Repetitive sequence environment distinguishes housekeeping genes

Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes by their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (> 400-bp) repetitive sequences (“repeats”), including Long Interspersed Nuclear Element-1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, was used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes.     

Insights into electron leakage in the reaction cycle of cytochrome P450 BM3 revealed by kinetic modeling and mutagenesis

As a single polypeptide, cytochrome P450 BM3 fuses oxidase and reductase domains and couples each domain's function to perform catalysis with exceptional activity upon binding of substrate for hydroxylation. Mutations introduced into the enzyme to change its substrate specificity often decrease coupling efficiency between the two domains, resulting in unproductive consumption of cofactors and formation of water and/or reactive species. This phenomenon can correlate with leakage, in which P450 BM3 uses electrons from NADPH to reduce oxygen to water and/or reactive species even without bound substrate. The physical basis for leakage is not yet well understood in this particular member of the cytochrome P450 family. To clarify the relationship between leakage and coupling, we used simulations to illustrate how different combinations of kinetic parameters related to substrate‐free consumption of NADPH and substrate hydroxylation can lead to either minimal effects on coupling or a dramatic decrease in coupling as a result of leakage. We explored leakage in P450 BM3 by introducing leakage‐enhancing mutations and combining these mutations to assess whether doing so increases leakage further. The variants in this study provide evidence that while a transition to high spin may be vital for coupled hydroxylation, it is not required for enhanced leakage; substrate binding and the consequent shift in spin state are not necessary as a redox switch for catalytic oxidation of NADPH. Additionally, the variants in this study suggest a tradeoff between leakage and stability and thus evolvability, as the mutations we investigated were far more deleterious than other mutations that have been used to change substrate specificity.     

The Ca2+ response of a smart forisome protein is dependent on polymerization

Forisomes are giant self‐assembling mechanoproteins that undergo reversible structural changes in response to Ca²⁺ and various other stimuli. Artificial forisomes assembled from the monomer MtSEO‐F1 can be used as smart biomaterials, but the molecular basis of their functionality is not understood. To determine the role of protein polymerization in forisome activity, we tested the Ca²⁺ association of MtSEO‐F1 dimers (the basic polymerization unit) by circular dichroism spectroscopy and microscale thermophoresis. We found that soluble MtSEO‐F1 dimers neither associate with Ca²⁺ nor undergo structural changes. However, polarization modulation infrared reflection absorption spectroscopy revealed that aggregated MtSEO‐F1 dimers and fully‐assembled forisomes associate with Ca²⁺, allowing the hydration of poorly‐hydrated protein areas. A change in the signal profile of complete forisomes indicated that Ca²⁺ interacts with negatively‐charged regions in the protein complexes that only become available during aggregation. We conclude that aggregation is required to establish the Ca²⁺ response of forisome polymers.     

Xylem hydraulic safety and construction costs determine tropical tree growth

Faster growth in tropical trees is usually associated with higher mortality rates, but the mechanisms underlying this relationship are poorly understood. In this study, we investigate how tree growth patterns are linked with environmental conditions and hydraulic traits, by monitoring the cambial growth of 9 tropical cloud forest tree species coupled with numerical simulations using an optimization model. We find that fast‐growing trees have lower xylem safety margins than slow‐growing trees and this pattern is not necessarily linked to differences in stomatal behaviour or environmental conditions when growth occurs. Instead, fast‐growing trees have xylem vessels that are more vulnerable to cavitation and lower density wood. We propose the growth ‐ xylem vulnerability trade‐off represents a wood hydraulic economics spectrum similar to the classic leaf economic spectrum, and show through numerical simulations that this trade‐off can emerge from the coordination between growth rates, wood density, and xylem vulnerability to cavitation. Our results suggest that vulnerability to hydraulic failure might be related with the growth‐mortality trade‐off in tropical trees, determining important life history differences. These findings are important in furthering our understanding of xylem hydraulic functioning and its implications on plant carbon economy.     

The molecular cloning and expression of two CRABP cDNAs from human skin

Retinoic acid (RA) is known to have a profound effect on the growth and differentiation of human epidermal cells in vivo and in vitro. One of the proteins thought to be involved in mediating the action of RA is the cellular retinoic acid-binding protein (CRABP). We have used PCR technology to generate cDNAs for two distinct CRABPs from human skin and skin-derived cells. One is highly homologous to the CRABP I cDNAs previously cloned from bovine and murine sources. The second shares extensive deduced amino acid homology with CRABP II, a protein recently described in newborn rat and embryonic chick. Although both mRNAs can be detected in neonatal foreskin, CRABP II mRNA is the predominant one in this tissue, as well as in cultured newborn fibroblasts and keratinocytes. Northern blot analysis showed CRABP II mRNA level was only slightly reduced by addition of 10(-6) or 10(-5) M RA to cultures of neonatal foreskin-derived fibroblasts, as was the CRABP I mRNA level in cultured human gut epithelial cells. In contrast, expression of CRABP II mRNA by cultured neonatal keratinocytes was strongly downregulated by RA. We conclude that CRABP II is the predominant CRABP in human skin, at least in the newborn period, and that it is differentially regulated in fibroblasts versus keratinocytes. Our data are consistent with a role for CRABP in regulating the amount of RA delivered to the nucleus.     

Verbreitung und Ökologie derVaucheria-Arten (Tribophyceae) des Elbe-Ästuars und der angrenzenden Küste

From the Elbe estuary and the adjacent North Sea coast, 19 species ofVaucheria are on record. Their horizontal and vertical distribution pattern as well as their association with macrophyte communities are described. With regard to ecological salinity tolerance and distribution below or above mean high water, 7 ecological groups ofVaucheria species are defined. Dominating species which form extensive algal mats in the upper eulittoral zone areVaucheria compacta var.dulcis (freshwater and oligohalinic section of the estuary),V. compacta var.compacta (mesohalinic section) andV. velutina together withV. subsimplex (polyhalinic and euhalinic section). The rare speciesV. vipera is recorded for the first time from the German coast.

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Herrn Dr. Dr. h. c. Peter Kornmann zum 80. Geburtstag gewidmet.

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Adressat für Sonderdruckwünsche: Prof. Dr. L. Kies.     

Nitrogen dioxide fixation in bacterial chromatin studies

Eller, Charles (St. John's University, Jamaica, N.Y.), and William H. Beckert. Nitrogen dioxide fixation in bacterial chromatin studies. J. Bacteriol. 90:1710-1712. 1965.-Satisfactory chromatin staining was obtained with two Bacillus species when nitrogen dioxide was used for fixation in conjunction with either the acid Giemsa or Feulgen staining methods. An impression method was employed for the transfer of bacilli to a new environment as well as for smears. Advantages of nitrogen dioxide fixation are discussed.