The primary structure and the functional domains of an elongation factor-1 alpha from Mucor racemosus

Extra- and intracellular lactose catabolism in Penicillium chrysogenum: phylogenetic and expression analysis of the putative permease and hydrolase genes

Penicillium chrysogenum is used as an industrial producer of penicillin. We investigated its catabolism of lactose, an abundant component of whey used in penicillin fermentation, comparing the type strain NRRL 1951 with the high producing strain AS-P-78. Both strains grew similarly on lactose as the sole carbon source under batch conditions, exhibiting almost identical time profiles of sugar depletion. In silico analysis of the genome sequences revealed that P. chrysogenum features at least five putative β-galactosidase (bGal)-encoding genes at the annotated loci Pc22g14540, Pc12g11750, Pc16g12750, Pc14g01510 and Pc06g00600. The first two proteins appear to be orthologs of two Aspergillus nidulans family 2 intracellular glycosyl hydrolases expressed on lactose. The latter three P. chrysogenum proteins appear to be distinct paralogs of the extracellular bGal from A. niger, LacA, a family 35 glycosyl hydrolase. The P. chrysogenum genome also specifies two putative lactose transporter genes at the annotated loci Pc16g06850 and Pc13g08630. These are orthologs of paralogs of the gene encoding the high-affinity lactose permease (lacpA) in A. nidulans for which P. chrysogenum appears to lack the ortholog. Transcript analysis of Pc22g14540 showed that it was expressed exclusively on lactose, whereas Pc12g11750 was weakly expressed on all carbon sources tested, including D-glucose. Pc16g12750 was co-expressed with the two putative intracellular bGal genes on lactose and also responded on L-arabinose. The Pc13g08630 transcript was formed exclusively on lactose. The data strongly suggest that P. chrysogenum exhibits a dual assimilation strategy for lactose, simultaneously employing extracellular and intracellular hydrolysis, without any correlation to the penicillin-producing potential of the studied strains.

Cloning and molecular characterization of CnTEF1 which encodes translation elongation factor 1alpha in Cryptococcus neoformans

Degenerate PCR primers were synthesized based upon known translation factor 1alpha (TEF1) sequences. Touchdown PCR with these primers utilizing Cryptococcus neoformans strain M1-106 genomic DNA as template produced a DNA fragment containing a portion of CnTEF1. This DNA fragment was used as a hybridization probe to clone a cDNA version of CnTEF1 from C. neoformans strain B3501. Comparison of the genomic and cDNA nucleotide sequences revealed the presence of six introns in CnTEF1. The nucleotide sequence of CnTEF1 from these two strains of C. neoformans were 98% identical. Codon bias for most amino acids encoded by CnTEF1 was similar to that observed in Saccharomyces cerevisiae for highly expressed genes. This codon bias was also observed in the C. neoformans ACT gene. CnTEF1 encoded a protein (CnEF-1alpha) consisting of 459 amino acids with a calculated MW of 50.3 kDa from C. neoformans strain B3501. CnTEF1 from strain M1-106 encoded a protein with one additional aa. Both C. neoformans proteins possessed a high degree of identity throughout their length to fungal, human, and plant EF-1alpha proteins.

Protein phylogeny of translation elongation factor EF-1 alpha suggests microsporidians are extremely ancient eukaryotes

Partial regions of the mRNA encoding a major part of translation elongation factor 1 alpha (EF-1 alpha) from a mitochondrion-lacking protozoan, Glugea plecoglossi, that belongs to microsporidians, were amplified by polymerase chain reaction (PCR) and their primary structures were analyzed. The deduced amino acid sequence was highly divergent from typical EF-1 alpha's of eukaryotes, although it clearly showed a eukaryotic feature when aligned with homologs of the three primary kingdoms. Maximum likelihood (ML) analyses on the basis of six different stochastic models of amino acid substitutions and a maximum parsimony (MP) analysis consistently suggest that among eukaryotic species being analyzed, G. plecoglossi is likely to represent the earliest offshoot of eukaryotes. Microsporidians might be the extremely ancient eukaryotes which have diverged before an occurrence of mitochondrial symbiosis.

