We studied the temporal succession of vertical profiles of Emiliania huxleyi and their specific viruses (EhVs) during the progression of a natural phytoplankton bloom in the North Sea in June 1999. Genotypic richness was assessed by exploiting the variations in a gene encoding a protein with calcium-binding motifs ( GPA ...

Aldehyde oxidase (AO) is a complex molybdoflavoprotein that belongs to the xanthine oxidase family. AO is active as a homodimer and each 150 kDa monomer binds two distinct [2Fe2S] clusters, FAD and the molybdenum cofactor (Moco). AO has an important role in the metabolism of drugs based on its broad ...

5-Aminolevulinic acid (ALA) is the universal precursor for tetrapyrrole biosynthesis and is synthesized in plants in three enzymatic steps: ligation of glutamate (Glu) to tRNA(Glu) by glutamyl-tRNA synthetase, reduction of activated Glu to Glu-1-semialdehyde by glutamyl-tRNA reductase (GluTR), and transamination to ALA by Glu 1-semialdehyde aminotransferase. ALA formation controls the ...

Caenorhabditis elegans and human HRG-1-related proteins are conserved, membrane-bound permeases that bind and translocate heme in metazoan cells via a currently uncharacterized mechanism. Here, we show that cellular import of heme by HRG-1-related proteins from worms and humans require strategically located amino acids that are topologically conserved across species. We ...

A new DyP-type peroxidase from Pseudomonas aeruginosa PKE117 was identified and characterized. The dypPa was first identified via sequence analysis and then cloned in Escherichia coli. Subsequently, the recombinant protein DyPPa was expressed and purified. Its DNA sequence analysis revealed an open reading frame of 897 bp, encoding a protein monomer ...

Campylobacter jejuni, a microaerophilic bacterium, is the most frequent cause of human bacterial gastroenteritis. C. jejuni is exposed to harmful reactive oxygen species (ROS) produced during its own normal metabolic processes and during infection from the host immune system and from host intestinal microbiota. These ROS will damage DNA, proteins, ...

The mitochondria-associated membrane (MAM) is a domain of the endoplasmic reticulum (ER) that mediates the exchange of ions, lipids and metabolites between the ER and mitochondria. ER chaperones and oxidoreductases are critical components of the MAM. However, the localization motifs and mechanisms for most MAM proteins have remained elusive. Using ...

Cytochromes c are widespread respiratory proteins characterised by the covalent attachment of heme. The formation of c-type cytochromes requires, in all but a few exceptional cases, the formation of two thioether bonds between the two cysteine sulfurs in a CXXCH motif in the protein and the vinyl groups of heme. ...

Biogenesis of the mitochondrial cytochrome c oxidase (COX) is a highly complex process involving subunits encoded both in the nuclear and the organellar genome; in addition, a large number of assembly factors participate in this process. The soil bacterium Paracoccus denitrificans is an interesting alternative model for the study of ...

The function of holocytochrome c synthase (HCCS, also called heme lyase) is to attach covalently the heme cofactor to cytochromes c in the mitochondria of animals, fungi and protozoa. Little is known about how the protein functions but CP motifs, commonly found in heme-binding proteins, are present. Here we examine ...

Pathogenic bacteria require iron to replicate inside mammalian hosts. Recent studies indicate that heme acquisition in Gram-positive bacteria is mediated by proteins containing one or more NEAr-iron Transporter (NEAT) domains. B. anthracis is a spore-forming, Gram-positive pathogen and the causative agent of anthrax disease. The rapid, extensive and efficient replication ...

Hemoglobins (Hb) are the major protein components of erythrocytes circulating in the red blood, but can serve additional functions besides the transport of oxygen. Here, the cDNA of the bloody clam (Tegillarca granosa) Hb dimer (designated Tg-HbI) was cloned and was found to be 748 bp in length, consisting of an ...

