scholarly journals New light on ancient enzymes – in vitro CO 2 Fixation by Pyruvate Synthase of Desulfovibrio africanus and Sulfolobus acidocaldarius

FEBS Journal ◽  
2019 ◽  
Vol 286 (22) ◽  
pp. 4494-4508 ◽  
Author(s):  
Andreas Witt ◽  
Roberta Pozzi ◽  
Stephan Diesch ◽  
Oliver Hädicke ◽  
Hartmut Grammel
Keyword(s):  
Sulfolobus Acidocaldarius ◽  
Pyruvate Synthase

scholarly journals High positive supercoiling in vitro catalyzed by an ATP and polyethylene glycol-stimulated topoisomerase from Sulfolobus acidocaldarius.

1985 ◽  
Vol 4 (8) ◽  
pp. 2123-2128 ◽  
Author(s):  
P. Forterre ◽  
G. Mirambeau ◽  
C. Jaxel ◽  
M. Nadal ◽  
M. Duguet
Keyword(s):  
Polyethylene Glycol ◽  
Sulfolobus Acidocaldarius ◽  
Positive Supercoiling

scholarly journals DNA Polymerase B1 Binding Protein 1 Is Important for DNA Repair by Holoenzyme PolB1 in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius

2021 ◽  
Vol 9 (2) ◽  
pp. 439
Author(s):  
Hiroka Miyabayashi ◽  
Hiroyuki D. Sakai ◽  
Norio Kurosawa
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Dna Polymerase ◽  
Binding Protein ◽  
Polymerase Activity ◽  
Sulfolobus Acidocaldarius ◽  
Deletion Strain ◽  
Synthesis Activity ◽  
Core Activity

DNA polymerase B1 (PolB1) is a member of the B-family DNA polymerase family and is a replicative DNA polymerase in Crenarchaea. PolB1 is responsible for the DNA replication of both the leading and lagging strands in the thermophilic crenarchaeon Sulfolobus acidocaldarius. Recently, two subunits, PolB1-binding protein (PBP)1 and PBP2, were identified in Saccharolobus solfataricus. Previous in vitro studies suggested that PBP1 and PBP2 influence the core activity of apoenzyme PolB1 (apo-PolB1). PBP1 contains a C-terminal acidic tail and modulates the strand-displacement synthesis activity of PolB1 during the synthesis of Okazaki fragments. PBP2 modestly enhances the DNA polymerase activity of apo-PolB1. These subunits are present in Sulfolobales, Acidilobales, and Desulfurococcales, which belong to Crenarchaea. However, it has not been determined whether these subunits are essential for the activity of apo-PolB1. In this study, we constructed a pbp1 deletion strain in S. acidocaldarius and characterized its phenotypes. However, a pbp2 deletion strain was not obtained, indicating that PBP2 is essential for replication by holoenzyme PolB1. A pbp1 deletion strain was sensitive to various types of DNA damage and exhibited an increased mutation rate, suggesting that PBP1 contribute to the repair or tolerance of DNA damage by holoenzyme PolB1. The results of our study suggest that PBP1 is important for DNA repair by holoenzyme PolB1 in S. acidocaldarius.

Preribosomal RNA processing in Archaea: characterization of the RNP endonuclease mediated processing of precursor 16S rRNA in the thermoacidophile Sulfolobus acidocaldarius

1995 ◽  
Vol 73 (11-12) ◽  
pp. 813-823 ◽  
Author(s):  
Simon Potter ◽  
Peter Durovic ◽  
Anthony Russell ◽  
Xin Wang ◽  
Deidre de Jong-Wong ◽  
...  
Keyword(s):  
16S Rrna ◽  
Processing System ◽  
Pcr Amplification ◽  
Rnase H ◽  
Micrococcal Nuclease ◽  
Sulfolobus Acidocaldarius ◽  
U3 Snorna ◽  
Processing Activity

