Structural modifications in Rhizobium meliloti Nod factors influence their stability against hydrolysis by root chitinases

Acylated chitooligosaccharide signals (Nod factors) trigger the development of root nodules on leguminous plants and play an important role in determining host specificity in the Rhizobium-plant symbiosis. Here, the ability of plant chitinases to hydrolyze different Nod factors and the potential significance of the structural modifications of Nod factors in stabilizing them against enzymatic inactivation were investigated. Incubation of the sulfated Nod factors of Rhizobium meliloti, NodRm-IV(S) and NodRm-V(S), as well as their desulfated derivatives NodRm-IV and NodRm-V, with purified chitinases from the roots of the host plant Medicago and the nonhost plant Vicia resulted in the release of the acylated lipotrisaccharide NodRm-III from NodRm-V, NodRm-IV and NodRm-V(S), whereas NodRm-IV(S) was completely resistant to digestion by both chitinases. Kinetic analysis showed that the structural parameters determining host specificity, the length of the oligosaccharide chain, the acylation at the nonreducing end and the sulfatation at the reducing end of the lipooligosaccharide, influence the stability of the molecule against degradation by chitinases. When the Nod factors were incubated in the presence of intact roots of Medicago, as well as of Vicia, the acylated lipotrisaccharide was similarly released in vivo from all Nod factors except NodRm-IV(S). In addition, a dimer-forming activity was observed in intact roots which also cleaved NodRm-IV(S). This activity was much greater in Medicago than in Vicia and increased upon incubation. The initial overall degradation rate of the Nod factors on Medicago was inversely correlated with their biological activities on Medicago roots. These results open the possibility that the activity of Nod factors on Medicago may partly be determined by the action of chitinases.     

Nod signal-induced plasma membrane potential changes in alfalfa root hairs are differentially sensitive to structural modifications of the lipochitooligosaccharide

Lipochitooligosaccharide Nod signals are important determinants of host specificity in the Rhizobium -legume symbiosis. The most rapid response of plant cells to the R. meliloti Nod signal NodRm-IV(C16:2,S) reported so far is the depolarization of the plasma membrane potential in alfalfa root hairs. In order to investigate whether this response may be part of a specific signal transduction cascade involved in the nodulation process, its specificity was studied with respect to host-specific modifications of the lipochitooligosaccharide. Five different Nod factors displaying different degrees of activity in inducing root hair deformation or cortical cell divisions on alfalfa were tested. The ability of the Nod factors to elicit plasma membrane depolarization correlated well with their activity in the bioassays. Removal of the sulfate group (NodRm-IV(C16:2)) led to inactivation of the Nod factor. An increase in the length of the chitooligosaccharide backbone (NodRm-V(C16:2,S)) or saturation of the acyl chain (NodRm-IV(C16:0,S)) resulted in severely reduced activity. In contrast, the O -acetyl group at the non-reducing terminus in NodRm-IV(Ac,C16:2,S), which confers substantially higher activity in long-term bioassays, did not enhance plasma membrane depolarization significantly in comparison with the non- O -acetylated factor. Thus, the rapid plasma membrane response is differentially sensitive to various structural motifs of the lipochitooligosaccharide. These data suggest that the different substituents modifying the basic Nod factor structure may have distinct functions, not all of them contributing to the interaction with a putative receptor in root hair cells. However, the overall specificity of the membrane depolarization for the cognate Nod factors raises the possibility that it is involved in a Nod signal transduction pathway.     

