Ribosomal protein L25 from Trypanosoma brucei: phylogeny and molecular co-evolution of an rRNA-binding protein and its rRNA binding site

Characterization of silk gland ribosomes from a bivoltine caddisfly, Stenopsyche marmorata: translational suppression of a silk protein in cold conditions

Larval Stenopsyche marmorata constructs food capture nets and fixed retreats underwater using self-produced proteinaceous silk fibers. In the Chikuma River (Nagano Prefecture, Japan) S. marmorata has a bivoltine life cycle; overwintering larvae grow slowly with reduced net spinning activity in winter. We recently reported constant transcript abundance of S. marmorata silk protein 1 (Smsp-1), a core S. marmorata silk fiber component, in all seasons, implying translational suppression in the silk gland during winter. Herein, we prepared and characterized silk gland ribosomes from seasonally collected S. marmorata larvae. Ribosomes from silk glands immediately frozen in liquid nitrogen (LN2) after dissection exhibited comparable translation elongation activity in spring, summer, and autumn. Conversely, silk glands obtained in winter did not contain active ribosomes and Smsp-1. Ribosomes from silk glands immersed in ice-cold physiological saline solution for approximately 4 h were translationally inactive, despite summer collection and Smsp-1 expression. The ribosomal inactivation occurs because of defects in the formation of 80S ribosomes, presumably due to splitting of 60S subunits containing 28S rRNA with central hidden break, in response to cold stress. These results suggest a novel-type ribosome-regulated translation control mechanism.

Molecular characterization and phylogenetic analysis of the eukaryotic translation initiation factor 4A gene in Antheraea pernyi (Lepdoptera: Saturniidae)

Eukaryotic initiation factor 4A (eIF-4A) is an essential component for protein translation in eukaryotes. The eIF-4A gene (ApeIF-4A) was isolated and characterized from Antheraea pernyi (Guérin-Méneville) (Lepidoptera: Saturniidae). The obtained cDNA sequence was 1,435-bp long with an open reading frame of 1,266 bp encoding 421 amino acids. The predicted amino acid sequence shared several conserved features as found in known eIF-4As and revealed 74 and 78% identities with eIF-4As of Homo sapiens L. and Drosophila melanogaster (Meigen), respectively. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that ApeIF-4A was transcribed at four developmental stages and in all tissues tested, suggesting that it plays an important role in development of A. pernyi. Homologous alignment suggested that eIF-4As are highly conserved throughout evolution of eukaryote organisms. Phylogenetic trees based on the amino acid and nucleotide sequences of eIF-4A demonstrated a similar topology with the classical systematics, suggesting that it has the potential value in phylogenetic inference of eukaryotes.

On the phylogenetic position of Myzostomida: can 77 genes get it wrong?

BACKGROUND

Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.

RESULTS

Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data.

CONCLUSION

We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.

Functional conservation between structurally diverse ribosomal proteins from Drosophila melanogaster and Saccharomyces cerevisiae: fly L23a can substitute for yeast L25 in ribosome assembly and function

The proposed Drosophila melanogaster L23a ribosomal protein features a conserved C-terminal amino acid signature characteristic of other L23a family members and a unique N-terminal extension [Koyama et al. (Poly(ADP-ribose) polymerase interacts with novel Drosophila ribosomal proteins, L22 and l23a, with unique histone-like amino-terminal extensions. Gene 1999; 226: 339-345)], absent from Saccharomyces cerevisiae L25 that nearly doubles the size of fly L23a. The ability of fly L23a to replace the role of yeast L25 in ribosome biogenesis was determined by creating a yeast strain carrying an L25 chromosomal gene disruption and a plasmid-encoded FLAG-tagged L23a gene. Though affected by a reduced growth rate, the strain is dependent on fly L23a-FLAG function for survival and growth, demonstrating functional compatibility between the fly and yeast proteins. Pulse-chase experiments reveal a delay in rRNA processing kinetics, most notably at a late cleavage step that converts precursor 27S rRNA into mature 25S rRNA, likely contributing to the strain's slower growth pattern. Yet, given the essential requirement for L23(a)/L25 in ribosome biogenesis, there is a remarkable tolerance for accommodating the fly L23a N-terminal extension within the structure of the yeast ribosome. A search of available databases shows that the unique N-terminal extension is shared by multiple insect lineages. An evolutionary perspective on L23a structure and function within insect lineages is discussed.

