scholarly journals An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12.

1992 ◽  
Vol 12 (1) ◽  
pp. 56-67 ◽  
Author(s):  
D A Maslov ◽  
N R Sturm ◽  
B M Niner ◽  
E S Gruszynski ◽  
M Peris ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Sequence Similarity ◽  
Rich Region ◽  
Leishmania Tarentolae ◽  
Significant Sequence Similarity ◽  
The Family ◽  
Intergenic Regions ◽  
Ribosomal Protein S12

Six short G-rich intergenic regions in the maxicircle of Leishmania tarentolae are conserved in location and polarity in two other kinetoplastid species. We show here that G-rich region 6 (G6) represents a pan-edited cryptogene which contains at least two domains edited independently in a 3'-to-5' manner connected by short unedited regions. In the completely edited RNA, 117 uridines are added at 49 sites and 32 uridines are deleted at 13 sites, creating a translated 85-amino-acid polypeptide. Similar polypeptides are probably encoded by pan-edited G6 transcripts in two other species. The G6 polypeptide has significant sequence similarity to the family of S12 ribosomal proteins. A minicircle-encoded gRNA overlaps 12 editing sites in G6 mRNA, and chimeric gRNA/mRNA molecules were shown to exist, in agreement with the transesterification model for editing.

An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12

1992 ◽  
Vol 12 (1) ◽  
pp. 56-67
Author(s):  
D A Maslov ◽  
N R Sturm ◽  
B M Niner ◽  
E S Gruszynski ◽  
M Peris ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Sequence Similarity ◽  
Rich Region ◽  
Leishmania Tarentolae ◽  
Significant Sequence Similarity ◽  
The Family ◽  
Intergenic Regions ◽  
Ribosomal Protein S12

Six short G-rich intergenic regions in the maxicircle of Leishmania tarentolae are conserved in location and polarity in two other kinetoplastid species. We show here that G-rich region 6 (G6) represents a pan-edited cryptogene which contains at least two domains edited independently in a 3'-to-5' manner connected by short unedited regions. In the completely edited RNA, 117 uridines are added at 49 sites and 32 uridines are deleted at 13 sites, creating a translated 85-amino-acid polypeptide. Similar polypeptides are probably encoded by pan-edited G6 transcripts in two other species. The G6 polypeptide has significant sequence similarity to the family of S12 ribosomal proteins. A minicircle-encoded gRNA overlaps 12 editing sites in G6 mRNA, and chimeric gRNA/mRNA molecules were shown to exist, in agreement with the transesterification model for editing.

scholarly journals Legionella pneumophila CRISPR-Cas suggests recurrent encounters with one or more phages in the family Microviridae .

2021 ◽  
Author(s):  
Shayna R. Deecker ◽  
Malene L. Urbanus ◽  
Beth Nicholson ◽  
Alexander W. Ensminger
Keyword(s):  
Legionella Pneumophila ◽  
Sequence Similarity ◽  
Mobile Element ◽  
Current Data ◽  
Significant Sequence Similarity ◽  
Remediation Strategies ◽  
The Family ◽  
Legionnaires Disease ◽  
Outstanding Question