How alfalfa root hairs discriminate between Nod factors and oligochitin elicitors

Using ion-selective microelectrodes, the problem of how signals coming from symbiotic partners or from potential microbial intruders are distinguished was investigated on root hairs of alfalfa (Medicago sativa). The Nod factor, NodRm-IV(C16:2,S), was used to trigger the symbiotic signal and (GlcNAc)(8) was selected from (GlcNAc)(4-8), to elicit defense-related reactions. To both compounds, root hairs responded with initial transient depolarizations and alkalinizations, which were followed by a hyperpolarization and external acidification in the presence of (GlcNAc)(8). We propose that alfalfa recognizes tetrameric Nod factors and N-acetylchitooligosaccharides (n = 4-8) with separate perception sites: (a) (GlcNAc)(4) and (GlcNAc)(6) reduced the depolarization response to (GlcNAc)(8), but not to NodRm-IV(C16:2, S); and (b) depolarization and external alkalization were enhanced when NodRm-IV(C16:2,S) and (GlcNAc)(8) were added jointly without preincubation. We suggest further that changes in cytosolic pH and Ca(2+) are key events in the transduction, as well as in the discrimination of signals leading to symbiotic responses or defense-related reactions. To (GlcNAc)(8), cells responded with a cytosolic acidification, and they responded to NodRm-IV(C16:2,S) with a sustained alkalinization. When both agents were added jointly, the cytosol first alkalized and then acidified. (GlcNAc)(8) and NodRm-IV(C16:2,S) transiently increased cytosolic Ca(2+) activity, whereby the response to (GlcNAc)(8) exceeded the one to NodRm-IV(C16:2,S) by at least a factor of two.     

Nod factors modulate the concentration of cytosolic free calcium differently in growing and non-growing root hairs of Medicago sativa L.

Using Ca²⁺-selective microelectrodes, the concentration of free calcium ([Ca²⁺]) in the cytosol has been measured in root hair cells of Medicago sativa L. in the presence of nodulation (Nod) factors. Growing root hairs of M. sativa displayed a steep apical [Ca²⁺] gradient, i.e. 604–967 nM in the tip compared with 95–235 nM in the basal region. When tested within the first 5 to 10 μm of the tip, addition of NodRm-IV(C16:2,S) decreased the cytosolic [Ca²⁺], whereas an increase was observed when tested behind the tip. Overall, this led to a partial dissipation of the [Ca²⁺] gradient. The Ca²⁺ response was specific: it was equally well observed in the presence of NodRm-IV(Ac,C16:2,S), reduced with NodRm-IV(C16:0,S), but not with chitotetraose, the nonactive glucosamine backbone. In contrast to growing root hairs, non-growing root hairs without a tip-to-base cytosolic [Ca²⁺] gradient responded to NodRm-IV(C16:2,S) with an increase in cytosolic [Ca²⁺] at the tip as well as at the root hair base. We suggest that the response to Nod factors depends on the stage of development of the root hairs, and that changes in cytosolic [Ca²⁺] may play different roles in Nod-factor signaling: changes of cytosolic [Ca²⁺] in the apical part of the root hair may be related to root hair deformation, while the increase in [Ca²⁺] behind the tip may be essential for the amplification of the Nod signal, for its propagation and transduction to trigger downstream events. Received: 5 January 1999 / Accepted: 14 April 1999     

Elevation of the cytosolic free [Ca2+] is indispensable for the transduction of the Nod factor signal in alfalfa.

In root hairs of alfalfa (Medicago sativa), the requirement of Ca(2+) for Nod factor signaling has been investigated by means of ion-selective microelectrodes. Measured 50 to 100 microm behind the growing tip, 0.1 microM NodRm-IV(C16:2,S) increased the cytosolic free [Ca2+] by about 0.2 pCa, while the same concentration of chitotetraose, the nonactive glucosamine backbone, had no effect. We demonstrate that NodRm-IV(C16:2,S) still depolarized the plasma membrane at external Ca(2+) concentrations below cytosolic values if the free EGTA concentration remained low (相似文献   

Rapid alkalinization in alfalfa root hairs in response to rhizobial lipochitooligosaccharide signals

