Molecular evolution and secondary structural conservation in the B-cell lymphoma leukemia 2 (bcl-2) family of proto-oncogene products

The nature of the bcl-2 family of proto-oncogenes was analyzed by sequence alignment, secondary structure prediction, and phylogenetic techniques. Phylogenies were inferred from both the nucleic acid and amino acid sequences of the human, murine, rat, and chicken sequences for BCL-2 and BCL-X, human MCL1, murine A1, the nematode Caenorhabditis elegans and Caenorhabditis briggsiae ced-9 proteins, and the sequences BHRF1 from Epstein-Barr and LMW5-HL from African swine fever viruses. Both sequence alignment and secondary structure prediction techniques supported the conservation of both the overall secondary structure and the carboxy-terminal transmembrane domain in all members of the family. All the treeing methods employed (distance matrix, maximum likelihood, and parsimony) supported a tree in which the proapoptotic proteins BCL-2 and BCL-X represent the most recent additions to the group. All the trees also indicated that the viral proteins BHRF1 and LMW-HL arose from a common ancestor, an ancestor they shared in common with the pro-apoptotic control protein BAX, indicating that this function of BAX evolved only recently. The most ancient branches are represented by the nematode ced-9 protein and by the control genes MCL1 and A1, which in the treeing methods employed represent separate lineages within the most ancient grouping. These results demonstrate the evolution of a highly conserved family of developmental control genes from nematode to man--genes that encode proteins essential for normal development but which are highly conserved in terms of predicted structure and possible cellular localization. The evolutionary analysis also indicates that the family may be even larger than originally predicted and that other members are waiting to be discovered.

Determination of the folding topology of the SL1 RNA from Caenorhabditis elegans by multidimensional heteronuclear NMR

The process of trans-splicing involves the transfer of a short spliced leader (SL) RNA sequence to a consensus acceptor site on a separate pre-mRNA transcript. In this study, the first stem loop of the SL1 RNA from the nematode Caenorhabditis elegans was examined by homonuclear and heteronuclear NMR. Results of enzymatic cleavage patterns established that the first 36 nucleotides (which includes the splice site and a complementary base-paired region surrounding a nine-nucleotide hairpin loop) remain structurally independent of the rest of the 100-nucleotide full-length transcript. A comparison of exchangeable and non-exchangeable proton chemical shifts in the region of the splice site and loop between the native sequence and a modified 26-nucleotide fragment from which an asymmetric internal loop had been deleted was made. There was no significant difference between the resonance locations of the equivalent protons in the two molecules, establishing that there was no tertiary interaction between the hairpin and internal loops. Full chemical shift assignments of 1H, 13C, and 15N chemical shifts were obtained for the modified fragment by multidimensional homonuclear and heteronuclear NMR spectroscopy. The stem adopts an A-form helix typical of RNA. The A-type helical conformation of the stem appears to continue for the first three nucleotides of the 5' side of the loop, followed by a guanosine residue in a syn conformation about the glycosidic bond. Base stacking is not seen on the 3' side of the loop. There was no evidence for formation of Watson-Crick base-pairs within the loop, but several long distance NOEs indicated cross-loop contacts, indicative of a structured loop. The final loop residues, an adenine which is conserved among all known nematode SL RNA sequences, adopts an extrahelical conformation.

The culture of credit

Scientific ideals call for collaboration and sharing. But in today's competitive scientific enterprise, a tremendous premium is placed on individual credit, setting the stage for conflict.

Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation

A number of different intracellular signaling pathways have been shown to be activated by receptor tyrosine kinases. These activation events include the phosphoinositide 3-kinase, 70 kDa S6 kinase, mitogen-activated protein kinase (MAPK), phospholipase C-gamma, and the Jak/STAT pathways. The precise role of each of these pathways in cell signaling remains to be resolved, but studies on the differentiation of mammalian PC12 cells in tissue culture and the genetics of cell fate determination in Drosophila and Caenorhabditis suggest that the extracellular signal-regulated kinase (ERK-regulated) MAPK pathway may be sufficient for these cellular responses. Experiments with PC12 cells also suggest that the duration of ERK activation is critical for cell signaling decisions.

