Robustness, evolvability, and neutrality

Biological systems, from macromolecules to whole organisms, are robust if they continue to function, survive, or reproduce when faced with mutations, environmental change, and internal noise. I focus here on biological systems that are robust to mutations and ask whether such systems are more or less evolvable, in the sense that they can acquire novel properties. The more robust a system is, the more mutations in it are neutral, that is, without phenotypic effect. I argue here that such neutral change--and thus robustness--can be a key to future evolutionary innovation, if one accepts that neutrality is not an essential feature of a mutation. That is, a once neutral mutation may cause phenotypic effects in a changed environment or genetic background. I argue that most, if not all, neutral mutations are of this sort, and that the essentialist notion of neutrality should be abandoned. This perspective reconciles two opposing views on the forces dominating organismal evolution, natural selection and random drift: neutral mutations occur and are especially abundant in robust systems, but they do not remain neutral indefinitely, and eventually become visible to natural selection, where some of them lead to evolutionary innovations.     

Thermosensitive, extracellular neutral proteases in Bacillus subtilis: isolation, characterization, and genetics.

Two mutants (NT02 and NT17), each producing a thermosensitive neutral protease, were isolated from Bacillus subtilis NP58, a transformant which acquired the property of hyperproduction of neutral protease from Bacillus natto IAM 1212. The neutral proteases produced by these two mutants were partially purified and enzymologically characterized. The two mutant neutral proteases displayed increased thermosensitivity as well as altered pH optima compared with those of the NP58 enzyme. In addition, the hydrolytic activity of the thermosensitive neutral proteases on synthetic peptide substrates was found to be extremely different. These results strongly suggest that the site of mutation in each of the temperature-sensitive strains is located within the structural gene for neutral protease (nprE). Previous studies indicated the existence of a specific regulator gene (nprR) in addition to the structural gene for neutral protease. Phage PBS1-mediated transduction and deoxyribonucleic acid-mediated transformation studies with the parental and mutant strains suggest that the chromosomal order of these genes is recA-pyrA-nprR-nprE-fruB-metC. Moreover, the results of these genetic analyses imply that the mutations to thermosensitivity are located proximate to each other within the nprE gene.     

Connectivity of Neutral Networks,Overdispersion, and Structural Conservation in Protein Evolution

Abstract Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds, determining that an extended neutral network in sequence space is associated with each of them. Within our model, neutral evolution leads to a non-Poissonian substitution process, due to the broad distribution of connectivities in neutral networks. The observation that the substitution process has non-Poissonian statistics has been used to argue against the original Kimura neutral theory, while our model shows that this is a generic property of neutral evolution with structural conservation. Our model also predicts that the substitution rate can strongly fluctuate from one branch to another of the evolutionary tree. The average sequence similarity within a neutral network is close to the threshold of randomness, as observed for families of sequences sharing the same fold. Nevertheless, some positions are more difficult to mutate than others. We compare such structurally conserved positions to positions conserved in protein evolution, suggesting that our model can be a valuable tool to distinguish structural from functional conservation in databases of protein families. These results indicate that a synergy between database analysis and structurally based computational studies can increase our understanding of protein evolution.     

Human hemoglobin: polymorphism, neutrality of variants, evolutionary aspect

Integrated analysis of the polymorphism of human hemoglobin has been made using populational genetics, hematological, physiological, protein chemistry and molecular biology data. The known variants of human hemoglobin are conventionally classified as "widely common", "less common" and "rare", depending on their contribution to polymorphism. The importance of homeostasis and compensatory reactions for maintaining the resistance of the human body against mutant hemoglobins is emphasized. Hb D Punjab and Hb O Arab being relatively neutral, the genetic structure of populations may restrict their distribution. A hypothesis is put forward concerning the possible role of an increased local conformational mobility of protein in creating neutral protein variants. It is proposed to discriminate between truly neutral and pseudoneutral protein variants. In case of possible changes in the genetic and environmental factors, the former are not subject to selection, while the latter may be. Contribution to neutral evolution can be made only by truly neutral variants. In a compensated heterozygotic state the truly neutral and pseudoneutral variants may give rise to new functions and adaptively valuable properties in protein. The evolution of proteins is believed to proceed from a stage which is consistent with M. Kimura's concept of neutrality of protein polymorphism toward a stage which is consistent with the concept of selectionism. It is concluded, that the currently observed degree of polymorphism of human hemoglobin corresponds to the present stage of molecular evolution of the protein.     

Immigration,Local Dispersal Limitation,and the Repeatability of Community Composition under Neutral and Niche Dynamics

Repeatability of community composition has been a critical aspect for community structure, which is closely associated with community stability, predictability, conservation biology and ecological restoration. It has been shown that both immigration and local dispersal limitation can affect the community composition in both neutral and niche model. Hence, we use a spatially explicit individual-based model to investigate the potential influence of immigration rate and strength of local dispersal limitation on repeatability in both neutral and niche models. Similarity measures are used to quantify repeatability. We examine the repeatability of community composition among replicate communities (which means the same community repeats many times), and between niche and neutral replicate communities. We find the correlation between repeatability and immigration rate is positive in the neutral model and an inverted unimodal in the niche model. The correlation between repeatability and local dispersal distance is positive in the niche model and negative in the neutral model. High repeatability between niche communities and neutral communities is observed with high immigration rates or when high local dispersal distance appears in the niche model or low local dispersal distance in the neutral model. Our results show that repeatability of community composition is not only dependent on the types of community models (niche vs. neutrality) but also strongly determined by immigration rates and local dispersal limitation.     

