PubMed Health⌕ Search

Biomedical subjects

Dale Kaiser

Publications and source records attributed to Dale Kaiser.

At least 19 recordsLinked to original sources
PubMed2006

Mutations of the act promoter in Myxococcus xanthus.

Mutations within the -12 and -24 elements provide evidence that the act promoter is recognized by sigma-54 RNA polymerase. Deletion of the -20 base pair, which lies between the two conserved elements of sigma-54 promoters, decreased expression by 90%. In addition, mutation of a potential enhancer sequence, around -120, led to an 80% reduction in act gene expression. actB, the second gene in the act operon, encodes a sigma-54 activator protein that is proposed to be an enhancer-binding protein for the act operon. All act genes, actA to actE, are expressed together and constitute an operon, because an in-frame deletion of actB decreased expression of actA and actE to the same extent. After an initially slow phase of act operon expression, which depends on FruA, there is a rapid phase. The rapid phase is shown to be due to the activation of the operon expression by ActB, which completes a positive feedback loop. That loop appears to be nested within a larger positive loop in which ActB is activated by the C signal via ActA, and the act operon activates transcription of the csgA gene. We propose that, as cells engage in more C signaling, positive feedback raises the number of C-signal molecules per cell and drives the process of fruiting body development forward.

Amino Acid Sequence↗
PubMed2006

Gliding motility and polarized slime secretion.

Myxococcus leaves a trail of slime on agar as it moves. A filament of slime can be seen attached to the end of a cell, but it is seen only at one end at any particular moment. To identify genes essential for A motility, transposon insertion mutations with defective A motility were studied. Fifteen of the 33 mutants had totally lost A motility. All these mutant cells had filaments of slime emerging from both ends, indicating that bipolar secretion prevents A motility. The remaining 18 A motility mutants, also produced by gene knockout, secreted slime only from one pole, but they swarmed at a lower rate than A(+) and are called 'partial' gliding mutants, or pgl. For each pgl mutant, the reduction in swarm expansion rate was directly proportional to the reduction in the coefficient of elasticotaxis. The pgl mutants have a normal reversal frequency and normal gliding speed when they move. But their probability of movement per unit time is lower than pgl(+) cells. Many of the pgl mutants are produced by transposon insertions in glycosyltransferase genes. It is proposed that these glycosyltransferases carry out the synthesis of a repeat unit polysaccharide that constitutes the slime.

Bacterial Proteins↗
PubMed2006

A three-dimensional model of myxobacterial fruiting-body formation.

Myxobacterial cells are social; they swarm by gliding on surfaces as they feed cooperatively. When they sense starvation, tens of thousands of cells change their movement pattern from outward spreading to inward concentration and form aggregates that become fruiting bodies. Cells inside fruiting bodies differentiate into round, nonmotile, environmentally resistant spores. Traditionally, cell aggregation has been considered to imply chemotaxis, a long-range cell interaction that shares many features of chemical reaction-diffusion dynamics. The biological evidence, however, suggests that Myxococcus xanthus aggregation is the consequence of direct cell-contact interactions that are different from chemotaxis. To test whether local interactions suffice to explain the formation of fruiting bodies and the differentiation of spores within them, we have simulated the process. In this article, we present a unified 3D model that reproduces in one continuous simulation all the stages of fruiting-body formation that have been experimentally observed: nonsymmetric initial aggregates (traffic jams), streams, formation of toroidal aggregates, hemispherical 3D mounds, and finally sporulation within the fruiting body.

Cell Communication↗
PubMed2006

Distinguishing features of delta-proteobacterial genomes.

We analyzed several features of five currently available delta-proteobacterial genomes, including two aerobic bacteria exhibiting predatory behavior and three anaerobic sulfate-reducing bacteria. The delta genomes are distinguished from other bacteria by several properties: (i) The delta genomes contain two "giant" S1 ribosomal protein genes in contrast to all other bacterial types, which encode a single or no S1; (ii) in most delta-proteobacterial genomes the major ribosomal protein (RP) gene cluster is near the replication terminus whereas most bacterial genomes place the major RP cluster near the origin of replication; (iii) the delta genomes possess the rare combination of discriminating asparaginyl and glutaminyl tRNA synthetase (AARS) together with the amido-transferase complex (Gat CAB) genes that modify Asp-tRNA(Asn) into Asn-tRNA(Asn) and Glu-tRNA(Gln) into Gln-tRNA(Gln); (iv) the TonB receptors and ferric siderophore receptors that facilitate uptake and removal of complex metals are common among delta genomes; (v) the anaerobic delta genomes encode multiple copies of the anaerobic detoxification protein rubrerythrin that can neutralize hydrogen peroxide; and (vi) sigma(54) activators play a more important role in the delta genomes than in other bacteria. delta genomes have a plethora of enhancer binding proteins that respond to environmental and intracellular cues, often as part of two-component systems; (vii) delta genomes encode multiple copies of metallo-beta-lactamase enzymes; (viii) a host of secretion proteins emphasizing SecA, SecB, and SecY may be especially useful in the predatory activities of Myxococcus xanthus; (ix) delta proteobacteria drive many multiprotein machines in their periplasms and outer membrane, including chaperone-feeding machines, jets for slime secretion, and type IV pili. Bdellovibrio replicates in the periplasm of prey cells. The sulfate-reducing delta proteobacteria metabolize hydrogen and generate a proton gradient by electron transport. The predicted highly expressed genes from delta genomes reflect their different ecologies, metabolic strategies, and adaptations.