Identification of two new members of the tubulin family

Analysis of the delta- and epsilon-tubulin sequences indicates that they both consist of two structural domains of which the N-terminal domain can bind to alpha/beta heterodimers while the C-terminal domain probably binds to a non-tubulin protein. Both additional tubulins probably bind GTP but lack GTPase activity, while their synthesis requires the TCP1 chaperonine but is not autoregulated. Although these properties resemble those of gamma-tubulin, the low sequence identity (Table I) demonstrates that the gamma-, delta-, and epsilon-proteins should be classed as different members of the tubulin family. The identification of these additional members is unexpected. Examination of the cellular expression and distribution of the delta- and epsilon-tubulins, and whether other organisms contain homologous genes, may reveal further features of the eukaryotic cytoskeleton.

On global sequence alignment

We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.

Sequence of C. elegans lag-2 reveals a cell-signalling domain shared with Delta and Serrate of Drosophila

The lin-12 and glp-1 genes of Caenorhabditis elegans encode members of the Notch family of transmembrane proteins. Genetic studies indicate that the lin-12 and glp-1 proteins act as receptors in specific developmental cell interactions and that their functions are partially redundant. lin-12 glp-1 double mutants display certain embryonic defects not found in either single mutant. The phenotype of this double mutant is called Lag, and recessive mutations in either of the genes lag-1 or lag-2 can also result in the Lag phenotype, indicating that these two genes may participate in the same cell interactions that require lin-12 or glp-1. We report here that lag-2 encodes a predicted transmembrane protein of 402 amino acids. The predicted extracellular region of lag-2 is similar to amino-terminal regions of Delta and Serrate, two Drosophila proteins that are thought to function as ligands for Notch. The region of similarity includes sequences related to epidermal growth factor (EGF) repeats. We have isolated lag2(sa37), a dominant allele that shows specific genetic interactions with lin-12. The sa37 mutation causes a Gly-->Asp change in a conserved residue of an EGF motif. Because of its overall structure, its sequence similarity to Delta and Serrate, and its genetic interactions, we suggest that lag-2 encodes an intercellular signal for the lin-12 and glp-1 receptors.

Collection and storage of invertebrate samples

The validity of any comparative study is dependent on the reliability of the identification of the samples in the study. Not all researchers are experts in the field of identification of samples, nor do all researchers have quick and ready access to expert systematists who can accomplish the task of identification. The importance of verification of sample identity for comparative studies is vital. We describe several methods by which researchers can obtain and identify samples from the wild, and we suggest methods by which voucher samples can be obtained for future reference to these collected samples. We outline alternatives to collection of samples from the wild, such as purchase from stock centers and biological supply companies. Museum collections can also be extremely helpful in obtaining complete organismal samples for comparative studies.

Scaling up the nervous system of Caenorhabditis elegans: is one ape equal to 33 million worms?

Although vastly different, both the mammalian brain and the nematode Caenorhabditis elegans' nervous system must contribute critically to assure survival. Two quantitative conditions which place bounds on networks for connectedness and stability are tested on the published neural network of C. elegans and fit. Consideration of networks scaled up to mammalian size and confined between these bounds suggests that perhaps, the entire spectrum of brain size may be built between these bounds. Further consequences of increasing brain size relate to the trade-off between complexity, providing internal resistance to individual damage, and redundancy of population, as survival mechanisms.

Alternatively spliced transcripts of the flp-1 gene encode distinct FMRFamide-like peptides in Caenorhabditis elegans

We have isolated and characterized several cDNAs and the corresponding genomic region of a gene encoding multiple FMRFamide-like neuropeptides from the nematode Caenorhabditis elegans. The gene, named flp-1, consists of six exons of which four encode FMRFamide-like peptides. The cDNA and genomic sequences revealed that two distinct transcripts are generated by the use of an alternative 3' splice acceptor site between exons 3 and 4. This alternative splice results in the substitution of AGSDPNFLRFG for one of the copies of SADPNFLRFG found in the other translation product. Based on PCR analysis of RNA from mixed-stage animals, both transcripts are expressed. This gene is the first example of a distinct FMRFamide-like peptide being derived from alternative splicing, suggesting a unique role for the substituted peptide in the animal.

