Cloning and mapping of infA, the gene for protein synthesis initiation factor IF1

Complete chloroplast genomes of two medicinal Swertia species: the comparative evolutionary analysis of Swertia genus in the Gentianaceae family

The complete chloroplast genome of Swertia kouitchensis has been sequenced and assembled, compared with that of S. bimaculata to determine the evolutionary relationships among species of the Swertia in the Gentianaceae family. Swertia kouitchensis and S. bimaculata are from the Gentianaceae family. The complete chloroplast genome of S. kouitchensis was newly assembled, annotated, and analyzed by Illumina Hiseq 2500 platform. The chloroplast genomes of the two species encoded a total of 133, 134 genes, which included 88-89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA genes. One intron was contained in each of the eight protein-coding genes and eight tRNA-coding genes, whereas two introns were found in two genes (ycf3 and clpP). The most abundant codon of the two species was for isoleucine, and the least abundant codon was for cysteine. The number of microsatellite repeat sequences was twenty-eight and thirty-two identified in the chloroplast genomes of S. kouitchensis and S. bimaculata, respectively. A total of 1127 repeat sequences were identified in all the 23 Swertia chloroplast genomes, and they fell into four categories. Furthermore, five divergence hotspot regions can be applied to discriminate these 23 Swertia species through genomes comparison. One pair of genus-specific DNA barcodes primer has been accurately identified. Therefore, the diverse regions cloned by a specific primer may become an effective and powerful molecular marker for the identification of Swertia genus. Moreover, four genes (ccsA, ndhK, rpoC1, and rps12) were positive selective pressure. The phylogenetic tree showed that the 23 Swertia species were clustered into a large clade including four evident subbranches, whereas the two species of S. kouitchensis and S. bimaculata were separately clustered into the diverse but correlated species group.

Comparative Bioinformatics Analysis of the Chloroplast Genomes of a Wild Diploid Gossypium and Two Cultivated Allotetraploid Species

BACKGROUND

Gossypium thurberi is a wild diploid species that has been used to improve cultivated allotetraploid cotton.G. thurberi belongs to D genome, which is an important wild bio-source for the cotton breeding and genetic research. To a certain degree, chloroplast DNA sequence information are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. Present study was conducted in order to analyse the sequence of its chloroplast.

OBJECTIVES

Present study was conducted to study and compare the complete chloroplast sequence of G. thurberi, analyses of its genome structure, gene content and organization, repeat sequence and codon usage and comparison with two cultivated allotetraploid sequenced cotton species.

MATERIALS AND METHODS

The available sequence was assembled by DNAman (Version 8.1.2.378). Gene annotation was mainly performed by DOGMA. The map of genome structure and gene distribution were carried out using OGDRAW V1.1. Relative synonymous codon usage (RSCU) of different codons in each gene sample was calculated by codonW in Mobyle. To determine the repeat sequence and location, an online version of REPuter was used.

RESULTS

The G. thurberi chloroplast (cp) genome is 160264 bp in length with conserved quadripartite structure. Single copy region of cp genome is separated by the two inverted regions. The large single copy region is 88,737 bp, and the small single copy region is 20,271 bp whereas the inverted repeat is 25,628 bp each. The plastidic genome has 113 single genes and 20 duplicated genes. The singletones encode 79 proteins, 4 ribosomal RNA genes and 30 transfer RNA genes.

CONCLUSIONS

Amongst all plastidic genes only 18 genes appeared to have 1-2 introns and when compared with cpDNA of two cultivated allotetraploid, rps18 was the only duplicated gene in G.thurberi. Despite the high level of conservation in cp genome SSRs ,these are useful in analysis of genetic diversity due to their greater efficiency as opposed to genomic SSRs. Low GC content is a significant feature of plastidic genomes, which is possibly formed after endosymbiosis by DNA replication and repair.

Translation Initiation

Selection of correct start codons on messenger RNAs is a key step required for faithful translation of the genetic message. Such a selection occurs in a complex process, during which a translation-competent ribosome assembles, eventually having in its P site a specialized methionyl-tRNAMet base-paired with the start codon on the mRNA. This chapter summarizes recent advances describing at the molecular level the successive steps involved in the process. Special emphasis is put on the roles of the three initiation factors and of the initiator tRNA, which are crucial for the efficiency and the specificity of the process. In particular, structural analyses concerning complexes containing ribosomal subunits, as well as detailed kinetic studies, have shed new light on the sequence of events leading to faithful initiation of protein synthesis in Bacteria.

