell or a population of finite cells. It also demonstrates that the switch is exactly analogous to a thermodynamic phase transition and that ultrasensitivity is inevitably coupled to random ultravariation. As a consequence, the average response in a large population of cells will often be much more gradual than predicted from macroscopic descriptions.

Why mitochondrial genes are most often found in nuclei.

A very small fraction of the proteins required for the propagation and function of mitochondria are coded by their genomes, while nuclear genes code the vast majority. We studied the migration of genes between the two genomes when transfer mechanisms mediate this exchange. We could calculate the influence of differential mutation rates, as well as that of biased transfer rates, on the partitioning of genes between the two genomes. We observe no significant difference in partitioning for haploid and diploid cell populations, but the effective size of cell populations is important. For infinitely large effective populations, higher mutation rates in mitochondria than in nuclear genomes are required to drive mitochondrial genes to the nuclear genome. In the more realistic case of finite populations, gene transfer favoring the nucleus and/or higher mutation rates in the mitochondrion will drive mitochondrial genes to the nucleus. We summarize experimental data that identify a gene transfer process mediated by vacuoles that favors the accumulation of mitochondrial genes in the nuclei of modern cells. Finally, we compare the behavior of mitochondrial genes for which transfer to the nucleus is neutral or influenced by purifying selection.

Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation.

Many regulatory molecules are present in low copy numbers per cell so that significant random fluctuations emerge spontaneously. Because cell viability depends on precise regulation of key events, such signal noise has been thought to impose a threat that cells must carefully eliminate. However, the precision of control is also greatly affected by the regulatory mechanisms' capacity for sensitivity amplification. Here we show that even if signal noise reduces the capacity for sensitivity amplification of threshold mechanisms, the effect on realistic regulatory kinetics can be the opposite: stochastic focusing (SF). SF particularly exploits tails of probability distributions and can be formulated as conventional multistep sensitivity amplification where signal noise provides the degrees of freedom. When signal fluctuations are sufficiently rapid, effects of time correlations in signal-dependent rates are negligible and SF works just like conventional sensitivity amplification. This means that, quite counterintuitively, signal noise can reduce the uncertainty in regulated processes. SF is exemplified by standard hyperbolic inhibition, and all probability distributions for signal noise are first derived from underlying chemical master equations. The negative binomial is suggested as a paradigmatic distribution for intracellular kinetics, applicable to stochastic gene expression as well as simple systems with Michaelis-Menten degradation or positive feedback. SF resembles stochastic resonance in that noise facilitates signal detection in nonlinear systems, but stochastic resonance is related to how noise in threshold systems allows for detection of subthreshold signals and SF describes how fluctuations can make a gradual response mechanism work more like a threshold mechanism.

Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance.

Most types of antibiotic resistance impose a biological cost on bacterial fitness. These costs can be compensated, usually without loss of resistance, by second-site mutations during the evolution of the resistant bacteria in an experimental host or in a laboratory medium. Different fitness-compensating mutations were selected depending on whether the bacteria evolved through serial passage in mice or in a laboratory medium. This difference in mutation spectra was caused by either a growth condition-specific formation or selection of the compensated mutants. These results suggest that bacterial evolution to reduce the costs of antibiotic resistance can take different trajectories within and outside a host.

Hydrolysis of monodisperse phosphatidylcholines by phospholipase A2 occurs on vessel walls and air bubbles.

Hydrolysis of monodisperse short chain phosphatidylcholines, far below their critical micelle concentration, by phospholipase A2 (PLA2) and other interfacial enzymes is characterized. Results show that virtually all the observed hydrolysis by pancreatic and human inflammatory PLA2 occurs on surfaces of the reaction vessel or air bubbles. Conditions to eliminate such extraneous contributions at low substrate concentrations are established. Premicellar aggregates are apparently formed near the critical micelle concentration. The observation window at low substrate concentrations is used to obtain an upper limit estimate of the rate of hydrolysis through the monodisperse Michaelis complex. A limit estimate of <0.1 s-1 is obtained for the hydrolysis of monodisperse substrates by pig pancreatic phospholipase A2. These results show that the observed rate of hydrolysis of dihexanoyl- and diheptanoylphosphatidylcholines with pig pancreatic phospholipase A(2) through the monomer path is insignificant compared to the rate of >1000 s-1 seen at the saturating levels of the micellar substrate. These protocols should be useful for evaluating reactions catalyzed at vessel walls. Implications of these results for assays and models of interfacial activation of pancreatic PLA2 are discussed.

Synonymous nucleotide divergence and saturation: effects of site-specific variations in codon bias and mutation rates.