Comparison of the body wall myosin heavy chain sequences from Onchocerca volvulus and Brugia malayi

The complete coding sequence of Onchocerca volvulus myosin heavy chain has been determined from a series of overlapping cDNAs. The protein sequences from the 2 filarids, one responsible for subcutaneous filariasis, the other for lymphatic filariasis, show 92% identity, and are 1957 amino acids long. Each protein sequence is also equally related, with 75% identity, to MHC-B, the protein encoded by the unc-54 gene of the free-living nematode C.elegans. Such analysis is useful in phylogenetic studies among nematodes, as well as in structure-function relationships among myosin isolates.

Cyclic 2',3'-phosphates and nontemplated nucleotides at the 3' end of spliceosomal U6 small nuclear RNA's

Spliceosomal U6 small nuclear RNA (U6 RNA) in species as diverse as man, frog, fruitfly, and soybean have at their 3' ends a cyclic 2',3'-phosphate (greater than p) apparently derived from uridylic acid residues that were added post-transcriptionally. The 3' ends of U6 RNA's from various sources may be processed in different ways, or to different extents, depending on the organism or stage of development. The presence of a greater than p terminus on U6 RNA may influence the activity of U6 RNA either directly during splicing or indirectly by ensuring that the RNA has a defined length or proper conformation (or both).

Factors affecting habituation and recovery from habituation in the nematode Caenorhabditis elegans

In four experiments, the factors that affect the rate of habituation, the degree of habituation, and the rate of recovery from habituation in a simple reflex circuit in Caenorhabditis elegans were investigated. The results showed that habituation was more pronounced and faster, and that recovery from habituation was more rapid, with short interstimulus intervals (ISIs) than with longer ISIs. Rate of recovery differed in animals that had reached asymptotic response levels when compared with animals still in the descending portion of the habituation curve. Once animals reached asymptotic response levels, rate of recovery appeared to be determined by ISI and not by additional stimuli.

The yeast type II myosin heavy chain: analysis of its predicted polypeptide sequence

We have completed the nucleotide sequence of the yeast MYO1 gene and deduced its amino acid sequence. The gene is 5553 bp long and contains no introns. Analysis of the sequence, as well as its comparison with other myosins, demonstrate that the yeast protein is a type II myosin heavy chain with characteristic head and tail regions. The latter domain contains six proline residues in two clusters of three, at approximately two thirds from the start of the gene.

Death by suicide: one way to go in mammalian cellular development?

Cell deaths occur selectively in many types of tissues throughout development. These physiological deaths appear to follow an orderly process of internal cellular disintegration that is distinct from the process observed in cell death resulting from trauma. Studies of a variety of physiological cell deaths have revealed that this process appears generally to involve the active participation of the dying cell in its own death. In other words, physiological cell death seems to be a process of induced cellular self-destruction, or cell suicide. Whether a single, genetically determined mechanism is utilized in all cell suicides remains to be established. Nonetheless, while genome digestion and intracellular calcium rises are dissociable from, and thus neither necessary nor sufficient for, cell death, control of the cell cycle may be critical in all cases of induced cell suicide. It is proposed here that physiological cell death occurs through a process of abortive mitosis.

Brief cytochalasin-induced disruption of microfilaments during a critical interval in 1-cell C. elegans embryos alters the partitioning of developmental instructions to the 2-cell embryo

