Reproduction and life strategies in the Paleozoic tabulate coral Paleofavosites capax (Billings)

Asexual and sexual modes of colony formation in a tabulate coral Paleofavosites capax are recognized from the early Silurian Gun River Formation of Anticosti Island. Québee. Colonies produced by asexual fragmentation comprise monospecific 'clumped populations'. They are characterized by circular and concave bases, and lack a protocorallite origin of colony growth. Sexually produced colonies, where in situ , are always dispersed and characterized by conical bases with a definite protocorallite point origin of colony growth. Asexual colony formation by fragmentation in P. capax appears to have been an adaptation to a habitat of muddy substrates. Sexual reproduction in this species probably played a minor role but was necessary for the maintenance of gene diversity and long-distance dispersal. A comparison of corallite size distributions between populations demonstrates that intrapopulation variation in the 'dispersed population' and the conical colonies in 'transported populations' of P. capax is significantly larger than the variation in the 'clumped populations'. It is suggested that this difference reflects the two modes of reproduction. The above observations are significant to systematic studies because they show that estimates of species morphologic parameters can he seriously biased even when based on a relatively large sample size from a well-defined population if that population is largely a result of asexual colony formation.     

The tabulate coral Hyostragulum, an epizoan with bearing on hyolithid ecology and systematics

The main generic feature of the hyolithid genus Pterygotheca Novlk, 1891 - the fringe on the lateral edges and on the dorsal side of the conch - is interpreted here as a colony of a tabulate coral, Hyostragulum gen. n. This coral covered the living specimens of different hyolithid species in the Bohemian and Moravian Lower and Middle Devonian and occasionally also of nautiloids and gastropods. Because of this discovery it is necessary to withdraw the order Pterygothecida Syssoiev, 1968 and probably also the family Ptery-gothecidae Syssoiev, 1958. The genus Pterygotheca is questionable, but further study may prove its validity. The character of the epifaunal coral strongly supports the interpretation of a benthic life of hyolithids.     

Substrate specificity of chlorophyllase

Apparent Km and V_max values were obtained for hydrolysis of methyl and ethyl chlorophyllides a, methyl and ethyl pheophorbide a, and 9-hydroxymethyl pheophorbide a by chlorophyllase from Ailanthus altissima. Analysis of substrate specificity data for chlorophyllase indicates that the presence of a 9-keto group and a methyl alcohol group esterified at the 7-position in chlorophyll derivatives results in maximum binding affinity for substrates. Data on maximum reaction rates indicate that the rate-controlling step of hydrolysis occurs after release of the alcohol from the ester. Probable high affinity chlorophyllase inhibitors can be predicted on the basis of these specificity studies.     

纤维素酶的底物专一性

天然纤维素的有效酶解取决于外切葡聚糖纤维二糖水解酶（ＣＢＨ）和内切葡聚糖水解酶（ＥＧ）的协同作用。ＥＧ随机水解纤维素无定形区分子链内的β－１,４－糖苷键;ＣＢＨ则由分子链的还原性末端水解出纤维二糖。这种底物专一性差别的原因在于ＣＢＨ呈“桶状”的活性部痊表面存在２个“ｌｏｏｐ”结构,只能容许纤维素分子链的末端伸入到活性裂隙中。ＥＧ无“ｌｏｏｐ”结构在存在,对底物是充分可及的。ＥＧ催化结构域中底物结合     

Substrate specificity of the SecB chaperone

The bacterial chaperone SecB assists translocation of proteins across the inner membrane. The mechanism by which it differentiates between secretory and cytosolic proteins is poorly understood. To identify its binding motif, we screened 2688 peptides covering sequences of 23 proteins for SecB binding. The motif is approximately 9 residues long and is enriched in aromatic and basic residues, whereas acidic residues are disfavored. Its identification allows the prediction of binding regions within protein sequences with up to 87% accuracy. SecB-binding regions occur statistically every 20-30 residues. The occurrence and affinity of binding regions are similar in SecB-dependent and -independent secretory proteins and in cytosolic proteins, and SecB lacks specificity toward signal sequences. SecB cannot thus differentiate between secretory and non-secretory proteins via its binding specificity. This conclusion is supported by the finding that SecB binds denatured luciferase, thereby allowing subsequent refolding by the DnaK system. SecB may rather be a general chaperone whose involvement in translocation is mediated by interactions of SecB and signal sequences of SecB-bound preproteins with the translocation apparatus.     