The synonymous divergence between Escherichia coli and Salmonella typhimurium is explained in a model where there is a large variation between mutation rates at different nucleotide sites in the genome. The model is based on the experimental observation that spontaneous mutation rates can vary over several orders of magnitude at different sites in a gene. Such site-specific variation must be taken into account when studying synonymous divergence and will result in an apparent saturation below the level expected from an assumption of uniform rates. Recently, it has been suggested that codon preference in enterobacteria has a very large site-specific variation and that the synonymous divergence between different species, e.g., E. coli and Salmonella, is saturated. In the present communication it is shown that when site-specific variation in mutation rates is introduced, there is no need to invoke assumptions of saturation and a large variability in codon preference. The same rate variation will also bring average mutation rates as estimated from synonymous sequence divergence into numerical agreement with experimental values.

Cationic residues 53 and 56 control the anion-induced interfacial k*cat activation of pancreatic phospholipase A2.

Added NaCl or anionic amphiphiles increase the rate of hydrolysis of dispersions of zwitterionic phospholipid by pancreatic phospholipase A2 (PLA2). Two effects of the negative charge at the interface have been dissected: enhanced binding of the enzyme to the interface, and k*cat activation of the enzyme at the interface [Berg et al. (1997) Biochemistry 36, 14512-14530]. Results reported here show that the structural basis for the k*cat activation is predominantly through cationic K53 and K56 in bovine pancreatic PLA2 with the anionic interface. The maximum rate at saturating diheptanoylphosphatidylcholine micelles, VMapp, for WT, K56M, and K53M in 4 M NaCl is in the 800-1300 s-1 range. In contrast, VMapp at 0.1 M NaCl is considerably higher for K56M (400 s-1) and K53M (230 s-1) compared to the rate with WT (30 s-1) or K56E (45 s-1). The rate of hydrolysis of anionic dimyristoylphosphatidylmethanol vesicles is virtually the same with all these mutants (200-300 s-1) and it is not affected by added NaCl. The chemical step for the hydrolysis of anionic and zwitterionic substrates remains rate-limiting in the presence or absence of added NaCl. A modest (approximately 10-fold) effect of K56M substitution or of added NaCl is seen on the binding of the enzyme to the interface; however, the binding of the substrate or a substrate mimic to the active site of the enzyme at the interface is not affected by more than a factor of 2. Magnitudes of the primary rate and equilibrium parameters at the zwitterionic and anionic interfaces show that the effect of mutation or of added NaCl is primarily on k*cat at the zwitterionic interface. These results are interpreted in terms of a two-state model for the interfacial allosteric activation, where the enzyme-substrate complex at the zwitterionic interface becomes catalytically active only after the positive charge on cationic K56 and K53 has been removed by mutation or neutralized by anionic charges in the interface.

Interfacial activation of triglyceride lipase from Thermomyces (Humicola) lanuginosa: kinetic parameters and a basis for control of the lid.

A strategy is developed to analyze steady-state kinetics for the hydrolysis of a soluble substrate partitioned into the interface by an enzyme at the interface. The feasibility of this approach to obtain interfacial primary kinetic and equilibrium parameters is demonstrated for a triglyceride lipase. Analysis for phospholipase A2 catalyzed hydrolysis of rapidly exchanging micellar (Berg et al. (1997) Biochemistry 36, 14512-14530) and nonexchangeable vesicular (Berg et al., (1991) Biochemistry 30, 7283-7291) phospholipids is extended to include the case of a substrate that does not form the interface. The triglyceride lipase (tlTGL) from Thermomyces (formerly Humicola) lanuginosa hydrolyzes p-nitrophenylbutyrate or tributyrin partitioned in the interface of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) vesicles at a rate that is more than 100-fold higher than that for the monodispersed substrate or for the substrate partitioned into zwitterionic vesicles. Catalysis and activation is not seen with the S146A mutant without the catalytic serine-146; however, it binds to the POPG interface with the same affinity as the WT. Thus POPG acts as a diluent surface to which the lipase binds in an active, or "open", form for the catalytic turnover; however, the diluent molecules have poor affinity for the active site. Analysis of the substrate and the diluent concentration dependence of the rate of hydrolysis provides a basis for the determination of the primary interfacial catalytic parameters. As a competitive substrate, tributyrin provided a check for the apparent affinity parameters. Nonidealities from the fractional difference in the molecular areas in interfaces are expressed as the area correction factor and can be interpreted as a first-order approximation for the interfacial activity coefficient. The basis for the interfacial activation of tlTGL on anionic interface is attributed to cationic R81, R84, and K98 in the "hinge" around the 86-93 "lid" segment of tlTGL.

Thermodynamic and kinetic basis of interfacial activation: resolution of binding and allosteric effects on pancreatic phospholipase A2 at zwitterionic interfaces.

