Noriko Okazaki

A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier

Several studies have addressed the importance of various ubiquitin‐like (UBL) post‐translational modifiers. These UBLs are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. In this report, we describe the identification of a novel ubiquitin‐fold modifier 1 (Ufm1) with a molecular mass of 9.1 kDa, displaying apparently similar tertiary structure, although lacking obvious sequence identity, to ubiquitin. Ufm1 is first cleaved at the C‐terminus to expose its conserved Gly residue. This Gly residue is essential for its subsequent conjugating reactions. The C‐terminally processed Ufm1 is activated by a novel E1‐like enzyme, Uba5, by forming a high‐energy thioester bond. Activated Ufm1 is then transferred to its cognate E2‐like enzyme, Ufc1, in a similar thioester linkage. Ufm1 forms several complexes in HEK293 cells and mouse tissues, revealing that it conjugates to the target proteins. Ufm1, Uba5, and Ufc1 are all conserved in metazoa and plants but not in yeast, suggesting its potential roles in various multicellular organisms.

Interaction of the Unc-51-like kinase and microtubule-associated protein light chain 3 related proteins in the brain: possible role of vesicular transport in axonal elongation.

We identified two mammalian ULK1 (Unc-51-like kinase involved in neurite extension) binding proteins by yeast two-hybrid screening. Both proteins showed high structural similarity to microtubule-associated protein (MAP) light chain 3 (LC3). One is identical to the Golgi-associated ATPase Enhancer of 16 kDa (GATE-16), an essential factor for intra-Golgi transport [39]. The other is identical to the gamma 2-subunit of GABA-A receptor associated protein (GABARAP) which has a possible role in receptor transport [46]. Using the yeast two-hybrid system and the in vitro GST pull-down assay, we found that the N-terminal proline/serine rich (PS) domain of ULK1 (amino acid 287-416) is required for ULK1-GATE-16 and ULK1-GABARAP protein interactions. However, the kinase activity of ULK1 affected neither ULK1-GATE-16 nor ULK1-GABARAP interaction. Immunohistochemical analysis using ULK1 and GABARAP antibodies showed that the ULK1 and the GABARAP proteins co-localized to many kind of neurons such as pyramidal cells of the hippocampus, mitral cells of the olfactory bulb, and Purkinje cells of the cerebellum. In HeLa cells, endogenous ULK1 and tagged GABARAP showed punctate structures in the cytosol, and were colocalized. These results suggest that the interaction of ULK1 and GABARAP is important to vesicle transport and axonal elongation in mammalian neurons.

A new cdc gene required for S phase entry of Schizosaccharomyces pombe encodes a protein similar to the cdc 10+ and SWI4 gene products.

We have isolated a new cell division cycle gene (res1+) required for entry into S phase, as a multicopy dual suppressor of the pat1 and cdc10 mutants of the fission yeast Schizosaccharomyces pombe. The res1+ gene specifies a 72 kDa protein with two copies of the cdc10/SWI6 motif. A disruptant of res1+ grows poorly at 30 degrees C with severe heat‐ and cold‐sensitivities, and completely arrests in G1 at 36 degrees C and 23 degrees C. The arrested disruptant retains a full conjugation ability. In addition to the cdc10/SWI6 motif, Res1 and SWI4 proteins share a remarkable homology in their amino‐terminal region, whereas Cdc10 and SWI6 do so in their carboxy‐terminal region. Moreover, the amino‐terminal region is essential for the function of Res1 as it is for the function of SWI4. Furthermore, analogous to the relationship of SWI4 to SWI6, the res1+ gene effectively rescues cdc10 mutants, but the cdc10+ gene cannot rescue the res1‐ phenotype. Thus, striking similarities exist in both structural and functional relationships between Res1 and SWI4, and between Cdc10 and SWI6. In view of the fact that SWI4 and SWI6 form a transcription factor complex and activate promoters containing the SWI4/SWI6 dependent cell‐cycle box, Res1 might be a putative association partner of Cdc10 which appears to be involved at least in the activation of promoters containing a MluI cell‐cycle box.

