Intracellular localization of a group II chaperonin indicates a membrane-related function

Trent, Jonathan D.; Kagawa, Hiromi; Paavola, Chad D.; McMillan, R. Andrew; Howard, J.B.; Jahnke, L. L.; Lavin, Colleen; Embaye, Tsegereda; Henze, Christopher E.

doi:10.1073/pnas.2136795100

Cited by 29 publications

(20 citation statements)

References 51 publications

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“…Ths is pervasively PHX in archaeal genomes at a very high predicted expression level (Table 2). Ths also has been investigated experimentally and confirmed especially abundant in Sulfolobus species encompassing up to 20% of the cellular protein content (24)(25)(26). DnaK (HSP70) is found, so far, only in archaeal mesophiles or in moderate thermophiles (27), where it is PHX.…”

Section: Resultsmentioning

confidence: 98%

“…Because chaperones, especially thermosomes, are potently PHX in Archaea, we elaborate more on these classes of proteins. Chaperones play pivotal roles in protein folding, degradation of misfolded proteins, proteolysis, secretion, trafficking across membranes, facilitating the assembly of macromolecular structural complexes (22), and archaeal membrane stabilization (26). Molecular chaperone systems that promote the correct folding of nascent or misfolded proteins have evolved in all domains of life.…”

Section: Resultsmentioning

confidence: 99%

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Predicted highly expressed genes in archaeal genomes

Karlin

Mrázek

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Based primarily on 16S rRNA sequence comparisons, life has been broadly divided into the three domains of Bacteria, Archaea, and Eukarya. Archaea is further classified into Crenarchaea and Euryarchaea. Archaea generally thrive in extreme environments as assessed by temperature, pH, and salinity. For many prokaryotic organisms, ribosomal proteins (RP), transcription͞translation factors, and chaperone genes tend to be highly expressed. A gene is predicted highly expressed (PHX) if its codon usage is rather similar to the average codon usage of at least one of the RP, transcription͞ translation factors, and chaperone gene classes and deviates strongly from the average gene of the genome. The thermosome (Ths) chaperonin family represents the most salient PHX genes among Archaea. The chaperones Trigger factor and HSP70 have overlapping functions in the folding process, but both of these proteins are lacking in most archaea where they may be substituted by the chaperone prefoldin. Other distinctive PHX proteins of Archaea, absent from Bacteria, include the proliferating cell nuclear antigen PCNA, a replication auxiliary factor responsible for tethering the catalytic unit of DNA polymerase to DNA during highspeed replication, and the acidic RP P0, which helps to initiate mRNA translation at the ribosome. Other PHX genes feature Cell division control protein 48 (Cdc48), whereas the bacterial septation proteins FtsZ and minD are lacking in Crenarchaea. RadA is a major DNA repair and recombination protein of Archaea. Archaeal genomes feature a strong Shine-Dalgarno ribosome-binding motif more pronounced in Euryarchaea compared with Crenarchaea.acidic ribosomal proteins ͉ Archaea ͉ highly expressed proteins ͉ thermosome T he identity of the three domains of life (1) and their relationships are controversial (2-11). Archaea form a heterogeneous clade composed of a mosaic of bacterial, eukaryotic, and unique features. Archaea and Eukarya share many homologous genes involved in information processing (replication, transcription, and translation), whereas Archaea and Bacteria share many morphological structures and metabolic proteins (10, 12). Of 19 archaeal genomes completely sequenced (Table 1, mid-2004), 4 are from Crenarchaea and 14 are from Euryarchaea. Nanoarchaeum equitans, a parasitic archaeon that lives in coculture with the archaeon Ignicoccus, has been tentatively assigned to the separate group of Nanoarchaea. Most sequenced archaea, to date, are thermophilic, generally prefer extreme environments, and are found in most ecosystems. The four sequenced crenarchaea are all hyperthermophiles (optimal growth temperature, Ն75°C), although mesophilic crenarchaea have been putatively found in pelagic waters (3, 13). Among the Euryarchaea, six are methanogens, including three mesophiles, Methanosarcina acetivorans, Methanosarcina mazei, and Methanococcus maripaludis. Halobacterium NRC-1 is also mesophilic, thriving in high salt concentrations. Most sequenced archaea, excluding methanogens (lifestyle strictly anaerobic, meta...