Rhizobial lipochitooligosaccharides (Nod factors) function as symbiotic signals that trigger root hair deformations and cortical cell divisions on the roots of leguminous plants in a host-specific manner. By using pH-sensitive microelectrodes, it is shown that alfalfa root hair cells respond to Rhizobium meliloti Nod factors with a rapid intracellular alkalinization of 0.2–0.3 pH units. This alkalinization remained as long as the Nod factor was present, but slowly reversed after removal of the signal. The response was most sensitive to the sulfated tetrameric Nod factor, NodRm-IV(C16:2,S), which is morphogenic on the host plant alfalfa, suggesting a role in a signal transduction cascade. Non-sulfated Nod factor as well as chitooligosaccharides elicited a pH_c change only at elevated concentrations. The increase of PH_c in response to sulfated Nod factor was concomitant with a depolarization of the plasma membrane potential whereas the PH_c change in response to non-sulfated Nod factor occurred in the absence of membrane depolarization. In addition, whereas a first dose of sulfated Nod factor inhibited the subsequent response to a second dose of the same molecule, it did not significantly repress the activity of non-sulfated Nod factor. These results indicate that sulfated and non-sulfated Nod factors act independently and suggest the existence of two Nod signal perception systems, one transmitting the host-specific signal, the other representing an ancient reception system for a generic Nod factor structure.     

Distinct response of Medicago suspension cultures and roots to Nod factors and chitin oligomers in the elicitation of defense-related responses

The induction of plant defense-related responses by chitin oligomers and the Rhizobium meliloti lipo-chito-oligosaccharide nodulation signals (Nod factors) in Medicago cell cultures and roots was investigated by following the expression of genes encoding enzymes of the isoflavonoid biosynthetic pathway, such as chalcone synthase, chalcone reductase, isoflavone reductase, as well as genes encoding a pathogenesis-related protein and a peroxidase. In suspension-cultured cells, all genes except the peroxidase gene were induced by both the R. meliloti Nod factor NodRm-IV(C16:2,S) and chitin oligomers with a minimum of three sugar residues. However, activation of these genes was not elicited by the symbiotically inactive, desulfated NodRm-IV(C16:2). Moreover, the cells were more sensitive to the chitin oligosaccharides than to the Nod factor. Analysis of flavonoids in Medicago microcallus cultures revealed differences between cells treated with N -acetyl-chitotetraose and those treated with Nod factor and demonstrated increased production of the phytoalexin medicarpin in the presence of Nod factor. In Medicago roots, none of the tested genes was activated by the N -acetylchitotetraose, whereas the Nod factor at micro-molar concentration enhanced transient expression of the isoflavonoid biosynthetic genes. The differential responses to Nod factors and chitin oligomers suggest that Medicago cells possess distinct perception systems for these related molecules.     

The mode of action of cell wall-degrading enzymes and their interference with Nod factor signalling in <Emphasis Type="Italic">Medicago sativa</Emphasis> root hairs

Medicago sativa L. (alfalfa) root hairs respond to Nod factors [NodRm-IV(C16:2,S)] in a host-specific manner with depolarization and rapid ion fluxes. Protoplasts prepared from these cells using the cell wall-digesting enzymes pectolyase and cellulase do not, or to a rather small extent, respond to Nod factors. In an effort to understand this activity loss we analyzed the mode of action of both enzymes with respect to their effects on the root hairs as well as their interference with the Nod factor response. (i) In the presence of the enzymes, Nod factor at saturating concentrations neither depolarized the plasma membrane of root hairs nor caused ion fluxes. Even after removal of the enzymes, Nod factor responses were strongly refractory. (ii) After a lag-phase of 12-18 s, pectolyase depolarized the plasma membrane, alkalized the external space, acidified the cytosol and increased the cytosolic Ca(2+) activity. (iii) Cellulase, without a lag-phase, depolarized the plasma membrane, acidified the cytosol, but only marginally increased the cytosolic Ca(2+) activity. Unlike pectolyase, the cellulase response was only weakly refractory to a second addition. (iv) Neither enzyme increased the membrane conductance, but pectolyase inhibited the H(+)-pump. (v) Pectolyase shows all the signs of an elicitor, while cellulase yields a mixed response. (vi) Denatured enzymes yielded strong effects similar to those of untreated enzymes. We conclude that the effects shown do not originate from enzymatic activity, but from interactions of the proteins with cell wall or plasma membrane constituents. It is further concluded that these enzymes (pectolyase more so than cellulase) trigger defense-related signal pathways, which makes protoplasts prepared with such enzymes unsuitable for studies of symbiotic or defense-related signalling.     