The hyperthermophilic archaeon Sulfolobus acidocaldarius uses a novel RNA-containing endonuclease to excise and mature 16S rRNA from the precursor (pre) rRNA transcript. A cell-free processing system has been developed using an in vitro transcribed RNA substrate containing the entire 144 nucleotide 5′ external transcribed spacer (5′ ETS) and the first 72 nucleotides of 16S rRNA. The cell-free extract cleaves in the 5′ ETS at positions −99, −31, and +1 (i.e., the 5′ ETS–16S junction). These positions are at or near the positions cleaved in vivo during processing of the pre rRNA transcript. The processing activity has been purified between 100 and 200-fold and appears to contain five or six polypeptide components and perhaps as many as 10 different small RNA components. Using combined reverse transcription–PCR amplification, full or partial cDNA copies of two of the RNA components have been obtained. One of the RNAs exhibits sequence and structural similarities to eukaryotic U3 snoRNA. The processing activity has been shown to be inactivated by micrococcal nuclease. It can be reactivated by reconstituting using bulk RNA from S. acidocaldarius but not bulk RNA from distantly related organisms. The activity is also abolished by RNase H digestion in the presence of oligonucleotides complementary to the U3-like RNA. These results demonstrate that the U3-like RNA is an essential component of the pre rRNA processing RNP endonuclease. Furthermore, this RNP endonuclease is not a derived eukaryotic feature, instead its existence predates the divergence of archaea and eukaryotes.Key words: Sulfolobus acidocaldarius, archaebacteria, mature RNA, U3 snoRNA, ribonucleoprotein.

scholarly journals Electron cryotomography of ESCRT assemblies and dividing Sulfolobus cells suggests that spiraling filaments are involved in membrane scission

2013 ◽  
Vol 24 (15) ◽  
pp. 2319-2327 ◽  
Author(s):  
Megan J. Dobro ◽  
Rachel Y. Samson ◽  
Zhiheng Yu ◽  
John McCullough ◽  
H. Jane Ding ◽  
...  
Keyword(s):  
Leading Edge ◽  
Sulfolobus Acidocaldarius ◽  
Endosomal Sorting ◽  
Evolutionarily Conserved ◽  
Dividing Cells ◽  
Membrane Scission ◽  
Electron Cryotomography ◽  
Helical Tubes

The endosomal-sorting complex required for transport (ESCRT) is evolutionarily conserved from Archaea to eukaryotes. The complex drives membrane scission events in a range of processes, including cytokinesis in Metazoa and some Archaea. CdvA is the protein in Archaea that recruits ESCRT-III to the membrane. Using electron cryotomography (ECT), we find that CdvA polymerizes into helical filaments wrapped around liposomes. ESCRT-III proteins are responsible for the cinching of membranes and have been shown to assemble into helical tubes in vitro, but here we show that they also can form nested tubes and nested cones, which reveal surprisingly numerous and versatile contacts. To observe the ESCRT–CdvA complex in a physiological context, we used ECT to image the archaeon Sulfolobus acidocaldarius and observed a distinct protein belt at the leading edge of constriction furrows in dividing cells. The known dimensions of ESCRT-III proteins constrain their possible orientations within each of these structures and point to the involvement of spiraling filaments in membrane scission.

scholarly journals Substrate Requirements for a Novel Archaeal Endonuclease That Cleaves Within the 5′ External Transcribed Spacer of Sulfolobus acidocaldarius Precursor rRNA

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1373-1385
Author(s):  
Anthony G Russell ◽  
Holger Ebhardt ◽  
Patrick P Dennis
Keyword(s):  
Rna Processing ◽  
Ribosome Biogenesis ◽  
Consensus Sequence ◽  
Helical Structure ◽  
Sulfolobus Acidocaldarius ◽  
Phosphodiester Bond ◽  
External Transcribed Spacer ◽  
Single Stranded Region ◽  
Recognition Elements