Our previous work showed that in cucumber (Cucumis sativus), auxin rapidly induces heme oxygenase (HO) activity and the product of HO action, carbon monoxide (CO), then triggers the signal transduction events leading to adventitious root formation. In this study, the cucumber HO-1 gene (named as CsHO1) was isolated and sequenced. ...

Hepadnaviruses, including human hepatitis B virus (HBV) and duck hepatitis B virus (DHBV), replicate their DNA genome through reverse transcription. Although hepadnaviral polymerase (Pol) is distantly related to retroviral RTs, some of its features are distinct. In particular, besides the RT and RNase H domain, which are commonly encoded by ...

ABSTRACT The protein YfeX from Escherichia coli has been proposed to be essential for the process of iron removal from heme by carrying out a dechelation of heme without cleavage of the porphyrin macrocycle. Since this proposed reaction is unique and would represent the first instance of the biological dechelation ...

In animals and recently in plants, heme oxygenase-1 (HO1) has been found to confer protection against a variety of oxidant-induced cell and tissue injuries. In this study, a wheat (Triticum aestivum) HO1 gene TaHO1 was cloned and sequenced. It encodes a polypeptide of 31.7 kD with a putative N-terminal plastid ...

We report Trypanosoma cruzi infection rates of the native kissing bug Triatoma protracta in southern California. The rates are within the historically reported range, but differ significantly between the two sites (19% in Escondido and 36% in Glendora). Identification of T. cruzi in T. protracta was conducted for the first ...

The rate-limiting step in ribosome biogenesis is the transcription of ribosomal RNA, which is controlled by environmental conditions. The JmjC enzyme KDM2A/JHDM1A/FbxL11 demethylates mono- and dimethylated Lys 36 of histone H3, but its function is unclear. Here, we show that KDM2A represses the transcription of ribosomal RNA. KDM2A was localized ...

Proteins with Pumilio RNA binding domains (Puf proteins) are ubiquitous in eukaryotes. Some Puf proteins bind to the 3'-untranslated regions of mRNAs, acting to repress translation and promote degradation; others are involved in ribosomal RNA maturation. The genome of Trypanosoma brucei encodes eleven Puf proteins whose function cannot be predicted ...

Here, we present a new recurrent RNA arrangement, the so-called adenosine wedge (A-wedge), which is found in three places of the ribosomal RNA in both ribosomal subunits. The arrangement has a hierarchical structure, consisting of elements previously described as recurrent motifs, namely, the along-groove packing motif, the A-minor and the ...

UV-cross-linking and RNase protection, combined with high-throughput sequencing, have provided global maps of RNA sites bound by individual proteins or ribosomes. Using a stringent purification protocol, UV-CLIP (UV-cross-linking and immunoprecipitation) was able to identify intronic and exonic sites bound by splicing regulators in mouse brain tissue. Ribosome profiling has been ...

In this issue of Molecular Cell, Bohnsack et al. (2009) identify multiple binding sites of the RNA helicase Prp43 on preribosomal RNA. The target regions suggest distinct functions of Prp43 in ribosome biogenesis.

Dyskerin is a component of small nucleolar ribonucleoprotein complexes and acts as a pseudouridine synthase to modify newly synthesized ribosomal, spliceosomal, and possibly other RNAs. It is encoded by the DKC1 gene, the gene mutated in X-linked dyskeratosis congenita, and is also part of the telomerase complex. The yeast ortholog, ...

Mutations in the X-linked gene, DKC1, encoding dyskerin, cause dyskeratosis congenita by leading to decreased telomerase activity and causing short telomeres. Dyskerin is also a pseudouridine synthase that modifies nascent ribosomal and other RNAs and it is not known if this function is affected by the mutations. Here we show ...

H/ACA molecules are small nucleolar RNAs (snoRNAs) that guide the conversion of a uridine into a pseudouridine. This modification is crucial for ribosomal RNA (rRNA) function. In addition, H/ACA RNA also function in ribosomal RNA processing. Unlike the double hairpin structure of H/ACA molecules in other organisms, H/ACA molecules in ...