The NodA proteins of Rhizobium meliloti and Rhizobium tropici specify the N-acylation of Nod factors by different fatty acids

Rhizobia synthesize mono- N -acylated chitooligosaccharide signals, called Nod factors, that are required for the specific infection and nodulation of their legume hosts. The biosynthesis of Nod factors is under the control of nodulation ( nod ) genes, including the nodABC genes present in all rhizobial species. The N -acyl substitution can vary between species and can play a role in host specificity. In Rhizobium meliloti , an alfalfa symbiont, the acyl chain is a C16 unsaturated or a (ω-1) hydroxylated fatty acid, whereas in Rhizobium tropici , a bean symbiont, it is vaccenic acid (C18:1). We constructed R. meliloti derivatives having a non-polar deletion of nodA , and carrying a plasmid with either the R. meliloti or the R. tropici nodA gene. The strain with the R. tropici nodA gene produced Nod factors acylated by vaccenic acid, instead of the C16 unsaturated or hydroxylated fatty acids characteristic of R. meliloti Nod factors, and infected and nodulated alfalfa with a significant delay. These results show that NodA proteins of R. meliloti and R. tropici specify the N -acylation of Nod factors by different fatty acids, and that allelic variation of the common nodA gene can contribute to the determination of host range.     

Characterization of a binding site for chemically synthesized lipo-oligosaccharidic NodRm factors in particulate fractions prepared from roots

This paper describes the characteristics of a binding site for the major, lipo-oligosaccharide Nod factor of Rhizobium meliloti in roots of the symbiotic host plant, Medicago truncatula. Chemically synthesized NodRm-IV(Ac, S, C16:2) was labelled by tritiation to a specific activity of 56 Ci mmol^?1 and this ligand was shown to be biologically active in the root hair deformation assay at 10^?11 M. Binding of the ligand to a particulate fraction from roots of M. truncatula was found to be saturable and reversible with an affinity (K_d) of 86 nM and the binding characteristics were consistent with a single class of binding sites. Competition with modified Nod factors showed that the binding was independent of both the O-acetyl and the sulphyl group and did not depend on the unsaturation of the fatty acid. However, both moieties of the lipo-oligosaccharide are required for high-affinity binding since tetra-N-acetyl-chitotetraose and palmitate were found to be poor competitors of ligand binding. A binding site with analogous characteristics was also found in a similarly prepared particulate fraction of tomato roots. This binding site for Nod factors, termed NFBS1, which is present in both a leguminous and a non-leguminous plant, may have a more general role than symbiosis.     

Root Hair Deformation Activity of Nodulation Factors and Their Fate on Vicia sativa

We used a semiquantitative root hair deformation assay for Vicia sativa (vetch) to study the activity of Rhizobium leguminosarum bv viciae nodulation (Nod) factors. Five to 10 min of Nod factor-root interaction appears to be sufficient to induce root hair deformation. The first deformation is visible within 1 h, and after 3 h about 80% of the root hairs in a small susceptible zone of the root are deformed. This zone encompasses root hairs that have almost reached their maximal size. The Nod factor accumulates preferentially to epidermal cells of the young part of the root, but is not restricted to the susceptible zone. In the interaction with roots, the glucosamine backbone of Nod factors is shortened, presumably by chitinases. NodRlv-IV(C18:4,Ac) is more stable than NodRlv-V(C18:4,Ac). No correlation was found between Nod factor degradation and susceptibility. Degradation occurs both in the susceptible zone and in the mature zone. Moreover, degradation is not affected by NH4NO3 and is similar in vetch and in the nonhost alfalfa (Medicago sativa).     

Activation of the cell cycle machinery and the isoflavonoid biosynthesis pathway by active Rhizobium meliloti Nod signal molecules in Medicago microcallus suspensions.