Multifunctional proteins in Tetrahymena: 14-nm filament protein/citrate synthase and translation elongation factor-1 alpha

One gene encoding a protein has been shown to have two entirely different functions. Such a phenomenon, which has been called "gene sharing," was first known in crystallins. We found two multifunctional proteins in the ciliated protozoan Tetrahymena: 14-nm filament protein and protein translation elongation factor 1-alpha (EF-1 alpha). The 14-nm filament protein has dual functions as a citrate synthase in mitochondria and as a cytoskeletal protein in cytoplasm. In cytoplasm, the 14-nm filament protein was involved in oral morphogenesis and in pronuclear behavior during conjugation. The observation that Tetrahymena intramitochondrial filamentous inclusions contain the 14-nm filament protein and that the citrate synthase activity of the 14-nm filament protein is decreased by polymerization and increased by depolymerization, suggests a possible modulating mechanism of citrate synthase activity by monomer-polymer conversion in mitochondria in situ. The EF-1 alpha functions as an F-actin-bundling protein and a 14-nm filament-associated protein as well as an elongation factor in protein synthesis. The F-actin-bundling activity of EF-1 alpha was regulated by Ca2+ and calmodulin. Here we review the properties and functions of two multifunctional proteins in Tetrahymena.

Cloning and characterization of the gene encoding translation elongation factor 1 alpha from Aureobasidium pullulans

The gene (TEF1) encoding translation elongation factor 1 alpha from the dimorphic fungus Aureobasidium pullulans (Ap) strain R106 has been cloned using Candida albicans TEF1 as a heterologous hybridization probe. Electrophoretic molecular karyotype/hybridization analysis of Ap revealed eight chromosomal bands and suggested that TEF1 resides on chromosome VI. Comparison of the genomic DNA sequence with the cDNA sequence of TEF1 verified the presence of three introns, the first one occurring five nucleotides from the start of translation. The deduced amino acid (aa) sequence encoded a protein consisting of 459 aa (49,663 Da) possessing high identity to a variety of TEF1-encoded proteins. A strong codon bias, similar to that observed in highly expressed yeast genes, was evident in A. pullulans TEF1. The ApTEF1 promoter region showed some sequence similarity to the well-studied TEF1 promoter from Saccharomyces cerevisiae, including a region from -23 to -11. This region exhibited high homology to a promoter upstream activating sequence (UAS) in S. cerevisiae. Such sequences have been shown to be essential promoter elements in genes coding for the highly expressed components of the yeast translation apparatus.

Cloning, nucleotide sequence, and expression of tef-1, the gene encoding translation elongation factor 1 alpha (EF-1 alpha) of Neurospora crassa

The tef-1 gene encoding translation elongation factor 1 alpha was cloned from the ascomycete fungus Neurospora crassa. The sequences of genomic DNA and cDNA clones showed that the tef-1 gene contained one ORF of 1380 bp length that is interrupted by three short introns. The deduced polypeptide contained 460 amino acid residues, and the sequence had a high similarity with those of EF-1 alpha polypeptides from other species. The level of tef-1 mRNA was low in conidia but high in growing cells. When mycelia were transferred to poor nutrient media, the level of tef-1 gene mRNA decreased remarkably. The pattern of tef-1 expression was similar to the expression of genes for ribosomal proteins. The tef-1 gene was mapped between arg-3 and leu-4 loci on linkage group I by restriction fragment length polymorphism mapping. Southern blot analysis showed that Neurospora genomic DNA contained only one copy of the tef-1 gene in a genome.

Isolation and characterization of the EF-1 alpha gene of the filamentous fungus Puccinia graminis f. sp. tritici

A gene of Puccinia graminis f. sp. tritici, coding for the translation elongation factor 1 alpha (EF-1 alpha), was isolated from a P. graminis genomic library using the EF-1 alpha gene sequence of Absidia glauca. The coding region of 1389 nucleotides encodes a polypeptide of 463 amino acids and is interrupted by eight introns. An additional intron is located in the 5' untranslated region. A single transcription start point (tsp) was mapped by primer extension. A cDNA fragment corresponding to P. graminis EF-1 alpha mRNA hybridized with a 1.9-kb-long poly(A+)RNA, sufficient to encode the EF-1 alpha protein. Southern hybridization of digested genomic DNA revealed that two copies of the EF-1 alpha gene exist in the genome of P. graminis.