Differential promoter usage of infA in response to cold shock in Escherichia coli

Initiation factor 1 (IF1) is an essential protein in Escherichia coli involved in the initiation step of protein synthesis. The protein level of IF1 increases when E. coli cells are subjected to cold shock, however, it remains unclear as to how this increase occurs. The infA gene encoding IF1 contains two promoters, the distal P1 and the proximal P2 promoter. In this study, we found that infA mRNA was greatly increased, and that this increase resulted from transcriptional activation of P1, not P2, during cold shock although stability of transcripts from both promoters concomitantly increased.

In vivo involvement of mutated initiation factor IF1 in gene expression control at the translational level

The influence in vivo of mutated forms of translation initiation factor (IF1) on the expression of the lacZ or 3A' reporter genes, with different initiation and/or +2 codons, has been investigated. Reporter gene expression in these infA(IF1) mutants is similar to the wild-type strain. The results do not support the longstanding hypothesis that IF1 could perform discriminatory functions while blocking the aminoacyl-tRNA acceptor site (A-site) of the ribosome. One cold-sensitive IF1 mutant shows a general overexpression, in particular at low temperatures, of both reporter genes at the protein but not mRNA level.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Initiation factors IF1 and IF2 synergistically remove peptidyl-tRNAs with short polypeptides from the P-site of translating Escherichia coli ribosomes

A novel function of initiation factors IF1 and IF2 in Escherichia coli translation has been identified. It is shown that these factors efficiently catalyse dissociation of peptidyl-tRNAs with polypeptides of different length from the P-site of E. coli ribosomes, and that the simultaneous presence of both factors is required for induction of drop-off. The factor-induced drop-off occurs with both sense and stop codons in the A-site and competes with peptide elongation or termination. The efficiency with which IF1 and IF2 catalyse drop-off decreases with increasing length of the nascent polypeptide, but is quite significant for hepta-peptidyl-tRNAs, the longest polypeptide chains studied. In the absence of IF1 and IF2 the rate of drop-off varies considerably for different peptidyl-tRNAs, and depends both on the length and sequence of the nascent peptide. Efficient factor-catalysed drop-off requires GTP but not GTP hydrolysis, as shown in experiments without guanine nucleotides, with GDP or with the non-cleavable analogue GMP-PNP.Simultaneous overexpression of IF1 and IF2 in vivo inhibits cell growth specifically in some peptidyl-tRNA hydrolase deficient mutants, suggesting that initiation factor-catalysed drop-off of peptidyl-tRNA can occur on a significant scale in the bacterial cell. Consequences for the bacterial physiology of this previously unknown function of IF1 and IF2 are discussed.

Translation initiation factor IF2 of the myxobacterium Stigmatella aurantiaca: presence of a single species with an unusual N-terminal sequence

The structural gene for translation initiation factor IF2 (infB) was isolated from the myxobacterium Stigmatella aurantiaca on a 5.18-kb BamHI genomic restriction fragment. The infB gene (ca. 3.16 kb) encodes a 1,054-residue polypeptide with extensive homology within its G domain and C terminus with the equivalent regions of IF2s from Escherichia coli, Bacillus subtilis, Bacillus stearothermophilus, and Streptococcus faecium. The N-terminal region does not display any significant homology to other known proteins. The S. aurantiaca infB gene encodes a single protein which cross-reacted with antiserum to E. coli IF2 and was able to complement an E. coli infB mutant. The S. aurantiaca IF2 is distinguished from all other IF2s by a sequence of 160 residues near the N terminus that has an unusual composition, made up essentially of alanine, proline, valine, and glutamic acid. Within this sequence, the pattern PXXXAP is repeated nine times. Complete deletion of this sequence did not affect the factor's function in initiation of translation and even increased its capacity to complement the E. coli infB mutant.