We have shown that treatment of Medicago microcallus suspensions with the cognate Rhizobium meliloti Nod signal molecule NodRm-IV(C16:2,S) can modify gene expression both qualitatively and quantitatively. At concentrations of 10(-6) - 10(-9) M, this host specific plant morphogen but not the inactive non-sulfated molecule stimulated cell cycle progression as indicated by the significantly enhanced thymidine incorporation, elevated number of S phase cells, increase in kinase activity of the p34cdc2-related complexes and enhancement of the level of expression of several cell cycle marker genes, the histone H3-1, the cdc2Ms and the cyclin cycMs2. The presented data suggest that at least part of the physiological role of the Nod factor may be linked to molecular events involved in the control of the plant cell division cycle. In situ hybridization experiments with antisense H3-1 RNA probe indicated that only certain cells of the calli were able to respond to the Nod factor. High (10(-6) M) but not low (10(-9) M) concentrations of the active Nod factors induced the expression of the isoflavone reductase gene (IFR), a marker gene of the isoflavonoid biosynthesis pathway in most callus cells. Our results indicate that Medicago cell responses to the Nod signal molecules can be investigated in suspension cultures.     

N-deacetylation of Sinorhizobium meliloti Nod factors increases their stability in the Medicago sativa rhizosphere and decreases their biological activity

Nod factors excreted by rhizobia are signal molecules that consist of a chitin oligomer backbone linked with a fatty acid at the nonreducing end. Modifications of the Nod factor structures influence their stability in the rhizosphere and their biological activity. To test the function of N-acetyl groups in Nod factors, NodSm-IV(C16:2,S) from Sinorhizobium meliloti was enzymatically N-deacetylated in vitro with purified chitin deacetylase from Colletotrichum lindemuthianum. A family of partially and completely deacetylated derivatives was produced and purified. The most abundant chemical structures identified by mass spectrometry were GlcN(C16:2)-GlcNAc-GlcNH2-GlcNAc(OH)(S), GlcN(C16,2)-GlcNAc-GlcNH2-GlcNH2(OH)(S), and GlcN(C16:2)-GlcNH2-GlcNH2-GlcNH2(OH)(S). In contrast to NodSm-IV(C16:2,S), the purified N-deacetylated derivatives were stable in the rhizosphere of Medicago sativa, indicating that the N-acetyl groups make the carbohydrate moiety of Nod factors accessible for glycosyl hydrolases of the host plant. The N-deacetylated derivatives displayed only a low level of activity in inducing root hair deformation. Furthermore, the N-deacetylated molecules were not able to stimulate Nod factor degradation by M. sativa roots, a response elicited by active Nod factors. These data show that N-acetyl groups of Nod factors are required for biological activity.     

Nod factors stimulate plasma membrane delimited phospholipase C activity in vitro

Nod factors are lipo-chito-oligosaccharides secreted by Rhizobium to initiate deformation of root hairs and other changes in host plants. Since Nod factor-induced changes in intracellular calcium occur in responsive root hairs, we tested if phospholipase C (PLC) activity is stimulated by Nod factors. Plasma membranes were isolated from the nodulation-competent zone of roots of Vigna unguiculata to assay PLC activity in vitro. Nod factors isolated from Rhizobium sp. NGR234, NodNGR[S] and NodNGR[Ac] significantly increased PLC activity and this increase in activity was inhibited in the presence of the PLC inhibitors, neomycin and U-73122. The response appears specific as PLC activity was not significantly induced neither by the 4-sugar, N,N',N',N' -tetracetylchitotetraose (TACT), or the five-sugar, penta- N -acetylchitopentaose (PACT), backbone of Nod factors. The G-protein activators, GTP γ S and the aluminium fluoride complex, had no effect on PLC activity in the presence or absence of NodNGR[S], suggesting that Nod factors act independently of G-proteins in vitro. However, the combination of oleic acid and TACT mimicked the effect of Nod factors on PLC activity indicating that the presence of the lipid tail may be critical. Also this combination of compounds acted synergistically together to evoke root hair deformation in vivo. Our results indicate that Nod factors can modulate membrane delimited PLC activity and indicate that PLC is likely to be a component of the Nod factor-signalling pathway.     