Evolution of small nucleolar RNAs in nematodes

In contrast to mRNAs, which are templates for translating proteins, non-protein coding (npc) RNAs (also known as ‘non-coding’ RNA, ncRNA), exhibit various functions in different compartments and developmental stages of the cell. Small nucleolar RNAs (snoRNAs), one of the largest classes of npcRNAs, guide post-transcriptional modifications of other RNAs that are crucial for appropriate RNA folding as well as for RNA–RNA and RNA–protein interactions. Although snoRNA genes comprise a significant fraction of the eutherian genome, identifying and characterizing large numbers of them is not sufficiently accessible by classical computer searches alone. Furthermore, most previous investigations of snoRNAs yielded only limited indications of their evolution. Using data obtained by a combination of high-throughput cDNA library screening and computational search strategies based on a modified DNAMAN program, we characterized 151 npcRNAs, and in particular 121 snoRNAs, from Caenorhabditis elegans and extensively compared them with those in the related, Caenorhabditis briggsae. Detailed comparisons of paralog snoRNAs in the two nematodes revealed, in addition to trans-duplication, a novel, cis-duplication distribution strategy with insertions near to the original loci. Some snoRNAs coevolved with their modification target sites, demonstrating the close interaction of complementary regions. Some target sites modified by snoRNAs were changed, added or lost, documenting a high degree of evolutionary plasticity of npcRNAs.

Molecular modeling approaches for determining gene function: application to a putative poly-A binding protein from Leishmania amazonensis (LaPABP)

The great expansion in the number of genome sequencing projects has revealed the importance of computational methods to speed up the characterization of unknown genes. These studies have been improved by the use of three dimensional information from the predicted proteins generated by molecular modeling techniques. In this work, we disclose the structure-function relationship of a gene product from Leishmania amazonensis by applying molecular modeling and bioinformatics techniques. The analyzed sequence encodes a 159 amino acids polypeptide (estimated 18 kDa) and was denoted LaPABP for its high homology with poly-A binding proteins from trypanosomatids. The domain structure, clustering analysis and a three dimensional model of LaPABP, basically obtained by homology modeling on the structure of the human poly-A binding protein, are described. Based on the analysis of the electrostatic potential mapped on the model's surface and conservation of intramolecular contacts responsible for folding stabilization we hypothesize that this protein may have less avidity to RNA than it's L. major counterpart but still account for a significant functional activity in the parasite. The model obtained will help in the design of mutagenesis experiments aimed to elucidate the mechanism of gene expression in trypanosomatids and serve as a starting point for its exploration as a potential source of targets for a rational chemotherapy.

Analysis of the 60 S ribosomal protein L27a (L29) gene of Trypanosoma brucei

The Trypanosoma brucei gene encoding the 60 S ribosomal protein L27a (L29) homologue has been cloned and characterised. The complete open reading frame encodes a small basic protein of 145 amino acids with a predicted molecular weight of 15,950. The L27a amino acid sequence shares 45-58% identity with other L27a (L29) homologues. Southern blot hybridisation suggests that the gene is present in multiple copies. Northern blot analysis of RNA from three T. brucei life cycle stages show that mRNA levels are two-fold higher in procyclic than in early or late bloodstream stages. This infers that this highly conserved ribosomal protein may play an important role in translational regulation through the life cycle of trypanosomes.