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Section: Resultsmentioning

confidence: 98%

Section: Resultsmentioning

confidence: 99%

Predicted highly expressed genes in archaeal genomes

Karlin

Mrázek

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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“…In addition, homologues of the Hsp60 family are present in the genomes of all archaea, and their upregulation as part of multiprotein complexes known as thermosomes during stress response has been demonstrated (19,21). The archaeal thermosomes form large homooligomeric rings consisting of 7 to 9 subunits that assist in protein folding as well as in other functions (6,16,20). Genomic mining also revealed the presence of prefoldin homologues in all archaeal species studied so far, but the gene encoding the prefoldin ␤-subunit was downregulated in Pyrococcus upon heat shock (19).…”

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confidence: 99%

Genome-Wide Identification of Targets for the Archaeal Heat Shock Regulator Phr by Cell-Free Transcription of Genomic DNA

et al. 2010

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The hyperthermophilic archaeon Pyrococcus furiosus grows optimally near 100°C and undergoes a heat shock response at 105°C, mediated at least in part by the heat shock regulator Phr. Genes encoding a small heat shock protein (HSP20) and a member of the AAA ؉ ATPase are the only known targets of the regulator, but a genetic mutant of Phr has yet to be characterized. We describe here an alternative approach for the identification of the regulon of Phr based on cell-free transcription of fragmented chromosomal DNA in the presence or absence of the regulator and hybridization of in vitro RNA to P. furiosus whole-genome microarrays. Our results confirmed the phr, the hsp20, and the aaa ؉ ATPase genes as targets of Phr and also identified six additional open reading frames, PF0624, PF1042, PF1291, PF1292, PF1488, and PF1616, as Phr-responsive genes, which include that encoding di-myo-inositol phosphate synthase. Transcription of the identified novel genes was inhibited by Phr in standard transcription assays, and the novel consensus sequence 5-TTTAnnn ACnnnnnGTnAnnAAAA-3 (uppercase letters denote a high conservation of the bases) was inferred from our data as the Phr recognition motif. Mutational evidence for the significance of this sequence as Phr recognition was provided in DNA-binding experiments.

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“…For example, Hsp70 (DnaK), Hsp40 (DnaJ), and Hsp60 (GroEL) are absent in members of the Crenarchaeota, although they are found in some members of the Euryarchaeota. The Crenarchaeota have a separate class of Hsp60s that is related to a eucaryotic protein known as TCP1 and only distantly related to the highly conserved bacterial Hsp60s (42,43). Some crenarchaeal Hsp60s are heat inducible (16,19), but others are regulated by low temperatures (17) as has also been shown for the related TCP1 proteins in yeast (39).…”

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confidence: 90%

“…It is well established that heat and other cell stresses modulate the expression of genes encoding the so-called heat shock proteins (HSPs), which are involved in a variety of cellular processes, including membrane transport and stability, protein folding, and cell signaling (11,12,29,42). The predominant HSPs are classified by their molecular masses as Hsp104, Hsp90, Hsp70, Hsp60, Hsp40, Hsp20, and Hsp10 or as heat-inducible proteases, such as Clp and Lon (21).…”

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confidence: 99%

Heat Shock Response ofArchaeoglobus fulgidus

et al. 2005

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The heat shock response of the hyperthermophilic archaeon Archaeoglobus fulgidus strain VC-16 was studied using whole-genome microarrays. On the basis of the resulting expression profiles, approximately 350 of the 2,410 open reading frames (ORFs) (ca. 14%) exhibited increased or decreased transcript abundance. These span a range of cell functions, including energy production, amino acid metabolism, and signal transduction, where the majority are uncharacterized. One ORF called AF1298 was identified that contains a putative helix-turn-helix DNA binding motif. The gene product, HSR1, was expressed and purified from Escherichia coli and was used to characterize specific DNA recognition regions upstream of two A. fulgidus genes, AF1298 and AF1971. The results indicate that AF1298 is autoregulated and is part of an operon with two downstream genes that encode a small heat shock protein, Hsp20, and cdc48, an AAA ؉ ATPase. The DNase I footprints using HSR1 suggest the presence of a cis-binding motif upstream of AF1298 consisting of CTAAC-N5-GTTAG. Since AF1298 is negatively regulated in response to heat shock and encodes a protein only distantly related to the N-terminal DNA binding domain of Phr of Pyrococcus furiosus, these results suggest that HSR1 and Phr may belong to an evolutionarily diverse protein family involved in heat shock regulation in hyperthermophilic and mesophilic Archaea organisms.

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Intracellular localization of a group II chaperonin indicates a membrane-related function

Cited by 29 publications

References 51 publications

Predicted highly expressed genes in archaeal genomes

Predicted highly expressed genes in archaeal genomes

Genome-Wide Identification of Targets for the Archaeal Heat Shock Regulator Phr by Cell-Free Transcription of Genomic DNA

Heat Shock Response ofArchaeoglobus fulgidus

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