We are investigating the involvement of the microfilament cytoskeleton in the development of early Caenorhabditis elegans embryos. We previously reported that several cytoplasmic movements in the zygote require that the microfilament cytoskeleton remain intact during a narrow time interval approximately three-quarters of the way through the first cell cycle. In this study, we analyze the developmental consequences of brief, cytochalasin D-induced microfilament disruption during the 1-cell stage. Our results indicate that during the first cell cycle microfilaments are important only during the critical time interval for the 2-cell embryo to undergo the correct pattern of subsequent divisions and to initiate the differentiation of at least 4 tissue types. Disruption of microfilaments during the critical interval results in aberrant division and P-granule segregation patterns, generating some embryos that we classify as ‘reverse polarity’, ‘anterior duplication’, and ‘posterior duplication’ embryos. These altered patterns suggest that microfilament disruption during the critical interval leads to the incorrect distribution of developmental instructions responsible for early pattern formation. The strict correlation between unequal division, unequal germ-granule partitioning, and the generation of daughter cells with different cell cycle periods observed in these embryos suggests that the three processes are coupled. We hypothesize that (1) an ‘asymmetry determinant’, normally located at the posterior end of the zygote, governs asymmetric cell division, germ-granule segregation, and the segregation of cell cycle timing elements during the first cell cycle, and (2) the integrity or placement of this asymmetry determinant is sensitive to microfilament disruption during the critical time interval.

Mutations affecting axonal growth and guidance of motor neurons and mechanosensory neurons in the nematode Caenorhabditis elegans

In the nematode Caenorhabditis elegans, each of its 302 individual neurons is an identified neuron. We have screened more than 100 mutations affecting locomotion in C. elegans immunocytochemically, using monoclonal antibodies that recognize specific subsets of neurons. Mutations in 25 genes affect the axonal outgrowth and guidance of a set of 6 mechanosensory receptor neurons (ALML, ALMR, AVM, PVM, PLML and PLMR). Similarly, mutations in 14 genes alter the axonal growth and process placement of two classes of inhibitory motor neurons (DD and VD). Most of these genes affect both embryonic and postembryonic development of the C. elegans nervous system, and have variable expressivity. Our results suggest that different neuron types are specified by a combination of genes that are activated in different cell types. Molecular characterization of such genes could lead to the identification of molecules critical in axonal outgrowth and guidance in higher organisms.

The ubiquitous nuclear protein, NHP1, binds with high affinity to different sequences of the chicken vitellogenin II gene

In gel shift assays, affinity chromatography-purified NHP1 forms a stable complex with different sequences of the chicken vitellogenin II gene. The apparent KD of NHP1 with the estrogen response element (ERE) containing 5-methylcytosine is 1 X 10(-11) M. NHP1 does not form a complex with the Xenopus vitellogenin ERE where the GCG bases are replaced by CAG. NHP1 is closely related if not identical to the other ubiquitous proteins NHP2, NHP3 and NHP4 that bind specifically to different sequences. All four proteins behave identically on chromatography and give identical patterns in proteolytic bandshift assays. NHP1, NHP2 and NHP3 have a native molecular weight of 170,000 and are composed of two polypeptides of 85 and 75 kDa. The possible function of NHP1 is discussed.

Anti-tubulin monoclonal antibodies that bind to specific neurons in Caenorhabditis elegans

We have identified 2 anti-tubulin monoclonal antibodies that bind to 2 different subpopulations of identified neurons in the simple nervous system of the nematode Caenorhabditis elegans. The antibodies also recognize specific tubulin isotypes from C. elegans that were separated by isoelectric focusing. Antibody 6-1 1B-1 intensely stained the mechano-sensory neurons ALML, ALMR, PLML, PLMR, PVM, and AVM, plus neuron PVR by indirect immunofluorescence, and it bound to 1 of 2 major alpha-tubulin isotypes separated by iso-electric focusing. The epitope for antibody (Ab) 6-1 1B-1 is acetylated alpha-tubulin (Piperno and Fuller, 1985). Antibody 2-28-33 stained a set of neurons that contain the neurotransmitter GABA. It bound to the 2 major and 1 of the minor beta-tubulin isotypes of C. elegans. These results suggest that specific alpha- and beta-tubulin isotypes are greatly enriched in the subsets of neurons recognized by these antibodies. Most (possibly all) of the neurons in each subset are functionally related. The antibodies should allow us to examine whether specific tubulin isotypes have specific functions in these neurons. They may also be useful for examining neuron morphologies in mutants of C. elegans which affect nerve development.