Cloning and characterisation of cDNA encoding the Trypanosoma brucei ribosomal protein L24

A cDNA encoding ribosomal protein L24 was amplified by PCR from the protozoan parasite, Trypanosoma brucei. The 621 nucleotide cDNA had an open reading frame of 375 nucleotides, predicting a highly basic protein of 125 aa. Database searches revealed 33-40% identity between the T. brucei RPL24 protein and several eukaryotic RPL24 homologues. Southern blot analysis indicated that the gene was present as a single copy, and a transcript of approximately 620 nucleotides was detected in procyclic forms of the parasite. Interestingly, T. brucei PRL24 is the smallest eukaryotic RPL24 protein described to date. It is also the most divergent of the known kinetoplastid ribosomal proteins.

The molecular karyotype of the megabase chromosomes of Trypanosoma brucei and the assignment of chromosome markers

We present the molecular karyotype of the megabase chromosomes of Trypanosoma brucei stock TREU927/4 (927). We have identified 11 diploid chromosomes ranging in size from 1 to 5.2 Mb approximately and pairs of homologues differ in size by up to 15%. A total of 401 cDNA probes were hybridised to T. brucei stock 927 chromosomes and 168 chromosome-specific markers were defined. Most of these markers were hybridised to the separated chromosomal DNA of two other cloned field isolates and four F1 progeny clones from a laboratory cross. The chromosomes vary in size by up to two and a half times between stocks and the DNA content of the 11 pairs of homologues varies by up to 33% in different stocks. Stock 927 contains the smallest chromosomes and the least nuclear genomic DNA. Nevertheless, all 11 syntenic groups of cDNA probes are maintained in all stocks. In the F1 hybrids only we have identified one extra PFG band to which none of our probes hybridise. We have shown that probes thought to be specific for the bloodstream-form variant surface glycoprotein expression sites hybridise to different chromosomes in different stocks and may hybridise to either one or both of a homologous pair of chromosomes. We have also determined the chromosomal location of the ribosomal RNA gene arrays.

Trypanosoma brucei: the dynamics of calcium movement between the cytosol, nucleus, and mitochondrion of intact cells

Targeted aequorins (CYT-AEQ, NUC-AEQ, and MT-AEQ) were used to measure Ca2+ concentrations within organelles of live trypanosomes. We determined that the nuclear envelope is a slight barrier to the free diffusion of Ca2+. This situation was especially evident when Ca2+ influx across the plasma membrane was stimulated with 200 nM melittin ([Ca2+]cyt = 1.2 +/- 0.4 microM and [Ca2+]nuc = 0.85 +/- 0.15 microM). By contrast, the ionophores nigericin (2.7 microM) or monensin (2 microg/ml) were used to induce Ca2+ efflux from the acidic storage compartment. Small transient elevations in [Ca2+]cyt were observed (peaking at 660 +/- 200 and 580 +/- 120 nM, respectively). Parallel and equivalent changes in [Ca2+1]nuc were recorded. Active accumulation of Ca2+ into the nucleus was not observed. Nigericin or monensin did not disrupt mitochondrial Ca2+ transport in vivo. Instead, the mitochondrion actively sequestered large quantities of Ca2+ in the presence of these ionophores, with peak values of 2.7 +/- 1.4 and 4.4 +/- 1.1 microM, respectively. Overall, these data demonstrate that significant quantities of Ca2+ enter the nucleus following influx across the plasma membrane or following efflux from an intracellular acidic storage compartment. However, the magnitude of change for [Ca2+]cyt and [Ca2+]nuc is small compared to the total amount of exchangeable Ca2+ since the majority of released Ca2+ is actively sequestered by the mitochondrion.