Legionella pneumophila is a ubiquitous freshwater pathogen and the causative agent of Legionnaires’ disease. L. pneumophila growth within protists provides a refuge from desiccation, disinfection, and other remediation strategies. One outstanding question has been whether this protection extends to phages. L. pneumophila isolates are remarkably devoid of prophages and to date no Legionella phages have been identified. Nevertheless, many L. pneumophila isolates maintain active CRISPR-Cas defenses. So far, the only known target of these systems is an episomal element that we previously named Legionella Mobile Element-1 (LME-1). The continued expansion of publicly available genomic data promises to further our understanding of the role of these systems. We now describe over 150 CRISPR-Cas systems across 600 isolates to establish the clearest picture yet of L. pneumophila ’s adaptive defenses. By searching for targets of 1,500 unique CRISPR-Cas spacers, LME-1 remains the only identified CRISPR-Cas targeted integrative element. We identified 3 additional LME-1 variants - all targeted by previously and newly identified CRISPR-Cas spacers - but no other similar elements. Notably, we also identified several spacers with significant sequence similarity to microviruses, specifically those within the subfamily Gokushovirinae . These spacers are found across several different CRISPR-Cas arrays isolated from geographically diverse isolates, indicating recurrent encounters with these phages. Our analysis of the extended Legionella CRISPR-Cas spacer catalog leads to two main conclusions: current data argue against CRISPR-Cas targeted integrative elements beyond LME-1, and the heretofore unknown L. pneumophila phages are most likely lytic gokushoviruses. IMPORTANCE Legionnaires’ disease is an often-fatal pneumonia caused by Legionella pneumophila , which normally grows inside amoebae and other freshwater protists. L. pneumophila trades diminished access to nutrients for the protection and isolation provided by the host. One outstanding question is whether L. pneumophila is susceptible to phages, given the protection provided by its intracellular lifestyle. In this work, we use Legionella CRISPR spacer sequences as a record of phage infection to predict that the “missing” L. pneumophila phages belong to the microvirus subfamily Gokushovirinae . Gokushoviruses are known to infect another intracellular pathogen, Chlamydia . How do gokushoviruses access L. pneumophila (and Chlamydia ) inside their “cozy niches”? Does exposure to phages happen during a transient extracellular period (during cell-to-cell spread) or is it indicative of a more complicated environmental lifestyle? One thing is clear, 100 years after their discovery, phages continue to hold important secrets about the bacteria upon which they prey.

Ribosomal proteins from goose reticulocytes are not histones

1968 ◽  
Vol 46 (12) ◽  
pp. 1507-1514 ◽  
Author(s):  
J. M. Neelin ◽  
G. Vidali
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Ribosomal Proteins ◽  
Cross Contamination ◽  
Guanidinium Chloride ◽  
Electrophoretic Patterns ◽  
Starch Gel ◽  
Cell Fractions

Ribosomes were isolated from goose reticulocytes after lysis with saponin in 50 mM KCl, 1.5 mM MgCl2, 1 mM Tris, pH 7.5. Maximum yields of ribosomes were obtained about 4 days after injection of the birds with Phenylhydrazine, but ribosomal proteins did not vary with the stage of recovery.Ribosomal proteins (extracted with either HCl–urea or LiCl–urea) differed generally from histones (extracted with either HCl or HCl–urea) according to amino acid composition and to electrophoretic patterns in starch gel and in Polyacrylamide gel, but a few zones of ribosomal protein appeared to coincide electrophoretically with the main histone components. Since all of the former proteins were eluted unretarded from Amberlite CG-50 in 9% guanidinium chloride, in which all histones are adsorbed, we conclude that histones and ribosomal proteins are different classes of protein.The hazards of assuming chemical identities of proteins on the basis of limited electrophoretic evidence and the risks of misleading cross-contamination of cell fractions were demonstrated.

scholarly journals Activity and genomic organization of human glucose transporter 9 (GLUT9), a novel member of the family of sugar-transport facilitators predominantly expressed in brain and leucocytes

2000 ◽  
Vol 350 (3) ◽  
pp. 771-776 ◽  
Author(s):  
Holger DOEGE ◽  
Andreas BOCIANSKI ◽  
Hans-Georg JOOST ◽  
Annette SCHÜRMANN
Keyword(s):  
Amino Acid ◽  
Glucose Transporter ◽  
Sequence Similarity ◽  
Organic Anion ◽  
Sugar Transport ◽  
Amino Acid Identity ◽  
Transport Activity ◽  
Anion Transporters ◽  
The Family ◽  
Glucose Transporter 9