Substrate specificity in thiamin diphosphate-dependent decarboxylases

Thiamin diphosphate (ThDP) is the biologically active form of vitamin B₁, and ThDP-dependent enzymes are found in all forms of life. The catalytic mechanism of this family requires the formation of a common intermediate, the 2α-carbanion–enamine, regardless of whether the enzyme is involved in C–C bond formation or breakdown, or even formation of C−N, C−O and C−S bonds. This demands that the enzymes must screen substrates prior to, and/or after, formation of the common intermediate. This review is focused on the group for which the second step is the protonation of the 2α-carbanion, i.e., the ThDP-dependent decarboxylases. Based on kinetic data, sequence/structure alignments and mutagenesis studies the factors involved in substrate specificity have been identified.     

Substrate specificity in hydrocarbon utilizing microorganisms

Three bacteria (designated stram JOB5, 7E4, and 7E1C) isolated from soil by elective culture techniques and capable of growth on a wide variety of hydrocarbons were tested for substrate specificity. Non-proliferating cells of strain JOB5 grown on each of the C₁ to C_N series of normal ahphatic hydrocarbons were assayed for the capacity to oxidize all the alkanes, alcohols, fatty acids, and methyl-ketones in the homologous series of straight chain compounds. Cells of strain 7E4 grown on the gaseous alkanes (C₁ C₄) and strain 7E1C grown on propane were tested for the ability to oxidize the C₁ to C₄ n-alkanes, alcohols, and fatty acids.Contribution from Microbiology, North Carolina Agricultural Experiment Station, Raleigh, North Carolina Published with the approval of the Director of Research as paper No 2395 of the Journal Series.Part of this work was done while the author was associated with the late Dr. Jackson W. Foster, at the University of Texas, Austin.     

Substrate specificity of potato lipoxygenase

The substrate specificity of potato lipoxygenase was examined using a partially purified enzyme preparation from tubers of a potato variety with low lipolytic acyl hydrolase activity. Potato lipoxygenase is fully active only on free linoleic acid or linolenic acid, and only acts directly on more complex glyceride moieties in the absence of any significant endogenous lipolytic acyl hydrolase activity.     

Substrate specificity of formylglycinamidine synthetase

Formylglycinamidine ribonucleotide (FGAM) synthetase, which catalyzes the conversion of formylglycinamide ribonucleotide (FGAR), glutamine, and ATP to FGAM, ADP, glutamate, and Pi, has been purified to homogeneity (sp act. 0.20 mumol min-1 mg-1) from chicken liver by an alternative procedure to that of Buchanan et al. [Buchanan, J. M., Ohnoki, S., & Hong, B. S. (1978) Methods Enzymol. 51, 193-201] (sp act. 0.12 mumol min-1 mg-1). A variety of new analogues of formylglycinamide ribonucleotide have been prepared in which the formylglycinamide arm (R = CH2NHCHO) has been replaced by R = CH3, CH2OH, CH2Cl, CH2NH3, CH2NHCOCH3, CH2NHCOCH2Cl, CH2NHCO2CH2Ph, and L-CHC-H3NHCHO. These compounds have been characterized by 1H and 13C NMR spectroscopy. With compounds R = CH3, CH2OH, and CH2NHCOCH3 and ATP, in the presence or absence of glutamine, FGAM synthetase catalyzes the production of Pi at 4.5, 48, and 20%, respectively, the rate of production of Pi from formylglycinamide ribonucleotide. Only R = CH2NHCOCH3 causes glutaminase activity as well as ATPase activity and has been shown to be converted to the amidine analogue. Both FGAR (R = CH2NHCHO) and the FGAR analogue (R = CH2NHCHOCH3) in the presence of ATP and FGAM synthetase and in the absence of glutamine form a complex isolable by Sephadex G-50 chromatography. FGAM synthetase is thus highly specific for its formylglycine side chain. [18O]-beta-FGAR was prepared biosynthetically, and FGAM synthetase was shown by 31P NMR spectroscopy to catalyze the transfer of amide 18O to inorganic phosphate.     