The structure of the translational initiation factor IF1 from E.coli contains an oligomer-binding motif

The structure of the translational initiation factor IF1 from Escherichia coli has been determined with multidimensional NMR spectroscopy. Using 1041 distance and 78 dihedral constraints, 40 distance geometry structures were calculated, which were refined by restrained molecular dynamics. From this set, 19 structures were selected, having low constraint energy and few constraint violations. The ensemble of 19 structures displays a root-mean-square deviation versus the average of 0.49 A for the backbone atoms and 1.12 A for all atoms for residues 6-36 and 46-67. The structure of IF1 is characterized by a five-stranded beta-barrel. The loop connecting strands three and four contains a short 3(10) helix but this region shows considerably higher flexibility than the beta-barrel. The fold of IF1 is very similar to that found in the bacterial cold shock proteins CspA and CspB, the N-terminal domain of aspartyl-tRNA synthetase and the staphylococcal nuclease, and can be identified as the oligomer-binding motif. Several proteins of this family are nucleic acid-binding proteins. This suggests that IF1 plays its role in the initiation of protein synthesis by nucleic acid interactions. Specific changes of NMR signals of IF1 upon titration with 30S ribosomal subunit identifies several residues that are involved in the interaction with ribosomes.

Genetic and transcriptional organization of the Bacillus subtilis spc-alpha region

We used chromosomal walking methods to isolate a 10.8-kb region from the major ribosomal protein (r-protein) gene cluster of Bacillus subtilis (Bs). The gene order in this region, given by gene product, was r-proteins L16-L29-S17-L14-L24-L5-S14-S8-L6-L18-S5-L30-L15-SecY-adenylate kinase (Adk)-methionine aminopeptidase (Map)-initiation factor 1 (IF1)-L36-S13-S11-alpha subunit of RNA polymerase-L17. The region cloned, therefore, contains the homologues for the last three genes of the Escherichia coli (Ec) S10 operon, together with entire spc and alpha operons. This Bs organization differs from the corresponding region in Ec by the inclusion of the genes encoding Adk, Map and IF1 between the genes encoding SecY and L36. Plasmid integration experiments indicated that all 22 genes comprise a single large transcriptional unit controlled from a major promoter which lies upstream from the gene encoding r-protein L16. Promoter probe experiments located lesser activities internal to this large transcriptional unit, the secY and map promoters. The secY promoter region (psecY) contained two activities, each principally functioning in the stationary growth phase when high protein export is required. Thus, the Bs S10-spc-alpha region differs from its Ec counterpart in both genetic and transcriptional organization. Given this difference in transcriptional organization, the mechanisms coordinating expression of the translational apparatus are also likely to differ between Ec and Bs.

Characterization and expression of a gene encoding serine tRNA5 from Escherichia coli

The genes for translational components frequently are located together on the Escherichia coli genome. We have reported previously that the gene for a serine tRNA lies directly downstream from infA, the gene encoding initiation factor IF1. Here we characterize this tRNA gene, named serW. The serW gene expresses a minor form of serine tRNA(GGA) which recognizes the most frequently used serine codons, UCC and UCU. Two promoters were identified by S1 nuclease mapping: P1, which lies about 72 bp upstream from the structural gene; and P2, which lies about 35 bp upstream. Expression from P1 and P2 is comparable under conditions of rapid growth. The P2 promoter is followed by a GC-rich element characteristic of promoters regulated by ppGpp. A putative hairpin structure followed by a stretch of U residues about 25 nucleotides following the mature tRNA sequence resembles a rho-independent termination signal. The upstream gene, infA, is followed by a transcriptional terminator, but S1 mapping shows considerable readthrough. This serW expression appears to rely both on its own promoters and on promoters further upstream. The downstream gene, encoding an unidentified protein of about 100 kDa, is expressed in the opposite orientation and also is followed by a termination signal. Therefore serW is expressed both as a monocistronic gene and in combination with infA.

Translation initiation factor IF1 is essential for cell viability in Escherichia coli

Translation initiation factor IF1 is a highly conserved element of the prokaryotic translational apparatus. It has been demonstrated earlier that the factor stimulates in vitro the initiation phase of protein synthesis. However, no mutation in its gene, infA, has been identified, and a role for IF1 in translation has not been demonstrated in vivo. To elucidate the function of IF1 and determine if the protein is essential for cell growth, the chromosomal copy of infA was disrupted. Cell viability is maintained only when infA is expressed in trans from a plasmid, thereby demonstrating that IF1 is essential for cell growth in Escherichia coli. Cells depleted of IF1 exhibit few polysomes, suggesting that IF1 functions in the initiation phase of protein synthesis.