The nucleotide sequence of the gene coding for the elongation factor 1 alpha in Sulfolobus solfataricus. Homology of the product with related proteins

The cloning and sequencing of the gene coding for the archaebacterial elongation factor 1 alpha (aEF-1 alpha) was performed by screening a Sulfolobus solfataricus genomic library using a probe constructed from the eptapeptide KNMITGA that is conserved in all the EF-1 alpha/EF-Tu known so far. The isolated recombinant phage contained the part of the aEF-1 alpha gene from amino acids 1 to 171. The other part (amino acids 162-435) was obtained through the amplification of the S. solfataricus DNA by PCR. The codon usage by the aEF-1 alpha gene showed a preference for triplets ending in A and/or T. This behavior was almost identical to that of the S. acidocaldarius EF-1 alpha gene but differed greatly from that of EF-1 alpha/EF-Tu genes in other archaebacteria eukaryotes and eubacteria. The translated protein is made of 435 amino acid residues and contains sequence motifs for the binding of GTP, tRNA and ribosome. Alignments of aEF-1 alpha with several EF-1 alpha/EF-Tu revealed that aEF-1 alpha is more similar to its eukaryotic than to its eubacterial counterparts.

Sequence and promoter analysis of the highly expressed TEF gene of the filamentous fungus Ashbya gossypii

Ashbya gossypii carries only a single gene (TEF) coding for the abundant translation elongation factor 1 alpha. Cloning and sequencing of this gene and deletion analysis of the promoter region revealed an extremely high degree of similarity with the well studied TEF genes of the yeast Saccharomyces cerevisiae including promoter upstream activation sequence (UAS) elements. The open reading frames in both species are 458 codons long and show 88.6% identity at the DNA level and 93.7% identity at the protein level. A short DNA segment in the promoter, between nucleotides -268 and -213 upstream of the ATG start codon, is essential for high-level expression of the A. gossypii TEF gene. It carries two sequences, GCCCATACAT and ATCCATACAT, with high homology to the UASrpg sequence of S. cerevisiae, which is an essential promoter element in genes coding for highly expressed components of the translational apparatus. UASrpg sequences are binding sites for the S. cerevisiae protein TUF, also called RAP1 or GRF1. In gel retardation with A. gossypii protein extracts we demonstrated specific protein binding to the short TEF promoter segment carrying the UASrpg homologous sequences.

Identification of Tetrahymena 14-nm filament-associated protein as elongation factor 1 alpha

Tetrahymena 14-nm filament-forming protein has dual functions as a citrate synthase in mitochondria and as a cytoskeletal protein involved in oral morphogenesis and in pronuclear behavior during conjugation. By immunoblotting using monoclonal and polyclonal antibodies following two-dimensional gel electrophoresis, we demonstrated that the 14-nm filament protein fraction contained two 49-kDa proteins whose isoelectric points were 8.0 and 9.0; a monoclonal antibody (MAb) 26B4 and a polyclonal antibody 49KI reacted only to a pI 8.0 protein, while two other MAbs, 11B6 and 11B8, reacted only to a pI 9.0 protein. From the N-terminal amino acid sequences, the pI 8.0 protein was identified as the previously reported 14-nm filament-forming protein/citrate synthase, but the pI 9.0 protein N-terminal sequence had no similarity with that of the pI 8.0 protein. The pI 9.0 protein is considered to be a 14-nm filament-associated protein since the pI 9.0 protein copurifies with the pI 8.0 protein during two cycles of an assembly and disassembly purification protocol. Cloning and sequencing the pI 9.0 protein gene from a Tetrahymena pyriformis cDNA library, we identified the pI 9.0 protein as elongation factor 1 alpha (EF-1 alpha) based on it sharing 73-76% sequence identity with EF-1 alpha from several species.