Amino Acyl-tRNA Synthetases↗
PubMed2006

Polar assembly of the type IV pilus secretin in Myxococcus xanthus.

The type IV pilus filament of Myxococcus xanthus penetrates the outer membrane through a gated channel--the PilQ secretin. Assembly of the channel and formation of PilQ multimeric complexes that resist disassembly in heated detergent is correlated with the release of a 50 kDa fragment of PilQ. Tgl lipoprotein is required for PilQ assembly in M. xanthus, because PilQ monomers but no heat and detergent-resistant complexes are present in a strain from which tgl has been deleted. PilQ protein is often found in single patches at both poles of the cell. Tgl, however, is found in a patch at only one pole that most likely identifies the piliated cell pole. Tgl protein that has been transferred from another cell by contact stimulation leads to secretin assembly in the recipient. Pilus proteins PilQ, PilG, PilM, PilN, PilO and PilP are also required for the donation of Tgl by contact stimulation to a stimulation recipient. We suggest that these proteins are parts of a polar superstructure that holds PilQ monomers in a cluster and ready for Tgl to bring about secretin assembly.

Bacterial Proteins↗
PubMed2006

Straight-chain fatty acids are dispensable in the myxobacterium Myxococcus xanthus for vegetative growth and fruiting body formation.

Inactivation of the MXAN_0853 gene blocked the production in Myxococcus xanthus of straight-chain fatty acids which otherwise represent 30% of total fatty acids. Despite this drastic change in the fatty acid profile, no change in phenotype could be observed, which contrasts with previous interpretations of the role of straight-chain fatty acids in the organism's development.

3-Oxoacyl-(Acyl-Carrier-Protein) Synthase↗
PubMed2006

3-Hydroxy-3-methylglutaryl-coenzyme A (CoA) synthase is involved in biosynthesis of isovaleryl-CoA in the myxobacterium Myxococcus xanthus during fruiting body formation.

Isovaleryl-coenzyme A (IV-CoA) is the starting unit for some secondary metabolites and iso-odd fatty acids in several bacteria. According to textbook biochemistry, IV-CoA is derived from leucine degradation, but recently an alternative pathway that branches from the well-known mevalonate-dependent isoprenoid biosynthesis has been described for myxobacteria. A double mutant was constructed in Myxococcus xanthus by deletion of genes involved in leucine degradation and disruption of mvaS encoding the 3-hydroxy-3-methylglutaryl-coenzyme A synthase. A dramatic decrease of IV-CoA-derived iso-odd fatty acids was observed for the mutant, confirming mvaS to be involved in the alternative pathway. Additional quantitative real-time reverse transcription-PCR experiments indicated that mvaS is transcriptionally regulated by isovalerate. Furthermore, feeding studies employing an intermediate specific for the alternative pathway revealed that this pathway is induced during fruiting body formation, which presumably increases the amount of IV-CoA available when leucine is limited.

Acyl Coenzyme A↗
PubMed2006

A microbial genetic journey.

Fortunately, I began research in 1950 when the basic concepts of microbial genetics could be explored experimentally. I began with bacteriophage lambda and tried to establish the colinearity of its linkage map with its DNA molecule. My students and I worked out the regulation of lambda repressor synthesis for the establishment and maintenance of lysogeny. We also investigated the proteins responsible for assembly of the phage head. Using cell extracts, we discovered how to package DNA inside the head in vitro. Around 1972, I began to use molecular genetics to understand the developmental biology of Myxococcus xanthus. In particular, I wanted to learn how myxococcus builds its multicellular fruiting body within which it differentiates spores. We identified two cell-to-cell signals used to coordinate development. We have elucidated, in part, the signal transduction pathway for C-signal that directs the morphogenesis of a fruiting body.