Identification of functional surfaces of the zinc binding domains of intracellular receptors

Transcriptional regulatory factor complexes assemble on genomic response elements to control gene expression. To gain insights on the surfaces that determine this assembly in the zinc binding domains from intracellular receptors, we systematically analyzed the variations in sequence and function of those domains in the context of their invariant fold. Taking the intracellular receptor superfamily as a whole revealed a hierarchy of amino acid residues along the DNA interface that correlated with response element binding specificity. When only steroid receptors were considered, two additional sites appeared: the known dimer interface, and a novel putative interface suitably located to contact regulatory factors bound to the free face of palindromic response elements commonly used by steroid receptors. Surprisingly, retinoic acid receptors, not known to bind palindromic response elements, contain both of these surfaces, implying that they may dimerize at palindromic elements under some circumstances. This work extends Evolutionary Trace analysis of functional surfaces to protein-DNA interactions, suggests how coordinated exchange of trace residues may predictably switch binding specificity, and demonstrates how to detect functional surfaces that are not apparent from sequence comparison alone.

Purification, cloning, and expression of two closely related Trypanosoma brucei nucleic acid binding proteins

Nucleic acid binding proteins in the trypanosomatid family are of particular interest because of several unusual molecular phenomena discovered in these organisms. We have purified two closely related proteins, p34 and p37, from the procyclic from of T. brucei using high salt extraction and single-stranded-DNA (ssDNA) agarose chromatography. Antibodies raised against the p34 protein showed crossreactivity with p37, suggesting relatedness. High performance liquid chromatography analysis and microsequencing of tryptic peptides derived from p34 and p37 showed that the primary structures of the two proteins are nearly identical. We have cloned and sequenced the two genes encoding these two proteins. Protein sequences predicted from the cDNAs confirm the relatedness of the two proteins but also indicate the presence of an 18 amino acid insertion unique to one of the two proteins as well as several minor differences resulting from single amino acid changes. Three sequence motifs have been identified in both proteins: an N-terminal alanine, proline, and lysine rich domain, one and a half internal RNA-binding domains, and a C-terminal KKDX repeat region. Both proteins preferentially bind to heterogenous RNA and ssDNA versus double-stranded DNA and homopolymers. Both recombinant proteins have been expressed in E. coli and show properties indistinguishable from those observed with native p34/p37.

Incorporation of dinitrophenyl protein L23 into totally reconstituted Escherichia coli 50 S ribosomal subunits and its localization at two sites by immune electron microscopy

Escherichia coli ribosomal protein L23 was derivatized with [3H]2, 4-dinitrofluorobenzene both at the N terminus and at internal lysines. Dinitrophenyl-L23 (DNP-L23) was taken up into 50 S subunits from a reconstitution mixture containing rRNA and total 50 S protein depleted in L23. Unmodified L23 competed with DNP-L23 for uptake, indicating that each protein form bound in an identical or similar position within the subunit. Modified L23, incorporated at a level of 0.7 or 0.4 DNP groups per 50 S, was localized by electron microscopy of subunits complexed with antibodies to dinitrophenol. Antibodies were seen at two major sites with almost equal frequency. One site is beside the central protuberance, in a region previously identified as the peptidyltransferase center. The second location is at the base of the subunit, in the area of the exit site from which the growing peptide leaves the ribosome. Models derived from image reconstruction show hollows or canyons in the subunit and a tunnel that links the transferase and exit sites. Our results indicate that L23 is at the subunit interior, with separate elements of the protein at the subunit surface at or near both ends of this tunnel.

Nuclear calcium flux in Trypanosoma brucei can be quantified with targeted aequorin