The sequence of the gene encoding elongation factor Tu from Chlamydia trachomatis compared with those of other organisms

Nucleotide (nt) sequences encoding the elongation factor Tu (EF-Tu), tRNA(Thr) and tRNA(Trp) from Chlamydia trachomatis have been determined. The environment of the EF-Tu-encoding gene (tuf), between two tRNA gene sequences, suggests that it is part of a tufB locus. The nt sequence and the deduced amino acid (aa) sequence were aligned with comparable sequences from other organisms and the resulting data bases were used to infer phylogenies. Phylogenetic trees based on aa sequences and nt sequences are similar, but not completely congruent with rRNA gene-based phylogenies. Both the nt and aa sequence trees concur on the early divergence of Thermotoga and Chlamydia from the bacterial root. The aa alignment highlights the presence of four unique Cys residues in the chlamydial sequence which are found at strictly conserved positions in other sequences. Further peculiarities of the chlamydial and eubacterial sequences have been mapped to the X-ray crystallographic structure of the protein.

Functional aspects of ribosomal proteins

A short personal recollection of HG Wittmann is given with emphasis on his basic contribution to the structure of the ribosome, in particular the ribosomal proteins. With these considerations in mind, two interrelated problems are reviewed here. The first relates to the internal symmetry both in tRNA and in the tetrameric L12-protein complex. The second problem to be addressed relates to the dynamics of transfer RNA in the ribosome and the role of L12 proteins in this process. The importance of electrostatic repulsion in the maintenance of the mutual spatial orientation of tRNAs and L12 in the ribosome is emphasized in relation to a pendulum model for how L12 may steer translocation.

Structure comparison and evolutionary relations between elongation factors EF-Tu (EF-1 alpha) and SUP 2 proteins

On the basis of high homology and structural similarity, three genes, SUP2 Saccharomyces cerevisiae, SUP2 Pichia pinus and GST1 Homo sapiens, might be considered as members of one family named SUP2. Comparison of the primary structure of SUP2 proteins and elongation factors EF-Tu(EF-1 alpha) from 19 different species was performed. It was found that SUP2 proteins bear more homology to eukaryotic elongation factor than to procaryotic EF-Tu, though the degree of sequence conservation in SUP2 proteins is smaller than in EF-1 alpha factors. The extensive phylogenetic analysis of SUP2 and EF-Tu(EF-1 alpha) genes was performed by means of 3 methods, 2 phenetic and one cladystic (maximal parsimony). The data support the close relation of SUP2 genes to other elongation factor genes.

Divergence and conservation of SUP2 (SUP35) gene of yeast Pichia pinus and Saccharomyces cerevisiae

SUP2 (SUP35) is an omnipotent suppressor gene, coding for an EF-1 alpha-like protein factor, intimately involved in the control of translational accuracy in yeast Saccharomyces cerevisiae. In the present study a SUP2 gene analogue from yeast Pichia pinus was isolated by complementation of the temperature-sensitive sup2 mutation of S. cerevisiae. The nucleotide sequence of the SUP2 gene of P. pinus codes for a protein of 82.4 kDa, exceeding the Sup2 protein of S. cerevisiae by 6 kDa. Like the SUP2 gene product of S. cerevisiae, the Sup2 protein of P. pinus represents a fusion of a unique N-terminal part and a region homologous to EF-1 alpha. The comparison of amino acid sequences of the Sup2 proteins reveals high conservation (76%) of the C-terminal region and low conservation (36%) of the N-terminal part where, in addition, the homologous correspondence is ambiguous. Proteins related to the Sup2 of S. cerevisiae were found in P. pinus and some other yeast species by the immunoblotting technique. The relation between the evolutionary conservation of different regions of the Sup2 protein and their functional significance is discussed.