Linking dispersal, immigration and scale in the neutral theory of biodiversity

In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m . A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory.     

Cloning, sequencing and expression of the gene encoding the extracellular neutral protease, vibriolysin, of Vibrio proteolyticus.

The gene (nprV), encoding the extracellular neutral protease, vibriolysin (NprV), of the Gram- marine microorganism, Vibrio proteolyticus, was isolated from a V. proteolyticus DNA library constructed in Escherichia coli. The recombinant E. coli produced a protease that co-migrated with purified neutral protease from V. proteolyticus on non-denaturing polyacrylamide gels, and that demonstrated enzymatic specificity towards the neutral protease substrate N-[3-(2-furyl)acryloyl]-L-alanylphenylalanine amide. The nucleotide (nt) sequence of the cloned nprV gene revealed an open reading frame encoding 609 amino acids (aa) including a putative signal peptide sequence followed by a long 'pro' sequence consisting of 172 aa. The N-terminal aa sequence of NprV purified from cultures of V. proteolyticus, identified the beginning of the mature protein within the aa sequence deduced from the nt sequence. Comparative analysis of mature NprV to the sequences of the neutral proteases from Bacillus thermoproteolyticus (thermolysin) and Bacillus stearothermophilus identified extensive regions of conserved aa homology, particularly with respect to active-site residues, zinc-binding residues, and calcium-binding sites. NprV was overproduced in Bacillus subtilis by placing the DNA encoding the 'pro' and mature enzyme downstream from a Bacillus promoter and signal sequence.     

Subcellular distribution of acid and neutral alpha-glucosidases in normal, acid maltase deficient, and myophosphorylase deficient human skeletal muscle

The subcellular distribution of acid (pH 4.0) and neutral (pH 6.5) α-glucosidases was investigated in biopsy specimens of human skeletal muscle obtained from six normal subjects, four adult cases of acid maltase deficiency, and a case of myophosphorylase deficiency. The highest relative specific activity of acid glucosidase, as well as of other acid hydrolases, was observed in the light mitochondrial fraction. Relatively high acid phosphatase activity was also found in the microsomal fraction. In all muscles the highest relative specific activity of neutral glucosidase was in the microsomal fraction. In acid glucosidase deficient muscle no neutral glucosidase could be detected in the light and heavy mitochondrial fractions but in normal and myophosphorylase deficient muscle neutral glucosidase activity was also detectable in these fractions. The final supernatant of all muscles contained neutral glucoamylase activity. The relevance of these data to the pathogenesis of the different forms of type II glycogenosis is considered.     

New insight into the structure,reaction mechanism,and biological functions of neutral ceramidase

Ceramidase (CDase) is an enzyme that hydrolyzes the N-acyl linkage between the sphingoid base and fatty acid of ceramide. These enzymes are classified into three distinct groups, acid (Asah1), neutral (Asah2), and alkaline (Asah3) CDases, based on their primary structure and optimum pH. Acid CDase catabolizes ceramide in lysosomes and is found only in vertebrates. In contrast, the distribution of neutral and alkaline CDases is broad, with both being found in species ranging from lower eukaryotes to mammals; however, only neutral CDase is found in prokaryotes, including some pathogenic bacteria. Neutral CDase is thought to have gained a specific domain (mucin box) in the N-terminal region after the vertebrate split, allowing the enzyme to be stably expressed at the plasma membrane as a type II membrane protein. The X-ray crystal structure of neutral CDase was recently solved, uncovering a unique structure and reaction mechanism for the enzyme. Neutral CDase contains a zinc ion in the active site that functions as a catalytic center, and the hydrolysis of the N-acyl linkage in ceramide proceeds through a mechanism that is similar to that described for zinc-dependent carboxypeptidase. This review describes the structure, reaction mechanism, and biological functions of neutral CDase in association with the molecular evolution, topology, and mechanical conformation. This article is part of a Special Issue entitled New Frontiers in Sphingolipid Biology.     

Biochemical studies on an acidophilic, thermophilic bacterium, Bacillus acidocaldarius: isolation of bacteria, intracellular pH, and stabilities of biopolymers.

Acidophilic, thermophilic bacteria were isolated from Japanese acidic hot springs. They were spore-forming rods, identified as Bacillus acidocaldarius. DNA extracted from these acido-thermophiles showed no abnormality in chemical structure; it was instantly denatured and gradually decomposed giving rise to apurinic acid in a hot acid environment milder than the optimal conditions for the growth of the acido-thermophiles. Glyceraldehyde-3-phosphate dehydrogenase extracted from B. acidocaldarius was not active at pH 5 or less, and was resistant to heat at neutral but not acid pH. The intracellular pH was computed to be neutral by using dimethyl-2,4-oxazolidinedione. When uncouplers or inhibitors of respiration were added to the cells suspended in hot acid solution, the estimated pH was not changed and glyceraldehyde-3-phosphate dehydrogenase in the cells was not denatured. These results suggest that the cytoplasm of B. acidocaldarius is a hot neutral environment, and that a pH gradient across the cell envelope can be maintained even when oxidative phosphorylation or respiration is inhibited.