A general kinetic model for catalysis by interfacial enzymes is developed. It couples the Michaelis-Menten catalytic turnover cycle at the interface with that in the aqueous phase through the distribution equilibria between the interface and the surrounding aqueous phase. Analysis under two limiting conditions fully describes the steady-state kinetics of hydrolysis and resolves the allosteric effects from apparent modes of interfacial activation in terms of the primary rate and equilibrium parameters for pig pancreatic phospholipase A2 (PLA2). One limit is observed in dispersions of anionic phospholipid vesicles, in which intervesicle exchange of enzyme, substrate, and hydrolysis products is absent and reaction occurs only on vesicles containing enzyme. A complete analysis at this highly processive limit, called kinetics in the scooting mode, has been published [Berg et al. (1991) Biochemistry 30, 7283]. Here is reported the analysis in the other limit, PLA2-catalyzed hydrolysis of zwitterionic micelles of short-chain phosphatidylcholines, at which substrate and products are in rapid exchange. Hydrolysis occurs either in bulk aqueous solution with phospholipid monomers or at the micellar interface. Above the critical micelle concentration (cmc), the hydrolysis rate shows a hyperbolic dependence on the bulk substrate concentration present as micelles. This dependence, characterized by the fitting parameters KMapp and VMapp, is analyzed in terms of the primary rate and equilibrium constants. The kinetic analysis is based on the assumption that the microscopic steady-state condition is satisfied because substrate replenishment in the micro-environment of the enzyme is fast relative to the catalytic turnover time. Added NaCl and anionic interface increase the hydrolysis rate in zwitterionic micelles dramatically. The overall interfacial rate enhancement is attributed to three factors: (a) promotion of PLA2 binding by net anionic charge of the interface, (b) enhancement of substrate affinity of PLA2 at the interface (Ks* allostery), and (c) stimulation of the rate-limiting chemical step (kcat* allostery).

Growth rate-optimised tRNA abundance and codon usage.

The abundance of different tRNAs in Escherichia coli at different growth rates correlates strongly with the usage of the corresponding cognate codons. On the assumption that the investment in the translation system is optimised to provide a maximal growth rate, the relationship between tRNA levels and codon usage can be predicted. When the complications due to different degeneracies and different association rate constants for the different tRNA-codon combinations are accounted for, recent data from the literature indicate that the predicted relations hold up very well: the tRNA levels correlate with codon frequencies in a way that would support a maximal growth rate. The relations can also be used to predict the association rate constant between an A-site codon and the cognate ternary complex. In the cases where they can be compared, the results agree reasonably well with experimental results from the literature.

Codon bias in Escherichia coli: the influence of codon context on mutation and selection.

The codon bias in Escherichia coli for all two-fold degenerate amino acids was studied as dependent on the context from the six bases in the nearest surrounding codons. By comparing the results in genes at different expression levels, effects that are due to differences in mutation rates can be distinguished from those that are due to selection. Selective effects on the codon bias is found mostly from the first neighbouring base in the 3'direction, while neighbouring bases further away influence mostly the mutational bias. In some cases it is also possible to identify specific molecular processes, repair or avoidance of frame shift, that lead to the context dependence of the bias.

Use of an imperfect neutral diluent and outer vesicle layer scooting mode hydrolysis to analyze the interfacial kinetics, inhibition, and substrate preferences of bee venom phospholipase A2.

Interfacial catalytic constants for bee venom phospholipase A2 (bvPLA2) have been obtained for its action on vesicles of the anionic phospholipid 1,2-dimyristoylphosphatidylmethanol (DMPM) in the highly processive scooting mode. Spectroscopic measurements which directly measure transbilayer movement of membrane components show that this exchange does not occur in anionic vesicles that have undergone complete bvPLA2-catalyzed hydrolysis of all phospholipids in the outer vesicle monolayer. 3-Hexadecyl-sn-glycero-1-phosphocholine (D-LPC) is an adequate neutral diluent for bvPLA2, which is defined as an amphiphile that forms an aggregate to which enzyme binds but neutral diluent molecules bind weakly in the enzyme's active site. D-LPC has weak affinity for the active site of bvPLA2, and theory and protocols are developed that allow its use to determine equilibrium dissociation constants for competing active site ligands. Some of the properties of bvPLA2 are shared by other 14 kDa PLA2s. (1) Ca2+ is required for binding of ligands to the active site but not for the binding of enzyme to the interface. (2) bvPLA2 does not significantly discriminate between phospholipids with different polar head groups or acyl chains. (3) bvPLA2 does not bind to phosphatidylcholine vesicles, and binding occurs if anionic amphiphiles are present in the vesicle. Novel features of bvPLA2 include the following: (1) Neutral diluents for other 14 kDa phospholipases A2 are not neutral diluents for bvPLA2. (2) Saturation of the active site with a variety of different ligands does not completely prevent histidine alkylation by 2-bromo-4'-nitroacetophenone, and Ca2+ binding does not change the rate of histidine alkylation. Finally, the carbohydrate portion of bvPLA2 does not alter the interfacial catalytic properties of the enzyme. Kinetic analysis of bvPLA2 in the scooting mode together with previous studies with other 14 kDa PLA2s provides a paradigm for the quantitative analysis of interfacial catalysis.