Identification of an actin-binding protein from Dictyostelium as elongation factor 1a

Indirect evidence has implicated an interaction between the cytoskeleton and the protein synthetic machinery. Two recent reports have linked the elongation factor 1a (EF-1a) which is involved in protein synthesis, with the microtubular cytoskeleton. In situ hybridization has, however, revealed that the messages for certain cytoskeletal proteins are preferentially associated with actin filaments. ABP-50 is an abundant actin filament bundling protein of native relative molecular mass 50,000 (50K) isolated from Dictyostelium discoideum. Immunofluorescence studies show that ABP-50 is present in filopodia and other cortical regions that contain actin filament bundles. In addition, ABP-50 binds to monomeric actin in the cytosol of unstimulated cells and the association of ABP-50 with the actin cytoskeleton is regulated during chemotaxis. Through complementary DNA sequencing and subsequent functional analysis, we have identified ABP-50 as D. discoideum EF-1a. The ability of EF-1a to bind reversibly to the actin cytoskeleton upon stimulation could provide a mechanism for spatially and temporally regulated protein synthesis in eukaryotic cells.

Sequence analysis and expression of the two genes for elongation factor 1 alpha from the dimorphic yeast Candida albicans

Two Candida albicans genes that encode the protein synthesis factor elongation factor 1 alpha (EF-1 alpha) were cloned by using a heterologous TEF1 probe from Mucor racemosus to screen libraries of C. albicans genomic DNA. Sequence analysis of the two clones showed that regions of DNA flanking the coding regions of the two genes were not homologous, verifying the presence of two genes, called TEF1 and TEF2, for EF-1 alpha in C. albicans. The coding regions of TEF1 and TEF2 differed by only five nucleotides and encoded identical EF-1 alpha proteins of 458 amino acids. Both genes were transcribed into mRNA in vivo, as shown by hybridization of oligonucleotide probes, which bound specifically to the 3' nontranslated regions of TEF1 and TEF2, respectively, to C. albicans total RNA in Northern (RNA) blot analysis. The predicted EF-1 alpha protein of C. albicans was more similar to Saccharomyces cerevisiae EF-1 alpha than to M. racemosus EF-1 alpha. Furthermore, codon bias and the promoter and termination signals of the C. albicans EF-1 alpha proteins were remarkably similar to those of S. cerevisiae EF-1 alpha. Taken together, these results suggest that C. albicans is more closely related to the ascomycete S. cerevisiae than to the zygomycete M. racemosus.

Complete nucleotide sequences of seven eubacterial genes coding for the elongation factor Tu: functional, structural and phylogenetic evaluations

The nucleotide sequences of cloned genes coding for the elongation factor Tu of seven eubacteria have been determined. These genes were from Anacystis nidulans, Bacillus subtilis, Bacteroides fragilis, "Deinonema" spec., Pseudomonas cepacia, Shewanella putrefaciens and Streptococcus oralis. The primary structures of the genes were compared to the available sequences of prokaryotic elongation factors Tu and eukaryotic elongation factors 1 alpha. A conservation profile was determined for homologous amino acid residues. Sites of known or putative functions are usually located at highly conserved positions or within highly conserved sequence stretches. The aligned 24 amino acid sequences were used as basis for a phylogenetic analysis. The phylogenetic tree corroborates the kingdom as well as phylum concept deduced from 16S rRNA data.

Evolution of RNA genomes: does the high mutation rate necessitate high rate of evolution of viral proteins?

RNA genomes have been shown to mutate much more frequently than DNA genomes. It is generally assumed that this results in rapid evolution of RNA viral proteins. Here, an alternative hypothesis is proposed that close cooperation between positive-strand RNA viral proteins and those of the host cells required their coevolution, resulting in similar amino acid substitution rates. Constraints on compatibility with cellular proteins should determine, at any time, the covarion sets in RNA viral proteins. These ideas may be helpful in rationalizing the accumulating data on significant sequence similarities between proteins of positive-strand RNA viruses infecting evolutionarily distant hosts as well as between viral and cellular proteins.