Similar organization of the nusA-infB operon in Bacillus subtilis and Escherichia coli

We reported previously the cloning and sequence of the Bacillus subtilis infB gene which encodes the essential IF2 factor required for initiation of translation (K. Shazand, J. Tucker, R. Chiang, K. Stansmore, H. U. Sperling-Petersen, M. Grunberg-Manago, J. C. Rabinowitz, and T. Leighton, J. Bacteriol. 172:2675-2687, 1990). The location of the 5' border of the infB operon was investigated by using integrative plasmids carrying various DNA fragments from the region upstream of the infB gene. The lethal effect of disruption of the infB transcriptional unit could be suppressed when the integrated plasmid introduced the spac promoter upstream of the infB operon and transformants were selected in conditions of induction of spac expression. Such an integrated plasmid was used as a starting point to clone the promoter of the infB operon. Primer extension mapping suggests that a single sigma A-type promoter controls transcription of the infB operon. The sequence of a 5,760-bp region encompassing the infB gene was determined. The infB operon is located immediately downstream of the polC gene and comprises seven open reading frames, four of which appear to be the homologs of genes present in the same order in the Escherichia coli infB operon, including nusA. The striking similarity between the E. coli and B. subtilis infB operons suggests that the function of each gene pair is conserved and that the B. subtilis NusA homolog, which is 124 residues shorter than its E. coli counterpart, could play a role similar to its role in E. coli.

Molecular cloning of a gene involved in lipooligosaccharide biosynthesis and virulence expression by Haemophilus influenzae type B

A wild-type Haemophilus influenzae type b (Hib) genomic DNA library was constructed in the plasmid shuttle vector pGJB103. A virulence-deficient lipooligosaccharide (LOS) mutant of Hib was used as a recipient for genetic transformation to screen this Hib genomic DNA library for genes involved in LOS expression. A recombinant plasmid containing a 7.8 kb PstI fragment of Hib DNA was shown to transform this LOS mutant to reactivity with a monoclonal antibody (mAb) specific for a wild-type LOS epitope. Transformation of two different virulence-deficient LOS mutants with a 4.4 kb BglII fragment of this recombinant plasmid yielded transformants which expressed LOS that bound the wild-type LOS-specific mAb and yielded profiles in sodium dodecyl sulphate/polyacrylamide gradient gel electrophoresis different from those of the original LOS mutants. These transformants with structurally altered LOS molecules also exhibited increased virulence in an animal model for invasive Hib disease. The virulence-transforming ability was further localized to a 1.8 kb BglII-AlwNI fragment of the Hib DNA insert. Nucleotide sequence analysis indicated the presence of a single large open reading frame within this fragment. This open reading frame contained 19 consecutive repeats of the tetramer CAAT near the 5' end. Linker insertion mutagenesis was used to demonstrate directly the involvement of this open reading frame in both LOS biosynthesis and virulence expression by Hib.

Requirement of the RNA helicase-like protein PRP22 for release of messenger RNA from spliceosomes

The product of the yeast PRP22 gene acts late in the splicing of yeast pre-messenger RNA, mediating the release of the spliced mRNA from the spliceosome. The predicted PRP22 protein sequence shares extensive homology with that of PRP2 and PRP16 proteins, which are also involved in nuclear pre-mRNA splicing. The homologous region contains sequence elements characteristic of several demonstrated or putative ATP-dependent RNA helicases. A putative RNA-binding motif originally identified in bacterial ribosomal protein S1 and Escherichia coli polynucleotide phosphorylase has also been found in PRP22.

Isolation and molecular genetic characterization of the Bacillus subtilis gene (infB) encoding protein synthesis initiation factor 2