Substrate specificity of strictosidine synthase

Strictosidine synthase catalyzes a Pictet-Spengler reaction in the first step in the biosynthesis of terpene indole alkaloids to generate strictosidine. The substrate requirements for strictosidine synthase are systematically and quantitatively examined and the enzymatically generated compounds are processed by the second enzyme in this biosynthetic pathway.     

Substrate specificity of haloalkane dehalogenases

An enzyme's substrate specificity is one of its most important characteristics. The quantitative comparison of broad-specificity enzymes requires the selection of a homogenous set of substrates for experimental testing, determination of substrate-specificity data and analysis using multivariate statistics. We describe a systematic analysis of the substrate specificities of nine wild-type and four engineered haloalkane dehalogenases. The enzymes were characterized experimentally using a set of 30 substrates selected using statistical experimental design from a set of nearly 200 halogenated compounds. Analysis of the activity data showed that the most universally useful substrates in the assessment of haloalkane dehalogenase activity are 1-bromobutane, 1-iodopropane, 1-iodobutane, 1,2-dibromoethane and 4-bromobutanenitrile. Functional relationships among the enzymes were explored using principal component analysis. Analysis of the untransformed specific activity data revealed that the overall activity of wild-type haloalkane dehalogenases decreases in the following order: LinB~DbjA>DhlA~DhaA~DbeA~DmbA>DatA~DmbC~DrbA. After transforming the data, we were able to classify haloalkane dehalogenases into four SSGs (substrate-specificity groups). These functional groups are clearly distinct from the evolutionary subfamilies, suggesting that phylogenetic analysis cannot be used to predict the substrate specificity of individual haloalkane dehalogenases. Structural and functional comparisons of wild-type and mutant enzymes revealed that the architecture of the active site and the main access tunnel significantly influences the substrate specificity of these enzymes, but is not its only determinant. The identification of other structural determinants of the substrate specificity remains a challenge for further research on haloalkane dehalogenases.     

Substrate specificity of choline kinase

The substrate specificity of choline kinase (ATP:choline phosphotransferase, EC 2.7.1.32) from brewer's yeast has been examined using multiple analogs of choline, most of which have been reported to be a substrate of one or another choline-using system from other sources. In contrast to many such systems, choline kinase from brewer's yeast has been found to have relatively stringent and straight-forward structural requirements for its substrates. It is hypothesized that there are at least four points of interaction of the substrate with the enzyme--one for the hydroxyalkyl side chain and one for each of the three substituents on the quaternary nitrogen. Of the latter, one site seems relatively more sterically hindered than the other two. Short, single or double alkyl substitutions on the quaternary nitrogen are possible without a large loss of substrate capacity of the analog. Thus N,N-dimethyl-N-propylethanolamine had a relative Vmax of 116% and a relative Vmax 96% that of choline and a Km of 68 +/- 15 microM [nearly four times that of choline itself (18 microM)]. However, N-butyl-N,N-dimethylethanolamine and N,N,N-triethylethanolamine were very poor substrates. Analogs with substituents on the quaternary nitrogen of longer chain length were without activity as were aromatic derivatives. None of the bisquaternary compounds of the general structure HOCH2CH2N+(CH3)2-(CH2)n-N+(CH3)2CH2CH2OH (n = 2-10) showed any substrate capacity, as well. Restrictions on the hydroxyethyl side chain were also severe. One additional methylene group in this chain greatly reduced substrate capacity of the analog and two additional ones eliminated it entirely, as did almost any substituent on the beta carbon. A single (but not a double) substituent on the alpha carbon was moderately tolerated, however. Thus alpha-methylcholine and N-methyl-2-hydroxymethylpiperidine were substrates (although the latter one was a poor one) but beta-methylcholine and N-methyl-3-hydroxypiperidine were not. Such information may be of use toward designing cholinergic probes targeting specific enzyme or metabolic functions.