Abstract During ribosome biogenesis in the hyperthermophilic archaeon Sulfolobus acidocaldarius, at least three separate precursor endonucleolytic cleavages occur within the 144-nucleotide-long 5′ external transcribed spacer (5′ ETS) region of the rRNA operon primary transcript. The 5′ ETS sequence contains three regions of very stable helical structure. One cleavage (5′ to position -98) is in the single-stranded region between the 5′ and the central helical domains; a second cleavage (5′ to position -31) is in the single-stranded region between the central and the 3′ helical domains; and a third cleavage is at the 5′ ETS-16S junction (5′ to position +1). The three sites share a common consensus sequence around the position of cleavage. We have used an in vitro pre-RNA processing assay to define some of the sequence and structural recognition elements necessary for the two precursor cleavages 5′ to positions -98 and -31. Surprisingly, none of the three predominant helical domains are required for recognition or targeting of the cleavages, although their removal reduces the rate of cleavage site utilization. We show that the sequence AAG ↓ (CA)UU encompassing each site contains at least some of the essential features for recognition and efficient targeting of the cleavages. Cleavage depends on the presence of a purine 5′ and a uracil two nucleotides 3′ to the scissile phosphodiester bond. Mutations to other bases at these critical positions are either not cleaved or cleaved very poorly. Finally, on the basis of intermediates that are produced during a processing reaction, we can conclude that the cleavages at positions 98 and 31 are not ordered in vitro.

scholarly journals Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius

Catalysts ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 34
Author(s):  
Shoji Suzuki ◽  
Norio Kurosawa ◽  
Takeshi Yamagami ◽  
Shunsuke Matsumoto ◽  
Tomoyuki Numata ◽  
...  
Keyword(s):  
Information Exchange ◽  
Direct Evidence ◽  
Sulfolobus Acidocaldarius ◽  
Dna Duplexes ◽  
Branch Migration ◽  
Migration Activity ◽  
Strand Invasion ◽  
End Resection

Homologous recombination (HR) refers to the process of information exchange between homologous DNA duplexes and is composed of four main steps: end resection, strand invasion and formation of a Holliday junction (HJ), branch migration, and resolution of the HJ. Within each step of HR in Archaea, the helicase-promoting branch migration is not fully understood. Previous biochemical studies identified three candidates for archaeal helicase promoting branch migration in vitro: Hjm/Hel308, PINA, and archaeal long helicase related (aLhr) 2. However, there is no direct evidence of their involvement in HR in vivo. Here, we identified a novel helicase encoded by Saci_0814, isolated from the thermophilic crenarchaeon Sulfolobus acidocaldarius; the helicase dissociated a synthetic HJ. Notably, HR frequency in the Saci_0814-deleted strain was lower than that of the parent strain (5-fold decrease), indicating that Saci_0814 may be involved in HR in vivo. Saci_0814 is classified as an aLhr1 under superfamily 2 helicases; its homologs are conserved among Archaea. Purified protein produced in Escherichia coli showed branch migration activity in vitro. Based on both genetic and biochemical evidence, we suggest that aLhr1 is involved in HR and may function as a branch migration helicase in S. acidocaldarius.

scholarly journals PolB1 Is Sufficient for DNA Replication and Repair Under Normal Growth Conditions in the Extremely Thermophilic Crenarchaeon Sulfolobus acidocaldarius

2020 ◽  
Vol 11 ◽  
Author(s):  
Hiroka Miyabayashi ◽  
Rupal Jain ◽  
Shoji Suzuki ◽  
Dennis W. Grogan ◽  
Norio Kurosawa
Keyword(s):  
Dna Replication ◽  
Normal Growth ◽  
Growth Conditions ◽  
Sulfolobus Acidocaldarius ◽  
Single Deletion ◽  
Dna Replication And Repair ◽  
Normal Sensitivity ◽  
Y Family