Western blot (immunoblot) analysis of Bacillus subtilis cell extracts detected two proteins that cross-reacted with monospecific polyclonal antibody raised against Escherichia coli initiation factor 2 alpha (IF2 alpha). Subsequent Southern blot analysis of B. subtilis genomic DNA identified a 1.3-kilobase (kb) HindIII fragment which cross-hybridized with both E. coli and Bacillus stearothermophilus IF2 gene probes. This DNA was cloned from a size-selected B. subtilis plasmid library. The cloned HindIII fragment, which was shown by DNA sequence analysis to encode the N-terminal half of the B. subtilis IF2 protein and 0.2 kb of upstream flanking sequence, was utilized as a homologous probe to clone an overlapping 2.76-kb ClaI chromosomal fragment containing the entire IF2 structural gene. The HindIII fragment was also used as a probe to obtain overlapping clones from a lambda gt11 library which contained additional upstream and downstream flanking sequences. Sequence comparisons between the B. subtilis IF2 gene and the other bacterial homologs from E. coli, B. stearothermophilus, and Streptococcus faecium displayed extensive nucleic acid and protein sequence homologies. The B. subtilis infB gene encodes two proteins, IF2 alpha (78.6 kilodaltons) and IF2 beta (68.2 kilodaltons); both were expressed in B. subtilis and E. coli. These two proteins cross-reacted with antiserum to E. coli IF2 alpha and were able to complement in vivo an E. coli infB gene disruption. Four-factor recombination analysis positioned the infB gene at 145 degrees on the B. subtilis chromosome, between the polC and spcB loci. This location is distinct from those of the other major ribosomal protein and rRNA gene clusters of B. subtilis.

Localization of the ribosome-releasing factor gene in the Escherichia coli chromosome

The ribosome-releasing factor (RRF) gene was localized at a position between 2 and 6 min on the Escherichia coli chromosome by measuring the gene-dosage-dependent production of RRF in various E. coli F' merozygotes. This position was confirmed and refined by using a nucleotide probe corresponding to a 16-amino-acid sequence in RRF. It was found that the RRF gene was contained in pLC 6-32 of the Clark-Carbon Gene Bank. Restriction enzyme mapping of E. coli genomic DNA with the above probe led us to conclude that the RRF gene is situated in the 4-min region, somewhere downstream (clockwise) of the elongation factor Ts gene, tsf. A pLC 6-32-derived DNA fragment which carries the RRF gene was found to contain a partial sequence of tsf. The exact location of the translational initiation site of the RRF gene was determined to be 1.1 kilobases downstream from the translational termination site of tsf. The RRF gene is designated frr.

Gene encoding the alpha core subunit of Bacillus subtilis RNA polymerase is cotranscribed with the genes for initiation factor 1 and ribosomal proteins B, S13, S11, and L17

We describe the genetic and transcriptional organization of the promoter-distal portion of the Bacillus subtilis alpha operon. By DNA sequence analysis of the region surrounding rpoA, the gene for the alpha core subunit of RNA polymerase, we identified six open reading frames by the similarity of their products to their counterparts in the Escherichia coli transcriptional and translational apparatus. Gene order in this region, given by gene product, was IF1-B-S13-S11-alpha-L17. Gene order in E. coli is similar but not identical: SecY-B-S13-S11-S4-alpha-L17. The B. subtilis alpha region differed most strikingly from E. coli in the presence of IF1 and the absence of ribosomal protein S4, which is the translational regulator of the E. coli alpha operon. In place of the gene for S4, B. subtilis had a 177-base-pair intercistronic region containing two possible promoter sequences. However, experiments with S1 mapping of in vivo transcripts, gene disruptions in the alpha region, and a single-copy transcriptional fusion vector all suggested that these possible promoters were largely inactive during logarithmic growth, that the major promoter for the alpha operon lay upstream from the region cloned, and that the genes in the IF1 to L17 interval were cotranscribed. Thus, the transcriptional organization of the region resembles that of E. coli, wherein the alpha operon is transcribed primarily from the upstream spc promoter, but the absence of the S4 gene suggests that the translational regulation of the region may differ more fundamentally.

Identification, cloning and sequence of the Streptococcus faecium infB (translational initiation factor IF2) gene

The structural gene for translational initiation factor IF2 (infB) from Streptococcus faecium was identified by cross-hybridization with DNA probes derived from the corresponding gene of Bacillus stearothermophilus. The entire infB gene (ca. 2.8 kb) was cloned and sequenced. The amino acid sequence deduced from the nucleotide sequence shows that S. faecium initiation factor IF2 (785 amino acids, Mr 86,415) displays extensive homology (ca. 69% and 53%) with the region comprising three-quarters of the molecule from the carboxy-terminus of B. stearothermophilus and Escherichia coli IF2, respectively. The region comprising one-quarter of the molecule from the amino-terminus, on the other hand, does not display any significant homology.