The GLUT9 gene encodes a cDNA which exhibits significant sequence similarity with members of the glucose transporter (GLUT) family. The gene is located on chromosome 9q34 and consists of 10 exons separated by short introns. The amino acid sequence deduced from its cDNA predicts 12 putative membrane-spanning helices and all the motifs (sugar-transporter signatures) that have previously been shown to be essential for transport activity. A striking characteristic of GLUT9 is the presence of two arginines in the putative helices 7 and 8 at positions where the organic anion transporters harbour basic residues. The next relative of GLUT9 is the glucose transporter GLUT8/GLUTX1 (44.8% amino acid identity with GLUT9). A 2.6-kb transcript of GLUT9 was detected in spleen, peripheral leucocytes and brain. Transfection of COS-7 cells with GLUT9 produced expression of a 46-kDa membrane protein which exhibited reconstitutable glucose-transport activity and low-affinity cytochalasin-B binding. It is concluded that GLUT9 is a novel member of the family of sugar-transport facilitators with a tissue-specific function.

scholarly journals Nonstructural p26 proteins encoded by the 3’-proximal genes of velariviruses and criniviruses are orthologs

2019 ◽  
Vol 165 (2) ◽  
pp. 439-443
Author(s):  
I. B. Rogozin ◽  
A. A. Agranovsky
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Similarity ◽  
Structural Proteins ◽  
Amino Acid Sequence Similarity ◽  
High Plasticity ◽  
Amino Acid Sequence Alignment ◽  
Bioinformatic Tools ◽  
The Family ◽  
Share Amino Acid Sequence

AbstractThe 3’-most genes in RNA-2 of the Crinivirus genus members (family Closteroviridae) code for non-structural p26 proteins that share amino acid sequence similarity [Stewart LR, Hwang MS, Falk BW (2009) Virus Res 145:293-299]. In this study, sensitive bioinformatic tools have been used to identify the homologous p26 proteins encoded by the 3’ genes in monopartite genomes of the members of Velarivirus, another Closteroviridae genus, and mint vein banding-associated virus, an unassigned member of the family. The p26 proteins showed similarity in their predicted secondary structures, but an amino acid sequence alignment showed no strictly conserved positions, thus indicating a high plasticity of these non-structural proteins. The implications of the sequence analysis for possible functions of the crinivirus and velarivirus p26 proteins are discussed.

Gene organization and structure of two transcriptional units from Methanococcus coding for ribosomal proteins and elongation factors

1989 ◽  
Vol 35 (1) ◽  
pp. 200-204 ◽  
Author(s):  
Johannes Auer ◽  
Konrad Lechner ◽  
August Bock
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Sequence Similarity ◽  
Elongation Factor ◽  
Gene Organization ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Elongation Factors ◽  
Putative Gene ◽  
Transcriptional Units

Two transcriptional units coding for ribosomal proteins and protein synthesis elongation factors in Methanococcus vannielii have been cloned and analysed in detail. They correspond to the "streptomycin operon" and "spectinomycin operon" of the Escherichia coli chromosome. The following general conclusions can be drawn from comparison of the nucleotide and the derived amino acid sequences of ribosomal proteins from Methanococcus with those from eubacteria and eukaryotes. (i) Ribosomal protein and elongation factor genes in Methanococcus are clustered in transcriptional units corresponding closely to E. coli ribosomal protein operons with respect to both gene composition and organization. (ii) These transcriptional units contain, in addition, a few open reading frames whose putative gene products share sequence similarity with eukaryotic 80S but not with eubacterial, ribosomal proteins. They may correspond to "additional" ribosomal proteins of the Methanococcus ribosome, there being no functional homologues in the eubacterial ribosome. (iii) Methanococcus ribosomal proteins and elongation factors almost exclusively exhibit a higher sequence similarity to eukaryotic 80S ribosomal proteins than to those of eubacteria. (iv) Many Methanococcus ribosomal proteins have a size intermediate between those of their eukaryotic and eubacterial homologues. These results are discussed in terms of a hypothesis which implies that the recent eubacterial ribosome developed by a "minimization" process from a more complex organelle and that the archaebacterial ribosome has maintained features of this ancestor.Key words: archaebacteria, Methanococcus, transcription factors, clonal analysis.

