Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations

How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial mutations that altered enzyme levels in the central metabolism of Methylobacterium extorquens to uncover the fitness landscape defined by gene expression levels. We found strong antagonism and sign epistasis between these beneficial mutations. Mutations with the largest individual benefit interacted the most antagonistically with other mutations, a trend we also uncovered through analyses of datasets from other model systems. However, these beneficial mutations interacted multiplicatively (i.e., no epistasis) at the level of enzyme expression. By generating a model that predicts fitness from enzyme levels we could explain the observed sign epistasis as a result of overshooting the optimum defined by a balance between enzyme catalysis benefits and fitness costs. Knowledge of the phenotypic landscape also illuminated that, although the fitness peak was phenotypically far from the ancestral state, it was not genetically distant. Single beneficial mutations jumped straight toward the global optimum rather than being constrained to change the expression phenotypes in the correlated fashion expected by the genetic architecture. Given that adaptation in nature often results from optimizing gene expression, these conclusions can be widely applicable to other organisms and selective conditions. Poor interactions between individually beneficial alleles affecting gene expression may thus compromise the benefit of sex during adaptation and promote genetic differentiation.     

Insulin-induced expression of human heat-shock protein gene hsp70

In human hepatoma cell line Hep3B/T2, the human heat-shock-inducible gene hsp70 could be induced by insulin. The dose-dependent insulin effect correlates very well with the dissociation constant of the insulin receptor, indicating that the insulin effect is mediated by the insulin receptor. The expression of hsp70 gene was neither significantly induced by growth factors of epidermal and platelet-derived growth factors, nor by tumor promoter, calcium ionophore, cAMP, and glucocorticoids. These results indicate that the induction of expression of hsp70 gene by insulin is very specific and not cell cycle-related. Furthermore, the insulin-induced expression of hsp70 gene is transient, occurring specifically from 4 to 8 h after insulin addition.     

Pollen–plant–climate relationships in sub-Saharan Africa

Aim  To demonstrate that incorporating the bioclimatic range of possible contributor plants leads to improved accuracy in interpreting the palaeoclimatic record of taxonomically complex pollen types.
Location  North Tropical Africa.
Methods  The geographical ranges of selected African plants were extracted from the literature and geo-referenced. These plant ranges were compared with the pollen percentages obtained from a network of surface sediments. Climate-response surfaces were graphed for each pollen taxon and each corresponding plant species.
Results  Several patterns can be identified, including taxa for which the pollen and plant distributions coincide, and others where the range limits diverge. Some pollen types display a reduced climate range compared with that of the corresponding plant species, due to low pollen production and/or dispersal. For other taxa, corresponding to high pollen producers such as pioneer taxa, pollen types display a larger climatic envelope than that of the corresponding plants. The number of species contained in a pollen taxon is an important factor, as the botanical species included in a taxon may have different geographical and climate distributions.
Main conclusions  The comparison between pollen and plant distributions is an essential step towards more precise vegetation and climate reconstructions in Africa, as it identifies taxa that have a high correspondence between pollen and plant distribution patterns. Our method is a useful tool to reassess biome reconstructions in Africa and to characterize accurately the vegetation and climate conditions at a regional scale, from pollen data.     

Ion-Exchange Chromatography Separates Activities Synthesizing and Degrading Fructose 2,6-Bisphosphate from C3 and C4 Leaves but Not from Rat Liver

Fructose-6-phosphate,2-kinase and fructose-2,6-bisphosphatase were separated on the basis of charge from leaves of C₃ (spinach, lettuce, and pea) and C₄ (sorghum and amaranthus) plants but not from rat liver—a tissue known to contain a bifunctional enzyme with both activities. [2-³²P]Fructose 2,6-bisphosphate binding experiments also suggest that the major forms of these activities reside on different proteins in leaves.     

The biological functions of low-frequency vibrations (phonons). VI. A possible dynamic mechanism of allosteric transition in antibody molecules

By means of the quasi-continuity theory developed recently [Chou, K.-C. (1983) Biochem. J. 209 , 573–580; Chou, K.-C. (1984) Biochem. J. 221 , 27–31; Chou, K.-C. (1985) Biophys. J. 48 , 289–297], the low-frequency breathing motions of the β-barrels in the 12 domains of an IgG antibody molecule have been calculated. The results are in very good agreement with the observed low-frequency peaks in the Raman spectra. Based on this, the resonant couplings among the domains located at its different regions are discussed. It turns out that some very interesting functions of antibody molecules, such as the “chelate effect” and “trigger effect” whose dynamic principle has been so far unknown, can be clearly elucidated in terms of a fundamental natural law; i.e., it is through the channel of low-frequency resonance that the “signal” (or energy) in an antibody is transmitted from one location to the other, so as to be able to induce the relevant conformational change required for operating those important biological functions. The physical picture illustrated here once again provides us with a classic example that structure and function in nature are highly harmonized.     

Thermotolerance of isolated mitochondria associated with heat shock proteins

Mitochondria isolated from 2-day-old etiolated soybean (Glycine max) seedlings which had been subjected to various heat shock treatments, i.e. (A) 28°C (2 h), (B) 38°C (2 h), (C) 38°C (2 h)-42.5°C (0.5 h), and (D) 38°C (2 h)-42.5°C (0.5 h)-28°C (4 h), were monitored for O₂ uptake using an oxygen electrode. Mitochondria isolated after all four heat shock treatments were active in O₂ consumption at 28°C in response to succinate and ADP (derived P/O ratios were 1.6, 1.7, 1.3, and 1.3, respectively.) The mitochondria from all four treatments were also active in O₂ uptake at 42.5°C. However, only mitochondria isolated after treatment (C) were tightly coupling at 42.5°C (derived ADP/O ratio was about 1.4). Combined with our earlier findings on the subcellular localization of heat shock proteins, our present data demonstrate that association of heat shock proteins with mitochondria by treatment (C) enables them to phosphorylate at 42.5°C (i.e. they become thermotolerant). Isolated mitochondria from treatment (C) and treatment (A) were compared by electron microscopy. They appeared to be very similar and no significant ultrastructural differences were noted.     

Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA.

Formulae for calculating low-frequency twist-like and accordion-like modes of DNA molecules have been derived using a quasi-continuum model. The formulae can be employed in essentially all (viz. A, B, C, D, E, and Z) forms of DNA. Calculated results indicate that the experimentally observed low-frequency modes at 22 cm-1 for the A-form octanucleotide (d[CCCCGGGG]) and at 18 cm-1 for the B-form dodecanucleotide (d[CGCAA ATTTGCG]) may result from accordion-like motions, while those observed at 12 cm-1 and 15 cm-1 may result from combinations of twist-like oscillations excited in the intact segments of B- and A-DNA's, respectively. Frequency shifts in the low-frequency modes observed when DNA molecules undergo conformational changes among different forms are also discussed in terms of the current model.