Bacterial Proteins↗
PubMed2005

A three-dimensional model of myxobacterial aggregation by contact-mediated interactions.

Myxobacteria provide one of the simplest models of cell-cell interaction and organized cell movement leading to cellular differentiation. When starved, tens of thousands of cells change their movement pattern from outward spreading to inward concentration; they form aggregates that become fruiting bodies. Cells inside fruiting bodies differentiate into round, nonmotile, environmentally resistant spores. Traditionally, cell aggregation has been considered to imply chemotaxis; a long-range cell interaction. However, myxobacterial aggregation is the consequence of direct cell-contact interactions, not chemotaxis. We present here a 3D stochastic lattice-gas cellular automata model of cell aggregation based on local cell-cell contact, and no chemotaxis. We demonstrate that a 3D discrete stochastic model can simulate two stages of cell aggregation. First, a "traffic jam" forms embedded in a field of motile cells. The jam then becomes an aggregation center that accumulates more cells. We show that, at high cell density, cells stream around the traffic jam, generating a 3D hemispherical mound. Later, when the nuclear traffic jam dissolves, the aggregation center becomes a 3D ring of streaming cells.

Models, Biological↗
PubMed2005

Cell-to-cell transfer of bacterial outer membrane lipoproteins.

Myxococcus xanthus cells can glide forward by retracting type IV pili. Tgl, an outer membrane lipoprotein, is necessary to assemble pili. Tgl mutants can be transiently "stimulated" if brought into end-to-end contact with tgl+ donor cells. By separating the stimulated recipient cells from donor cells, we found that Tgl protein was transferred from the donors to the rescued recipient cells. Mutants lacking CglB lipoprotein, which is part of a second gliding engine, could also be stimulated, and CglB protein was transferred from donor to recipient cells. The high transfer efficiency of Tgl and CglB proteins suggests that donor and recipient cells briefly fuse their outer membranes.

Antigens, Bacterial↗
PubMed2005

Enhancer-binding proteins with a forkhead-associated domain and the sigma54 regulon in Myxococcus xanthus fruiting body development.

In response to starvation, Myxococcus xanthus initiates a developmental program that results in the formation of spore-filled, multicellular fruiting bodies. Many developmentally regulated genes in M. xanthus are transcribed from sigma(54) promoters, and these genes require enhancer-binding proteins. Here we report the finding of an unusual group of 12 genes encoding sigma(54)-dependent enhancer-binding proteins containing a forkhead-associated (FHA) domain as their N-terminal sensory domain. FHA domains in other proteins recognize phosphothreonine residues. An insertion mutation in one of these genes, Mx4885, caused a cell autonomous aggregation and sporulation defect. In-frame deletion mutants showed that the FHA domain is necessary for proper Mx4885 function. The altered pattern of developmental gene expression in the mutant implied that Mx4885 is on the pathway of response to the morphogenetic C-signal. Immunoblots specific for C-signal and FruA imply that the site of Mx4885 action is downstream of FruA synthesis on the C-signal transduction pathway. Mx4885 may help to coordinate the level of intracellular phosphorylated FruA (FruA-P) with the level of C-signal displayed on the signal donor cell. Because FHA domains respond to phosphothreonine-containing proteins, these results suggest a regulatory link to the abundant Ser/Thr protein kinases in M. xanthus.

Amino Acid Sequence↗
PubMed2005

Reversing cell polarity: evidence and hypothesis.

The long, rod-shaped cells of myxobacteria are polarized by their gliding engines. At the rear, A-engines push while pili pull the front end forward. An hypothesis is developed whereby both engines are partially dis-assembled, then re-assembled at the opposite pole when cells reverse their movement direction. Reversals are induced by an Mgl G-protein switch that controls engine polarity. The switch is driven by an oscillatory circuit of Frizzy proteins. In growing cells, the circuit gives rise to an occasional reversal that makes swarming possible. Then, as myxobacteria begin fruiting body development, a rising level of C-signal input drives the oscillator and changes the reversal pattern. Cells reverse regularly every eight minutes in traveling waves, the reversal period is then prolonged enabling cells to form streams that enlarge tiny random aggregates into fruiting bodies.

Bacterial Proteins↗
PubMed2005

Regulating pilin expression reveals a threshold for S motility in Myxococcus xanthus.

An isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible promoter was constructed in Myxococcus xanthus. The single-copy pilA gene encodes pilin, the monomer unit of M. xanthus type IV pili. To vary the level of pilA expression, we cloned its promoter in front of the lac operator, and a plasmid containing the construct was inserted into the chromosome of a DeltapilA strain. Induction of pilin expression increased smoothly as the dose of IPTG added to the culture was increased. IPTG-induced pilin rescued S motility of the DeltapilA strain to wild-type levels. The rate of S-motile swarming was found to be proportional to the number of pili (shear-sensitive pilin) produced rather than to the level of total pilin. In fact, S motility was not rescued until the total level of pilin was more than 50% of the wild-type level. This observation implies that a threshold concentration of pilin must be exceeded before the shear-sensitive material (pili) is polymerized in M. xanthus.

Base Sequence↗
PubMed2004

Computational prediction of human metabolic pathways from the complete human genome.

BACKGROUND: We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary first step toward quantitative modeling of metabolism. RESULTS: Our analysis assigns 2,709 human enzymes to 896 bioreactions; 622 of the enzymes are assigned roles in 135 predicted metabolic pathways. The predicted pathways closely match the known nutritional requirements of humans. This analysis identifies probable omissions in the human genome annotation in the form of 203 pathway holes (missing enzymes within the predicted pathways). We have identified putative genes to fill 25 of these holes. The predicted human metabolic map is described by a Pathway/Genome Database called HumanCyc, which is available at http://HumanCyc.org/. We describe the generation of HumanCyc, and present an analysis of the human metabolic map. For example, we compare the predicted human metabolic pathway complement to the pathways of Escherichia coli and Arabidopsis thaliana and identify 35 pathways that are shared among all three organisms. CONCLUSIONS: Our analysis elucidates a significant portion of the human metabolic map, and also indicates probable unidentified genes in the genome. HumanCyc provides a genome-based view of human nutrition that associates the essential dietary requirements of humans with a set of metabolic pathways whose existence is supported by the human genome. The database places many human genes in a pathway context, thereby facilitating analysis of gene expression, proteomics, and metabolomics datasets through a publicly available online tool called the Omics Viewer.

Arabidopsis↗
PubMed2004

A biochemical oscillator explains several aspects of Myxococcus xanthus behavior during development.

During development, Myxococcus xanthus cells produce a series of spatial patterns by coordinating their motion through a contact-dependent signal, the C-signal. C-signaling modulates the frequency at which cells reverse their gliding direction. It does this by interacting with the Frz system (a homolog of the Escherichia coli chemosensory system) via a cascade of covalent modifications. Here we show that introducing a negative feedback into this cascade results in oscillatory behavior of the signaling circuit. The model explains several aspects of M. xanthus behavior during development, including the nonrandom distribution of reversal times, and the differences in response of the reversal frequency to both moderate and high levels of C-signaling at different developmental stages. We also propose experiments to test the model.

Bacterial Proteins↗
PubMed2004

Waves and aggregation patterns in myxobacteria.

Under starvation conditions, a population of myxobacteria aggregates to build a fruiting body whose shape is species-specific and within which the cells sporulate. Early in this process, cells often pass through a "ripple phase" characterized by traveling linear, concentric, and spiral waves. These waves are different from the waves observed during slime mold aggregation that depend on diffusible morphogens, because myxobacteria communicate by direct contact. The difference is most dramatic when waves collide: rather than annihilating one another, myxobacterial waves appear to pass through one another unchanged. Under certain conditions, the spacing and location of the nascent fruiting bodies is determined by the wavelength and pattern of the waves. Later in fruiting body development, waves are replaced by streams of cells that circulate around small initial aggregates enlarging and rounding them. Still later, pairs of motile aggregates coalesce to form larger aggregates that develop into fruiting bodies. Here we present a mathematical model that quantitatively explains these wave and aggregation phenomena.

Models, Biological↗
PubMed2004

Sigma54 enhancer binding proteins and Myxococcus xanthus fruiting body development.

A search of the M1genome sequence, which includes 97% of the Myxococcus xanthus genes, identified 53 sequence homologs of sigma54-dependent enhancer binding proteins (EBPs). A DNA microarray was constructed from the M1genome that includes those homologs and 318 other M. xanthus genes for comparison. To screen the developmental program with this array, an RNA extract from growing cells was compared with one prepared from developing cells at 12 h. Previous reporter studies had shown that M. xanthus has initiated development and has begun to express many developmentally regulated genes by 12 h. The comparison revealed substantial increases in the expression levels of 11 transcription factors that may respond to environmental stimuli. Six of the 53 EBP homologs were expressed at significantly higher levels at 12 h of development than during growth. Three were previously unknown genes, and they were inactivated to look for effects on fruiting body development. One knockout mutant produced fruiting bodies of abnormal shape that depended on the composition of the medium.

Amino Acid Sequence↗