The thermophilic crenarchaeon Sulfolobus acidocaldarius has four DNA polymerases (DNAPs): PolB1, PolB2, PolB3, and Dbh (PolY). Previous in vitro studies suggested that PolB1 is the main replicative DNAP of Sulfolobales whereas PolB2 and Y-family polymerases Dpo4 (Saccharolobus solfataricus) or Dbh are involved in DNA repair and translesion DNA synthesis. On the other hand, there are various opinions about the role of PolB3, which remains to be clearly resolved. In order to examine the roles of the DNAPs of S. acidocaldarius through in vivo experiments, we constructed polB2, polB3, and dbh deletion strains and characterized their phenotypes. Efforts to construct a polB1 deletion strain were not successful; in contrast, it was possible to isolate triple gene-deletion strains lacking polB2, polB3, and dbh. The growth of these strains was nearly the same as that of the parent strains under normal growth conditions. The polB2, polB3, and dbh single-deletion strains were sensitive to some types of DNA-damaging treatments, but exhibited normal sensitivity to UV irradiation and several other damaging treatments. Overall, the genotype which exhibited the greatest sensitivity to the DNA-damaging treatments we tested was the ΔpolB2 ΔpolB3 combination, providing the first evidence of overlapping function for these two DNAPs in vivo. The results of our study strongly suggest that PolB1 is responsible for the DNA replication of both the leading and lagging strands and is sufficient to complete the repair of most DNA damage under normal growth conditions in S. acidocaldarius.

Ultrastructural Investigations of the Contractile Filaments of Amoebae

1974 ◽  
Vol 32 ◽  
pp. 188-189
Author(s):  
P.L. Moore
Keyword(s):  
Cytoplasmic Streaming ◽  
Three Dimensional ◽  
Freeze Fracture ◽  
Amoeboid Movement ◽  
Different Types ◽  
Chemical Conditions ◽  
Complete Interpretation

Previous freeze fracture results on the intact giant, amoeba Chaos carolinensis indicated the presence of a fibrillar arrangement of filaments within the cytoplasm. A complete interpretation of the three dimensional ultrastructure of these structures, and their possible role in amoeboid movement was not possible, since comparable results could not be obtained with conventional fixation of intact amoebae. Progress in interpreting the freeze fracture images of amoebae required a more thorough understanding of the different types of filaments present in amoebae, and of the ways in which they could be organized while remaining functional.The recent development of a calcium sensitive, demembranated, amoeboid model of Chaos carolinensis has made it possible to achieve a better understanding of such functional arrangements of amoeboid filaments. In these models the motility of demembranated cytoplasm can be controlled in vitro, and the chemical conditions necessary for contractility, and cytoplasmic streaming can be investigated. It is clear from these studies that “fibrils” exist in amoeboid models, and that they are capable of contracting along their length under conditions similar to those which cause contraction in vertebrate muscles.

In Vitro Induction of Crystals of MT Protein by Vinblastine-Colcemid in Mouse Spermatids

1974 ◽  
Vol 32 ◽  
pp. 132-133
Author(s):  
John J. Wolosewick ◽  
John H. D. Bryan
Keyword(s):  
Endoplasmic Reticulum ◽  
Smooth Endoplasmic Reticulum ◽  
Nuclear Ring ◽  
Rough Er ◽  
Distal Direction ◽  
In Vitro Induction

Early in spermiogenesis the manchette is rapidly assembled in a distal direction from the nuclear-ring-densities. The association of vesicles of smooth endoplasmic reticulum (SER) and the manchette microtubules (MTS) has been reported. In the mouse, osmophilic densities at the distal ends of the manchette are the organizing centers (MTOCS), and are associated with the SER. Rapid MT assembly and the lack of rough ER suggests that there is an existing pool of MT protein. Colcemid potentiates the reaction of vinblastine with tubulin and was used in this investigation to detect this protein.

Induction and Differentiation of Dental Epithelium in Vivo and in Vitro

1982 ◽  
Vol 40 ◽  
pp. 142-145
Author(s):  
E. J. Kollar
Keyword(s):  
Connective Tissue ◽  
Oral Mucosa ◽  
Basal Lamina ◽  
Functional Derivatives ◽  
Specific Source ◽  
Dental Epithelium ◽  
Connective Tissue Stroma

The differentiation and maintenance of many specialized epithelial structures are dependent on the underlying connective tissue stroma and on an intact basal lamina. These requirements are especially stringent in the development and maintenance of the skin and oral mucosa. The keratinization patterns of thin or thick cornified layers as well as the appearance of specialized functional derivatives such as hair and teeth can be correlated with the specific source of stroma which supports these differentiated expressions.

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