A knowledge base for predicting protein localization sites in eukaryotic cells

Nakai, Kenta; Kanehisa, Minoru

doi:10.1016/s0888-7543(05)80111-9

Cited by 1,435 publications

(884 citation statements)

References 64 publications

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“…The presence of integral transmembrane (TM) domains was analysed with TMHMM version 2.0 (http://www.cbs.dtu.dk/services/TMHMM/) and PSORT II (http://psort.nibb.ac.jp). TMHMM predicts TM domains with a Hidden Markov Model based on the presence of hydrophobic regions of at least 18 residues (Krogh et al, 2001) and PSORT II uses the method that was described by Nakai and Kanehisa (1992) …”

Section: In Silico Analysismentioning

confidence: 99%

Genome‐wide identification of fungal GPI proteins

Groot

Hellingwerf

Klis

2003

Yeast

254

283

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Glycosylphosphatidylinositol-modified (GPI) proteins share structural features that allow their identification using a genomic approach. From the known S. cerevisiae and C. albicans GPI proteins, the following consensus sequence for the GPI attachment site and its downstream region was derived: This consensus sequence, which recognized known GPI proteins from various fungi, was used to screen the genomes of the yeasts S. cerevisiae, C. albicans, Sz. pombe and the filamentous fungus N. crassa for putative GPI proteins. The subsets of proteins so obtained were further screened for the presence of an N-terminal signal sequence for the secretion and absence of internal transmembrane domains. In this way, we identified 66 putative GPI proteins in S. cerevisiae. Some of these are known GPI proteins that were not identified by earlier genomic analyses, indicating that this selection procedure renders a more complete image of the S. cerevisiae GPI proteome. Using the same approach, 104 putative GPI proteins were identified in the human pathogen C. albicans. Among these were the proteins Gas/Phr, Ecm33, Crh and Plb, all members of GPI protein families that are also present in S. cerevisiae. In addition, several proteins and protein families with no significant homology to S. cerevisiae proteins were identified, including the cell wallassociated Als, Csa1/Rbt5, Hwp1/Rbt1 and Hyr1 protein families. In Sz. pombe, which has a low level of (galacto)mannan in the cell wall compared to C. albicans and S. cerevisiae, only 33 GPI candidates were identified and in N. crassa 97. BLAST searches revealed that about half of the putative GPI proteins that were identified in Sz. pombe and N. crassa are homologous to known or putative GPI proteins from other fungi. We conclude that our algorithm is selective and can also be used for GPI protein identification in other fungi.

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Section: In Silico Analysismentioning

confidence: 99%

Genome‐wide identification of fungal GPI proteins

Groot

Hellingwerf

Klis

2003

Yeast

254

283

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“…The deduced amino acid sequence of alfalfa mMDH (1467 bp, 343 amino acids) is similar at 86% of the positions when compared to watermelon mMDH. A putative pre-sequence of 23 amino acids is 61% similar to the watermelon mMDH targeting peptide and is predicted by the PSORT program (Nakai and Kanehisa, 1992) to direct this protein to mitochondria.…”

Section: Characterization Of Alfalfa Mdh Cdnasmentioning

confidence: 99%

Alfalfa malate dehydrogenase (MDH): molecular cloning and characterization of five different forms reveals a unique nodule‐enhanced MDH

Miller¹,

Driscoll²,

Gregerson³

et al. 1998

The Plant Journal

153

100

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SummaryMalate dehydrogenase (MDH) catalyzes the readily reversible reaction of oxaloacetate ≤ malate using either NADH or NADPH as a reductant. In plants, the enzyme is important in providing malate for C 4 metabolism, pH balance, stomatal and pulvinal movement, respiration, β-oxidation of fatty acids, and legume root nodule functioning. Due to its diverse roles the enzyme occurs as numerous isozymes in various organelles. While antibodies have been produced and cDNAs characterized for plant mitochondrial, glyoxysomal, and chloroplast forms of MDH, little is known of other forms. Here we report the cloning and characterization of cDNAs encoding five different forms of alfalfa MDH, including a plant cytosolic MDH (cMDH) and a unique novel nodule-enhanced MDH (neMDH). Phylogenetic analyses show that neMDH is related to mitochondrial and glyoxysomal MDHs, but diverge from these forms early in land plant evolution. Four of the five forms could effectively complement an E. coli Mdh -mutant. RNA and protein blots show that neMDH is most highly expressed in effective root nodules. Immunoprecipitation experiments show that antibodies produced to cMDH and neMDH are immunologically distinct and that the neMDH form comprises the major form of total MDH activity and protein in root nodules. Kinetic analysis showed that neMDH has a turnover rate and specificity constant that can account for the extraordinarily high synthesis of malate in nodules.

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“…Analysis of the NOCT orthologs in Fig. 3 using NucPred [96], cNLS Mapper [97–99], and SeqNLS [100] tools did not predict nuclear localization, whereas PSORTII [101,102] predicted nuclear localization for Drosophila, X. laevis , and D. rerio NOCTB orthologs. Mitochondrial localization is predicted for several NOCT orthologs.…”

Section: Is Noct Activity Spatially Restricted?mentioning

confidence: 99%

“…Mitochondrial localization is predicted for several NOCT orthologs. PSORTII [101,102], TargetP [103], and MitoProt [104] all predict mitochondrial localization of X. tropicalis, R. norvegicus, H. sapiens, M. musculus , and D. rerio NOCTA. TargetP and MitoProt predictions indicate that D. rerio NOCTB is likely to be mitochondrial; however, this conflicts with the nuclear localization predicted by PSORTII.…”

Section: Is Noct Activity Spatially Restricted?mentioning

confidence: 99%

Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries

2018

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Post-transcriptional control of messenger RNA (mRNA) is an important layer of gene regulation that modulates mRNA decay, translation, and localization. Eukaryotic mRNA decay begins with the catalytic removal of the 3′ poly-adenosine tail by deadenylase enzymes. Multiple deadenylases have been identified in vertebrates and are known to have distinct biological roles; among these proteins is Nocturnin, which has been linked to circadian biology, adipogenesis, osteogenesis, and obesity. Multiple studies have investigated Nocturnin’s involvement in these processes; however, a full understanding of its molecular function remains elusive. Recent studies have provided new insights by identifying putative Nocturnin-regulated mRNAs in mice and by determining the structure and regulatory activities of human Nocturnin. This review seeks to integrate these new discoveries into our understanding of Nocturnin’s regulatory functions and highlight the important remaining unanswered questions surrounding its regulation, biochemical activities, protein partners, and target mRNAs.

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A knowledge base for predicting protein localization sites in eukaryotic cells

Cited by 1,435 publications

References 64 publications

Genome‐wide identification of fungal GPI proteins

Genome‐wide identification of fungal GPI proteins

Alfalfa malate dehydrogenase (MDH): molecular cloning and characterization of five different forms reveals a unique nodule‐enhanced MDH

Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries

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