Ribosomal proteins stabilize the folded structure of the ribosomal RNA and enable the recruitment of further proteins to the complex. Quantitative hydroxyl radical footprinting was used to measure the extent to which three different primary assembly proteins, S4, S17, and S20, stabilize the three-dimensional structure of the Escherichia coli 16S ...

The synthesis of the 6-O-DPC-2-N-methylguanosine (m(2)G) nucleoside and the corresponding 5'-O-DMT-2'-O-TOM-protected 6-O-DPC-2-N-methylguanosine phosphoramidite is reported [DPC, diphenyl carbamoyl; DMT, 4,4'-dimethoxytrityl; TOM, [(triisopropylsilyl)oxy]methyl]. The availability of the phosphoramidite allows for syntheses of hairpin RNAs with site-selective incorporation of 2-N-methylguanosine modification. Four 18-nt hairpin RNA analogues representing the 970-loop region (helix 31 ...

Short duplexes between the U3 small nucleolar RNA and the precursor ribosomal RNA must form quickly and with high yield to satisfy the high demand for ribosome synthesis in rapidly growing eukaryotic cells. These interactions, designated the U3-ETS (external transcribed spacer) and U3-18S duplexes, are essential to initiate the processing ...

Rapid and accurate assembly of new ribosomal subunits is essential for cell growth. Here we show that the ribosomal proteins make assembly more cooperative by discriminating against non-native conformations of the Escherichia coli 16S ribosomal RNA. We used hydroxyl radical footprinting to measure how much the proteins stabilize individual ribosomal ...

The ribosome is a complex macromolecular machine responsible for protein synthesis in the cell. It consists of two subunits, each of which contains both RNA and protein components. Ribosome assembly is subject to intricate regulatory control and is aided by a multitude of assembly factors in vivo, but can also ...

By the early 1960s, evidence had accumulated that proteins were synthesized from special RNA copies of genes, named "messenger RNAs" (mRNAs), not directly from the stable RNAs found in the ribosomes of the cytoplasm. Yet, precisely how the protein chains were assembled along the RNA and, in particular, the relationship ...

The genus Chenopodium contains many economically important species in the New World, but is relatively understudied and poorly understood, especially in terms of evolutionary relationships. A better understanding of the structure of this genus could significantly help in breeding efforts on its cultivated members, notably the tetraploid C. quinoa and ...

In the present study the ribosomal RNA of the leech Hirudo medicinalis has been characterized at the aim of identifying possible analogies with other invertebrates. Upon electrophoresis on denaturating gels, ribosomal RNA fraction of H. medicinalis exhibited a remarkable thermal instability by dissociating into two hydrogen-bonded components when heated at ...

Cover illustration: RNA-assisted Protein Folding. This special issue of BTJ covers the role of ribosomes in protein folding, the role of non-coding RNAs on neurodegeneration, the effect of small non-coding RNA on transcription elongation, and much more. Image of molecules targeting ribosomal RNA. Surface of the 50S subunit of H. ...

Programmed ribosomal frameshifting (PRF) is one of the multiple translational recoding processes that fundamentally alters triplet decoding of the messenger RNA by the elongating ribosome. The ability of the ribosome to change translational reading frames in the -1 direction (-1 PRF) is employed by many positive strand RNA viruses, including ...

GTPases are found in all domains of life and are highly conserved. In eukaryotes, they serve as signalling molecules for many cellular processes. However, the prokaryotic GTPases play a very different role and are found to be associated with ribosome function. Among the 11 conserved GTPases, Der is the most ...

Escherichia coli contains five members of the DEAD-box RNA helicase family, a ubiquitous class of proteins characterized by their ability to unwind RNA duplexes. Although four of these proteins have been implicated in RNA turnover or ribosome biogenesis, no cellular function for the RhlE DEAD-box protein has been described as ...