Yolk proteins from nematodes, chickens, and frogs bind strongly and preferentially to left-handed Z-DNA

Yolk proteins purified from the nematode Caenorhabditis elegans, from the frog Xenopus laevis, and from chicken eggs all have the unexpected property of binding strongly and preferentially to a left-handed Z-DNA probe, brominated poly(dG-dC). We estimate that the nematode proteins bind to Z-DNA with an association constant of at least 10(4) (M-1) and that this association constant is at least 40-50-fold higher than the association constant to B-DNA. Thus, yolk proteins have a higher Z-DNA specificity than most of the Z-DNA binding proteins previously isolated from other sources. Although yolk protein binding to Z-DNA is poorly competed by a wide variety of nucleic acids, the interaction is strongly competed by the phospholipids cardiolipin and phosphatidic acid (500-1000-fold better than by the same mass of B-DNA). We suggest that Z-DNA interacts with the yolk protein phospholipid binding site. In general, our results emphasize the danger of using physical properties to infer biological function. In particular, our results should raise serious questions about the biological relevance of previously isolated Z-DNA binding proteins.

Mutant expression of male copulatory bursa surface markers in Caenorhabditis elegans

In a search for molecular markers of male tail morphogenesis in C. elegans, we have detected two surface markers that are specifically observed in the copulatory bursa of adult males and the vulva of adult hermaphrodites. These markers are defined by binding of a monoclonal antibody (Ab117) and the lectin wheat germ agglutinin (WGA) to live intact animals. Expression of these markers is dependent on sex, stage and anterior-posterior position in the animal. Four of ten mutants with specific defects in bursal development show altered expression of one or both markers. Because the WGA marker can be expressed in intersexual animals with very little bursal development, posterior surface expression of this marker can serve as an indication of subtle masculinization of hermaphrodites. The timing of expression of these markers is not affected by heterochronic mutations that cause larval animals to express adult cuticles or adult animals to express larval cuticles, indicating that marker expression can be uncoupled from general cuticle development. Mutant lin-22 males, which have an anterior-to-posterior transformation of cell fates in the lateral hypodermis, ectopically express both markers in a manner consistent with a ‘posteriorization’ of positional information in these animals. These markers should be useful for the isolation and characterization of mutants defective in bursal and vulval development, sex determination and expression of anterior-posterior positional information.

Purified thick filaments from the nematode Caenorhabditis elegans: evidence for multiple proteins associated with core structures

The thick filaments of the nematode, Caenorhabditis elegans, arising predominantly from the body-wall muscles, contain two myosin isoforms and paramyosin as their major proteins. The two myosins are located in distinct regions of the surfaces, while paramyosin is located within the backbones of the filaments. Tubular structures constitute the cores of the polar regions, and electron-dense material is present in the cores of the central regions (Epstein, H.F., D.M. Miller, I. Ortiz, and G.C. Berliner. 1985. J. Cell Biol. 100:904-915). Biochemical, genetic, and immunological experiments indicate that the two myosins and paramyosin are not necessary core components (Epstein, H.F., I. Ortiz, and L.A. Traeger Mackinnon. 1986. J. Cell Biol. 103:985-993). The existence of the core structures suggests, therefore, that additional proteins may be associated with thick filaments in C. elegans. To biochemically detect minor associated proteins, a new procedure for the isolation of thick filaments of high purity and structural preservation has been developed. The final step, glycerol gradient centrifugation, yielded fractions that are contaminated by, at most, 1-2% with actin, tropomyosin, or ribosome-associated proteins on the basis of Coomassie Blue staining and electron microscopy. Silver staining and radioautography of gel electrophoretograms of unlabeled and 35S-labeled proteins, respectively, revealed at least 10 additional bands that cosedimented with thick filaments in glycerol gradients. Core structures prepared from wild-type thick filaments contained at least six of these thick filament-associated protein bands. The six proteins also cosedimented with thick filaments purified by gradient centrifugation from CB190 mutants lacking myosin heavy chain B and from CB1214 mutants lacking paramyosin. For these reasons, we propose that the six associated proteins are potential candidates for putative components of core structures in the thick filaments of body-wall muscles of C. elegans.