The role of ion fluxes in Nod factor signalling in Medicago sativa

Using ion-selective microelectrodes, the basis of Nod factor-induced changes in the plasma membrane potential was analysed by measuring the extracellular free concentrations of Ca²⁺, K⁺, H⁺ and Cl^– in the root hair zone of alfalfa. After addition of the Rhizobium meliloti Nod factor NodRm-IV(C16:2,S) at a concentration of 0.1 μM, a decrease in [Ca²⁺] was observed first, which was followed after a few seconds by an increase of [Cl^–], by an alkalinization, and then by a delayed increase of [K⁺], all of which were transient changes. Simultaneously with the appearance of Cl^– ions in the root hair zone, a decrease in cytosolic [Cl^–] was measured. It was concluded that the depolarization was caused by temporary short-circuiting of the proton pump through the rapid release of Cl^– ions along their steep electrochemical gradient. Since under resting conditions the driving force for K⁺ ions was inwardly directed, their release was delayed until their driving force was inverted. This indicates that K⁺ serves as a charge balance that eventually stops depolarization and initiates repolarization. Since the decrease in [Ca²⁺] was observed seconds before the increase in [Cl^–] and the depolarization, it is argued that Ca²⁺ entering into the cell does not cause the depolarization directly, but might initiate it by triggering the activation of an anion channel that then releases the chloride ions. The observations that the Ca²⁺ ionophore A23187 mimicks the Nod factor response, and that the Ca²⁺ channel antagonist nifedipine inhibits this response, support the idea that Ca²⁺ plays a primary role in the transduction of the Nod signal in alfalfa.     

Efficacy of chlorine and heat treatment in killing Salmonella stanley inoculated onto alfalfa seeds and growth and survival of the pathogen during sprouting and storage.

The efficacy of chlorine and hot water treatments in killing Salmonella stanley inoculated onto alfalfa seeds was determined. Treatment of seeds containing 10(2) to 10(3) CFU/g in 100-micrograms/ml active chlorine solution for 5 or 10 min caused a significant (P < or = 0.05) reduction in population, and treatment in 290-micrograms/ml chlorine solution resulted in a significant reduction compared with treatment in 100 micrograms of chlorine per ml. However, concentrations of chlorine of up to 1,010 micrograms/ml failed to result in further significant reductions. Treatment of seeds containing 10(1) to 10(2) CFU of S. stanley per g for 5 min in a solution containing 2,040 micrograms of chlorine per ml reduced the population to undetectable levels (< 1 CFU/g). Treatment of seeds in water for 5 or 10 min at 54 degrees C caused a significant reduction in the S. stanley population, and treatment at > or = 57 degrees C reduced populations to < or = 1 CFU/g. However, treatment at > or = 54 degrees C for 10 min caused a substantial reduction in viability of the seeds. Treatment at 57 or 60 degrees C for 5 min appears to be effective in killing S. stanley without substantially decreasing germinability of seeds. Storage of seeds for 8 to 9 weeks at 8 and 21 degrees C resulted in reductions in populations of S. stanley of about 1 log10 and 2 log10 CFU/g, respectively. The behavior of S. stanley on seeds during soaking germination, sprouting, and refrigerated storage of sprouts was determined. An initial population of 3.29 log10 CFU/g increased slightly during 6 h of soaking, by about 10(3) CFU/g during a 24-h germination period, and by an additional 10 CFU/g during a 72-h sprouting stage. A population of 10(7) CFU/g of mature alfalfa sprouts was detected throughout a subsequent 10-day storage period at 5 degrees C. These studies indicate that while populations of S. stanley can be greatly reduced, elimination of this organism from alfalfa seeds may not be reliably achieved with traditional disinfection procedures. If S. stanley is present on seeds at the initiation of the sprout production process, populations exceeding 10(7) CFU/g can develop and survive on mature sprouts exposed to handling practices used in commercial production and marketing.     