Ribosomal RNA: the message or matrix for ribosomal proteins

1976 ◽  
Vol 54 (2) ◽  
pp. 192-193
Author(s):  
D. R. Miller ◽  
A. T. Matheson ◽  
L. P. Visentin
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Ribosomal Protein ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
16S Ribosomal Rna ◽  
Degree Of Similarity

The known nucleotide sequence of Escherichia coli 16S ribosomal RNA has been converted to amino acid sequences in all possible ways, and compared to known ribosomal protein sequences. The degree of similarity is precisely what one would expect by chance alone, providing additional evidence that ribosomal proteins cannot be coded for by ribosomal RNA.

scholarly journals Search for Highly Divergent Tandem Repeats in Amino Acid Sequences

2021 ◽  
Vol 22 (13) ◽  
pp. 7096
Author(s):  
Valentina Rudenko ◽  
Eugene Korotkov
Keyword(s):  
Cluster Analysis ◽  
Amino Acid ◽  
Tandem Repeats ◽  
Sequence Similarity ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
The Other ◽  
Significant Sequence Similarity ◽  
Pairwise Correlations

We report a Method to Search for Highly Divergent Tandem Repeats (MSHDTR) in protein sequences which considers pairwise correlations between adjacent residues. MSHDTR was compared with some previously developed methods for searching for tandem repeats (TRs) in amino acid sequences, such as T-REKS and XSTREAM, which focus on the identification of TRs with significant sequence similarity, whereas MSHDTR detects repeats that significantly diverged during evolution, accumulating deletions, insertions, and substitutions. The application of MSHDTR to a search of the Swiss-Prot databank revealed over 15 thousand TR-containing amino acid sequences that were difficult to find using the other methods. Among the detected TRs, the most representative were those with consensus lengths of two and seven residues; these TRs were subjected to cluster analysis and the classes of patterns were identified. All TRs detected in this study have been combined into a databank accessible over the WWW.

Deficiency of dietary EAA preferentially inhibits mRNA translation of ribosomal proteins in liver of meal-fed rats

2001 ◽  
Vol 281 (3) ◽  
pp. E430-E439 ◽  
Author(s):  
Tracy G. Anthony ◽  
Ali K. Reiter ◽  
Joshua C. Anthony ◽  
Scot R. Kimball ◽  
Leonard S. Jefferson
Keyword(s):  
Protein Synthesis ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Serum Insulin ◽  
Control Diet ◽  
Mrna Translation ◽  
Initiation Factor ◽  
Liver Protein ◽  
Deficient Diet

The goal of these studies was to investigate the mechanisms by which amino acid supply regulates global rates of protein synthesis as well as the translation of ribosomal protein (rp) mRNAs in liver. In the experiments conducted, male weanling rats were trained over a 2-wk period to consume their daily food intake within 3 h. On day 14, rats were fed the control diet or an isocaloric, isonitrogenous diet lacking glycine, tryptophan, leucine, or the branched-chain amino acids (BCAA) for 1 h. Feeding Trp-, Leu-, or BCAA-deficient diets resulted in significant reductions in serum insulin, hepatic protein synthesis, eukaryotic initiation factor 2B (eIF2B) activity, and phosphorylation of eIF4E-binding protein 1 (4E-BP1) and ribosomal protein S6 kinase (S6K1). Phosphorylation of eIF2α was inversely related to eIF2B activity under all conditions. Alterations in the hepatic synthesis of rp were assessed by changes in the distribution of rp (S4, S8, L26) mRNAs across sucrose density gradients and compared with non-rp (β-actin, albumin) mRNAs. In all dietary treatments, non-rp mRNAs were mostly polysome associated. Conversely, the proportion of rp mRNAs residing in polysomes was two- to fivefold less in rats fed diets lacking tryptophan, leucine, or BCAA compared with rats fed the control diet. Total hepatic abundance of all mRNAs examined did not differ among treatment groups. For all parameters examined, there were no differences between rats fed the glycine-deficient diet and rats fed the control diet. The data suggest that essential amino acid (EAA) deficiency inhibits global rates of liver protein synthesis via a block in translation initiation. Additionally, the translation of rp mRNAs is preferentially repressed in association with decreased S6K1 phosphorylation.

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