Biology's new Rosetta stone

Das, Sudeshna; Yu, Lean; Gaitatzes, Chrysanthe; Rogers, Robert; Freeman, Jim; Bienkowska, Jadwiga; Adams, Rhys M.; Smith, Temple F.; Lindelien, James

doi:10.1038/385029a0

Cited by 50 publications

(36 citation statements)

References 6 publications

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“…Phosphoryl transfer is the most common enzymatic function encoded by the yeast genome (12), and the reaction is catalyzed by central regulatory enzymes, such as protein kinases, ATPases, and GTPases (7). A number of aspects of the mechanism of enzyme-catalyzed phosphoryl transfer are still incompletely understood and are a source of ongoing controversy (34).…”

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confidence: 99%

Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases

et al. 2001

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Acetate kinase, an enzyme widely distributed in the Bacteria and Archaea domains, catalyzes the phosphorylation of acetate. We have determined the three-dimensional structure of Methanosarcina thermophila acetate kinase bound to ADP through crystallography. As we previously predicted, acetate kinase contains a core fold that is topologically identical to that of the ADP-binding domains of glycerol kinase, hexokinase, the 70-kDa heat shock cognate (Hsc70), and actin. Numerous charged active-site residues are conserved within acetate kinases, but few are conserved within the phosphotransferase superfamily. The identity of the points of insertion of polypeptide segments into the core fold of the superfamily members indicates that the insertions existed in the common ancestor of the phosphotransferases. Another remarkable shared feature is the unusual, epsilon conformation of the residue that directly precedes a conserved glycine residue (Gly-331 in acetate kinase) that binds the ␣-phosphate of ADP. Structural, biochemical, and geochemical considerations indicate that an acetate kinase may be the ancestral enzyme of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases.

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confidence: 99%

Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases

et al. 2001

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“…Since the proteins of Category V did not show any homology with proteins contained in the databases, many of the sequences classified in this category may be novel. It is also suspected that this category may contain a high percentage of spurious ORFs, produced by false predictions (Das et al 1997). In fact, the distribution of predicted sequence lengths indicates that both Categories IV and V, in general, have much shorter ORFs than those of the other categories (Supplemental Fig.…”

Section: Curation Of Orf Functionsmentioning

confidence: 99%

Curated genome annotation ofOryza sativassp.japonicaand comparative genome analysis withArabidopsis thaliana

Itoh¹,

Tanaka²,

Barrero³

et al. 2007

Genome Res.

220

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We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

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“…The ''gray area'' surrounding the ad hoc 100-codon boundary presents two special problems for biologists: (1) ORFs of 100-150 codons include numerous artifactual ORFs (Fickett 1995;Das et al 1997); and (2) the set of ORFs of 1-99 codons, among which the probability of being biologically meaningless is exceedingly high, nevertheless contains numerous interesting genes, which are easily missed because of the sheer number of small ORFs. To illustrate the magnitude of this problem, we plotted the total number of ORFs in the yeast genome of all lengths between 2 and 1000 codons (Fig.…”

Section: The Difficulties Of Defining Meaningful Smorfsmentioning

confidence: 99%