The 970 loop (helix 31) of Escherichia coli 16S ribosomal RNA contains two modified nucleotides, m(2)G966 and m(5)C967. Positions A964, A969, and C970 are conserved among the Bacteria, Archaea, and Eukarya. The nucleotides present at positions 965, 966, 967, 968, and 971, however, are only conserved and unique within each ...

Thesis (Ph. D. in Agriculture)--University of Tsukuba, (A), no. 3091, 2003.3.25

Nucleoli are the prominent contrasted structures of the cell nucleus. In the nucleolus, ribosomal RNAs are synthesized, processed and assembled with ribosomal proteins. RNA polymerase I synthesizes the ribosomal RNAs and this activity is cell cycle regulated. The nucleolus reveals the functional organization of the nucleus in which the compartmentation ...

Although bystin has been identified as a protein potentially involved in embryo implantation (a process unique to mammals) in humans, the bystin gene is evolutionarily conserved from yeast to humans. DNA microarray data indicates that bystin is overexpressed in human cancers, suggesting that it promotes cell growth. We undertook RT ...

The pseudoknot is an important RNA structural element that provides an excellent model system for studying the contributions of tertiary interactions to RNA stability and to folding kinetics. RNA pseudoknots are also of interest because of their key role in the control of ribosomal frameshifting by viral RNAs. Their mechanical ...

MicroRNAs (miRNAs) are a class of small RNAs that act post-transcriptionally to regulate messenger RNA stability and translation. To elucidate how miRNAs mediate their repressive effects, we performed biochemical and functional assays to identify new factors in the miRNA pathway. Here we show that human RISC (RNA-induced silencing complex) associates ...

The interaction between the ribosomal protein S15 and its binding sites in the 16S RNA was examined from two points of view. First, the isolated protein S15 was studied by comparing NMR conformer sets, available in the PDB and recalculated using the CNS-ARIA protocol. Molecular dynamics (MD) trajectories were then ...

An RNA aptamer obtained by in vitro evolution can be used as an artificial molecular switch to regulate RNA function by additing a specific ligand. To construct novel translational control system in the cell, we created an "allosteric ribosome" consisted of 16S ribosomal (r) RNA that bears theophylline apatmer. The ...

Living systems have efficient degradative pathways for dealing with the fact that reactive oxygen species (ROS) derived from cellular metabolism and the environment oxidatively damage proteins and DNA. But aggregation and cross-linking can occur as well, leading to a series of problems including disruption of cellular regulation, mutations, and even ...

Eleven reference genes (18s ribosomal ribonucleic acid [RNA], 28s ribosomal RNA, ubiquitin, beta-actin, glycerine aldehyde dehydrogenase, ATP-synthase subunit 5B, hydroxymethyl-bilane synthase, hypoxanthine-phosphoribosyl transferase, ribosomal protein L32, tryptophan 5-monooxygenase activation protein (zeta polypeptide), and TATA-Box binding protein) were analyzed in use as references for gene expression profiling experiments using quantitative reverse ...

The RegB endoribonuclease participates in the bacteriophage T4 life cycle by favoring early messenger RNA breakdown. RegB specifically cleaves GGAG sequences found in intergenic regions, mainly in translation initiation sites. Its activity is very low but can be enhanced up to 100-fold by the ribosomal 30 S subunit or by ...

Bacteria possess a unique salvage mechanism for rescuing ribosomes stalled on aberrant mRNAs. A complex of SmpB protein and SsrA RNA orchestrates this salvage process. The specific and direct binding of SmpB facilitates recognition and delivery of SsrA RNA to stalled ribosomes. The SmpB protein is conserved throughout the bacterial ...

Ribosomal RNA from all organisms contains post-transcriptionally modified nucleotides whose function is far from clear. To gain insight into the molecular interactions of modified nucleotides, we investigated the modification status of Thermus thermophilus 5 S and 23 S ribosomal RNA by mass spectrometry and chemical derivatization/primer extension. A total of ...