AAA+: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes
TL;DR: Whole-genome analysis indicates that this class of proteins is ancient and has undergone considerable functional divergence prior to the emergence of the major divisions of life.
Abstract: Using a combination of computer methods for iterative database searches and multiple sequence alignment, we show that protein sequences related to the AAA family of ATPases are far more prevalent than reported previously. Among these are regulatory components of Lon and Clp proteases, proteins involved in DNA replication, recombination, and restriction (including subunits of the origin recognition complex, replication factor C proteins, MCM DNA-licensing factors and the bacterial DnaA, RuvB, and McrB proteins), prokaryotic NtrC-related transcription regulators, the Bacillus sporulation protein SpoVJ, Mg2+, and Co2+ chelatases, the Halobacterium GvpN gas vesicle synthesis protein, dynein motor proteins, TorsinA, and Rubisco activase. Alignment of these sequences, in light of the structures of the clamp loader delta' subunit of Escherichia coli DNA polymerase III and the hexamerization component of N-ethylmaleimide-sensitive fusion protein, provides structural and mechanistic insights into these proteins, collectively designated the AAA+ class. Whole-genome analysis indicates that this class is ancient and has undergone considerable functional divergence prior to the emergence of the major divisions of life. These proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. The hexameric architecture often associated with this class can provide a hole through which DNA or RNA can be thread; this may be important for assembly or remodeling of DNA-protein complexes.
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TL;DR: The significance of Hsps and chaperones in abiotic stress responses in plants is summarized, and the co-operation among their different classes and their interactions with other stress-induced components are discussed.
2,309 citations
TL;DR: This review describes the current understanding of the events of initiation of eukaryotic replication factors and how they are coordinated with cell cycle progression and emphasizes recent progress in determining the function of the different replication factors once they have been assembled at the origin.
Abstract: ▪ Abstract The maintenance of the eukaryotic genome requires precisely coordinated replication of the entire genome each time a cell divides. To achieve this coordination, eukaryotic cells use an ordered series of steps to form several key protein assemblies at origins of replication. Recent studies have identified many of the protein components of these complexes and the time during the cell cycle they assemble at the origin. Interestingly, despite distinct differences in origin structure, the identity and order of assembly of eukaryotic replication factors is highly conserved across all species. This review describes our current understanding of these events and how they are coordinated with cell cycle progression. We focus on bringing together the results from different organisms to provide a coherent model of the events of initiation. We emphasize recent progress in determining the function of the different replication factors once they have been assembled at the origin.
2,169 citations
TL;DR: Remarkably, fungi, parasites, plants, and animals have distinct subsets of Toolbox motors in their genomes, suggesting an underlying diversity of strategies for intracellular transport.
1,890 citations
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...Ad-as eukaryotes (Neuwald et al., 1999)....
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TL;DR: The ESCRT pathway can be viewed as a cargo-recognition and membrane-sculpting machine viewable from three distinct perspectives: the ESCRT proteins themselves, the cargo they sort, and the membrane they deform as mentioned in this paper.
1,189 citations
Cites background from "AAA+: A Class of Chaperone-Like ATP..."
...AAAATPases are involved in awide array of cellular processes, including membrane trafficking and fusion, DNA replication, proteolysis, and cytoskeletal reorganization (Barends et al., 2010; Neuwald et al., 1999; Striebel et al., 2009)....
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TL;DR: The structural organization of AAA+ proteins, the conformational changes they undergo, the range of different reactions they catalyse, and the diseases associated with their dysfunction are reviewed.
Abstract: The AAA+ (ATPases associated with various cellular activities) family is a large and functionally diverse group of enzymes that are able to induce conformational changes in a wide range of substrate proteins. The family's defining feature is a structurally conserved ATPase domain that assembles into oligomeric rings and undergoes conformational changes during cycles of nucleotide binding and hydrolysis. Here, we review the structural organization of AAA+ proteins, the conformational changes they undergo, the range of different reactions they catalyse, and the diseases associated with their dysfunction.
1,137 citations
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TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
70,111 citations
17,427 citations
TL;DR: This work has derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins, leading to marked improvements in alignments and in searches using queries from each of the groups.
Abstract: Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
6,553 citations
TL;DR: A new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence that performs significantly better than previous prediction schemes and can easily be applied on genome-wide data sets.
Abstract: We have developed a new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence. The method performs significantly better than previous prediction schemes and can easily be applied on genome-wide data sets. Discrimination between cleaved signal peptides and uncleaved N-terminal signal-anchor sequences is also possible, though with lower precision. Predictions can be made on a publicly available WWW server.
5,480 citations
01 Jan 1997
TL;DR: In this paper, a new method for the identification of in performance compared with the weight matrix method signal peptides and their cleavage sites based on neural (Arrigo et al., 1991; Ladunga et al, 1991; Schneider and networks trained on separate sets of prokaryotic and eukaryotic sequence.
Abstract: applicable prediction methods with significant improvements We have developed a new method for the identification of in performance compared with the weight matrix method signal peptides and their cleavage sites based on neural (Arrigo et al., 1991; Ladunga et al., 1991; Schneider and networks trained on separate sets of prokaryotic and Wrede, 1993). eukaryotic sequence. The method performs significantly better than previous prediction schemes and can easily be Materials and methods applied on genome-wide data sets. Discrimination between cleaved signal peptides and uncleaved N-terminal signal- The data were taken from SWISS-PROT version 29 (Bairoch anchor sequences is also possible, though with lower preci- and Boeckmann, 1994). The data sets were divided into sion. Predictions can be made on a publicly available prokaryotic and eukaryotic entries and the prokaryotic data sets WWW server.
5,191 citations