The mRNA encoding elongation factor 1-alpha (EF-1 alpha) is a major transcript at the midblastula transition in Xenopus

A Xenopus laevis gastrula cDNA library has been screened in order to identify sequences that are expressed early in development. We find that the mRNA encoding translation elongation factor 1-alpha (EF-1 alpha) is synthesized in very large amounts in the early embryo. Transcription of EF-1 alpha mRNA commences at the midblastula transition (MBT), and new EF-1 alpha protein is synthesized very soon after this, as determined by the association of EF-1 alpha mRNA with polysomes. The nucleotide sequence of a full-length EF-1 alpha cDNA clone and the deduced amino acid sequence of Xenopus EF-1 alpha protein are presented.

Polypeptide elongation factor Tu from Halobacterium marismortui

A GDP-binding protein of 60 kDa from Halobacterium marismortui has been purified to homogeneity. The purification has been carried out in high-salt buffers or in 50% glycerol buffers to protect the halophilic protein from denaturation. Evidence that this protein is the halophilic elongation factor Tu (hEF-Tu) is provided by the high homology of its N terminus with the corresponding sequences of other EF-Tus, and by immunological studies. Like some other EF-Tus the native protein can be cleaved with trypsin without concomitant loss of GDP-binding ability. The molecular mass of this hEF-Tu is higher than that for the corresponding factors from other sources including the halobacterium Halobacterium cutirubrum. The protein possesses typical halophilic characteristics, in that it is stable and active in 3 M KCl or 2 M (NH4)2SO4. Some other properties, like autofragmentation under sample treatment before SDS-PAGE, are described.

SUF12 suppressor protein of yeast. A fusion protein related to the EF-1 family of elongation factors

Mutations at the suf12 locus were isolated in Saccharomyces cerevisiae as extragenic suppressors of +1 frameshift mutations in glycine (GGX) and proline (CCX) codons, as well as UGA and UAG nonsense mutations. To identify the SUF12 function in translation and to understand the relationship between suf12-mediated misreading and translational frameshifting, we have isolated an SUF12+ clone from a centromeric plasmid library by complementation. SUF12+ is an essential, single-copy gene that is identical with the omnipotent suppressor gene SUP35+. The 2.3 x 10(3) base SUF12+ transcript contains an open reading frame sufficient to encode a 88 x 10(3) Mr protein. The pattern of codon usage and transcript abundance suggests that SUF12+ is not a highly expressed gene. The linear SUF12 amino acid sequence suggests that SUF12 has evolved as a fusion protein of unique N-terminal domains fused to domains that exhibit essentially co-linear homology to the EF-1 family of elongation factors. Beginning internally at amino acid 254, homology is more extensive between the SUF12 protein and EF-1 alpha of yeast (36% identity; 65% with conservative substitutions) than between EF-1 alpha of yeast and EF-Tu of Escherichia coli. The most extensive regions of SUF12/EF-1 alpha homology are those regions that have been conserved in the EF-1 family, including domains involved in GTP and tRNA binding. It is clear that SUF12 and EF-1 alpha are not functionally equivalent, since both are essential in vivo. The N-terminal domains of SUF12 are unique and may reflect, in part, the functional distinction between these proteins. These domains exhibit unusual amino acid composition and extensive repeated structure. The behavior of suf12-null/SUF12+ heterozygotes indicates that suf12 is co-dominantly expressed and suggests that suf12 allele-specific suppression may result from functionally distinct mutant proteins rather than variation in residual wild-type SUF12+ activity. We propose a model of suf12-mediated frameshift and nonsense suppression that is based on a primary defect in the normal process of codon recognition.

A conserved amino acid sequence around Arg-68 of Artemia elongation factor 1 alpha is involved in the binding of guanine nucleotides and aminoacyl transfer RNAs

The rate of trypsin cleavage of elongation factor 1 alpha having bound GDP is low and increases on exchange of GDP for GTP. The cleavage occurs at a unique position of the protein chain, namely at arginine-68 of Artemia EF-1 alpha. This increase in trypsin sensitivity is enhanced further in the presence of charged or uncharged transfer RNA. The local unfolding of EF-alpha at residue 68 is discussed in terms of a model in which GTP hydrolysis controls the positioning of a short 3'-terminal section of transfer RNA near the centre of peptide bond synthesis.