The following study was undertaken to determine if calcium ions move from the plasma membrane to the nucleus of Trypanosoma brucei. Nuclear and cytosolic calcium flux was measured with the calcium sensitive photoprotein, aequorin which was targeted to various locations in stably transformed procyclic cells. Immunoblots revealed that the recombinant proteins, CYT-AEQ and NUC-AEQ were translated in transformants, and that CYT-AEQ was contained in a soluble fraction. Immunolocalization demonstrated that NUC-AEQ was contained within the trypanosome nucleus. To evaluate calcium movement from the plasma membrane to the nucleus in live trypanosomes, aequorin was reconstituted in vivo with coelenterazine and luminescence was recorded. The resting levels of [Ca2+]cyt and [Ca2+]nuc were similar (314 +/- 43 and 287 +/- 28 nM, respectively). When calcium influx across the plasma membrane was initiated with 2 microM ionomycin, [Ca2+]cyt and [Ca2+]nuc each became elevated in parallel to a new steady state which was approximately 2-fold above the resting level. Compound 48/80 initiated a calcium flux across the plasma membrane by a different mechanism from ionomycin, and in a manner that was inhibited by the calcium channel antagonist, La3+. Compound 48/80 (8 micrograms/ml) transiently elevated [Ca2+]cyt to 1.73 +/- 0.3 microM over the course of 20 s, and also generated a transient rise in [Ca2+]nuc which peaked at 1.32 + 0.29 microM over the same time course. Overall, these data demonstrate that calcium moves into and out of the trypanosome nucleus in a manner which closely parallels changes in [Ca2+]cyt. A small calcium ion gradient between nucleus and cytoplasm was also observed.

Phylogenetic depth of S10 and spc operons: cloning and sequencing of a ribosomal protein gene cluster from the extremely thermophilic bacterium Thermotoga maritima

A segment of Thermotoga maritima DNA spanning 6,613 bp downstream from the gene tuf for elongation factor Tu was sequenced by use of a chromosome walking strategy. The sequenced region comprised a string of 14 tightly linked open reading frames (ORFs) starting 50 bp downstream from tuf. The first 11 ORFs were identified as homologs of ribosomal protein genes rps10, rpl3, rpl4, rpl23, rpl2, rps19, rpl22, rps3, rpl16, rpl29, and rps17 (which in Escherichia coli constitute the S10 operon, in that order); the last three ORFs were homologous to genes rpl14, rpl24, and rpl5 (which in E. coli constitute the three promoter-proximal genes of the spectinomycin operon). The 14-gene string was preceded by putative -35 and -10 promoter sequences situated 5' to gene rps10, within the 50-bp spacing between genes tuf and rps10; the same region exhibited a potential transcription termination signal for the upstream gene cluster (having tuf as the last gene) but displayed also the potential for formation of a hairpin loop hindering the terminator; this suggests that transcription of rps10 and downstream genes may start farther upstream. The similar organization of the sequenced rp genes in the deepest-branching bacterial phyla (T. maritima) and among Archaea has been interpreted as indicating that the S10-spc gene arrangement existed in the (last) common ancestor. The phylogenetic depth of the Thermotoga lineage was probed by use of r proteins as marker molecules: in all except one case (S3), Proteobacteria or the gram-positive bacteria, and not the genus Thermotoga, were the deepest-branching lineage; in only two cases, however, was the inferred branching order substantiated by bootstrap analysis.

Role of conserved nucleotides in building the 16S rRNA binding site of E. coli ribosomal protein S8

Ribosomal protein S8 specifically recognizes a helical and irregular region of 16S rRNA that is highly evolutionary constrained. Despite its restricted size, the precise conformation of this region remains a question of debate. Here, we used chemical probing to analyze the structural consequences of mutations in this RNA region. These data, combined with computer modelling and previously published data on protein binding were used to investigate the conformation of the RNA binding site. The experimental data confirm the model in which adenines A595, A640 and A642 bulge out in the deep groove. In addition to the already proposed non canonical U598-U641 interaction, the structure is stabilized by stacking interactions (between A595 and A640) and an array of hydrogen bonds involving bases and the sugar phosphate backbone. Mutations that alter the ability to form these interdependent interactions result in a local destabilization or reorganization. The specificity of recognition by protein S8 is provided by the irregular and distorted backbone and the two bulged adenines 640 and 642 in the deep groove. The third adenine (A595) is not a direct recognition site but must adopt a bulged position. The U598-U641 pair should not be directly in contact with the protein.