The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

The genome of the human hepatitis delta virus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal structure shows the dangling nucleotides 5′ of the cleavage site projecting away from the catalytic core. This 5′-sequence contains a clinically conserved U − 1 that we find to be essential for fast cleavage, as the order of activity follows U − 1 > C − 1 > A − 1 > G − 1, with a >25-fold activity loss from U − 1 to G − 1. Terbium(III) footprinting detects conformations for the P1.1 stem, the cleavage site wobble pair and the A-minor motif of the catalytic trefoil turn that depend on the identity of the N − 1 base. The most tightly folded catalytic core, resembling that of the reaction product, is found in the U − 1 wild-type precursor. Molecular dynamics simulations demonstrate that a U − 1 forms the most robust kink around the scissile phosphate, exposing it to the catalytic C75 in a previously unnoticed U-turn motif found also, for example, in the hammerhead ribozyme and tRNAs. Strikingly, we find that the common structural U-turn motif serves distinct functions in the HDV and hammerhead ribozymes.     

Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme

Many sequence variations of the 8–17 RNA-cleaving deoxyribozyme have been isolated through in vitro selection. In an effort to understand how these sequence variations affect cleavage site selectivity, we systematically mutated the catalytic core of 8–17 and measured the cleavage activity of each mutant deoxyribozyme against all 16 possible chimeric (RNA/DNA) dinucleotide junctions. We observed sequence-function relationships that suggest how the following non-conserved positions in the catalytic core influence selectivity at the dinucleotide (5′ rN₁₈-N_1.1 3′) cleavage site: (i) positions 2.1 and 12 represent a primary determinant of the selectivity at the 3′ position (N_1.1) of the cleavage site; (ii) positions 15 and 15.0 represent a primary determinant of the selectivity at the 5′ position (rN₁₈) of the cleavage site and (iii) the sequence of the 3-bp intramolecular stem has relatively little influence on cleavage site selectivity. Furthermore, we report for the first time that 8–17 variants have the collective ability to cleave all dinucleotide junctions with rate enhancements of at least 1000-fold over background. Three optimal 8–17 variants, identified from ~75 different sequences that were examined, can collectively cleave 10 of 16 junctions with useful rates of ≥0.1 min⁻¹, and exhibit an overall hierarchy of reactivity towards groups of related junctions according to the order NG > NA > NC > NT.     

Kinetics of Cellulose Digestion by Fibrobacter succinogenes S85

Growing cultures of Fibrobacter succinogenes S85 digested cellulose at a rapid rate, but nongrowing cells and cell extracts did not have detectable crystalline cellulase activity. Cells that had been growing exponentially on cellobiose initiated cellulose digestion and succinate production immediately, and cellulose-dependent succinate production could be used as an index of enzyme activity against crystalline cellulose. Cells incubated with cellulose never produced detectable cellobiose, and cells that were preincubated for a short time with thiocellobiose lost their ability to digest cellulose (competitive inhibition [K(infi)] of only 0.2 mg/ml or 0.56 mM). Based on these results, the crystalline cellulases of F. succinogenes were very sensitive to feedback inhibition. Different cellulose sources bound different amounts of Congo red, and the binding capacity was HCl-regenerated cellulose > ball-milled cellulose > Sigmacel > Avicel > filter paper. Congo red binding capacity was highly correlated with the maximum rates of metabolism of cellulose digestion and inversely related to K(infm). Congo red (250 (mu)g/ml) did not inhibit the growth of F. succinogenes S85 on cellobiose, but this concentration of Congo red inhibited the rate of ball-milled cellulose digestion. A Lineweaver-Burk plot of ball-milled cellulose digestion rate versus the amount of cellulose indicated that Congo red was a competitive inhibitor of cellulose digestion (K(infi) was 250 (mu)g/ml).