Mouse ULK2, a novel member of the UNC-51-like protein kinases: unique features of functional domains

The UNC-51 serine/threonine kinase of C. elegans plays an essential role in axonal elongation, and unc-51 mutants exhibit uncoordinated movements. We have previously identified mouse and human cDNAs encoding UNC-51-like kinase (ULK1). Here we report the identification and characterization of the second murine member of this kinase family, ULK2. Mouse ULK2 cDNA encodes a putative polypeptide of 1033 aa which has an overall 52% and 33% amino acid identity to ULK1 and UNC-51, respectively. ULKs and UNC-51 share a typical domain structure of an amino-terminal kinase domain, a central proline/serine rich (PS) domain, and a carboxy-terminal (C) domain. Northern blot analysis showed that ULK2 mRNA is widely expressed in adult tissues. In situ hybridization analysis indicated that ULK2 mRNA is ubiquitously localized in premature as well as mature neurons in developing nervous system. ULK2 gene was mapped to mouse chromosome 11B1.3 and rat chromosome 10q23 by FISH. HA-tagged ULK2 expressed in COS7 cells had an apparent molecular size of ∼150 kDa and was autophosphorylated in vitro. Truncation mutants suggested that the autophosphorylation occurs in the PS domain. Although expression of ULK2 failed to rescue unc-51 mutant of C. elegans, a series of ULK2/UNC-51 chimeric kinases revealed that function of the kinase and PS domains are conserved among species, while the C domain acts in a species-specific manner. These results suggest that ULK2 is involved in a previously uncharacterized signaling pathway in mammalian cells.

HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE

We have been developing a Human Unidentified Gene-Encoded (HUGE) protein database (http://www.kazusa.or.jp/huge) to summarize results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project. At present, HUGE contains 2031 cDNA entries (KIAA cDNAs), for each of which a gene/protein characteristic table has been prepared. Since we have been shifting our research attention from the identification and cloning of novel cDNAs to the functional analysis of the proteins encoded by these cDNAs (KIAA proteins), we have not substantially increased the number of cDNA entries in HUGE for some time. Instead, we have manually curated 451 KIAA cDNAs in order to prepare a set of genetic resources to facilitate the functional analysis of KIAA proteins. In addition, we have updated the contents of the corresponding gene/protein characteristic tables in HUGE and have constructed two subsidiary databases, HUGEppi (http://www. kazusa.or.jp/huge/ppi) and ROUGE (http://www. kazusa.or.jp/rouge), to make available the results from our study of KIAA protein function. HUGEppi shows detailed information on protein-protein interactions detected between 84 pairs of KIAA proteins by yeast two-hybrid screening. ROUGE summarizes the results of computer-assisted analyses of approximately 1000 mouse homologues of human large cDNAs that we identified.

Prediction of the Coding Sequences of Mouse Homologues of FLJ Genes: The Complete Nucleotide Sequences of 110 Mouse FLJ- Homologous cDNAs Identified by Screening of Terminal Sequences of cDNA Clones Randomly Sampled from Size-Fractionated Libraries

We have been conducting a human cDNA project to predict protein-coding sequences in long cDNAs (> 4 kb) since 1994. The number of these newly identified human genes exceeds 2000 and these genes are known as KIAA genes. As an extension of this project, we herein report characterization of cDNAs derived from mouse KIAA-homologous genes. A primary aim of this study was to prepare a set of mouse. KIAA-homologous cDNAs that could be used to analyze the physiological roles of KIAA genes in mice. In addition, comparison of the structures of mouse and human KIAA cDNAs might enable us to evaluate the integrity of KIAA cDNAs more convincingly. In this study, we selected mouse KIAA-homologous cDNA clones to be sequenced by screening a library of terminal sequences of mouse cDNAs in size-fractionated libraries. We present the entire sequences of 100 cDNA clones thus selected and predict their protein-coding sequences. The average size of the 100 cDNA sequences reached 5.1 kb and that of mouse KIAA-homologous proteins predicted from these cDNAs was 989 amino acid residues.

Novel Factor Highly Conserved among Eukaryotes Controls Sexual Development in Fission Yeast

ABSTRACT In the fission yeast Schizosaccharomyces pombe, the onset of sexual development is controlled mainly by two external signals, nutrient starvation and mating pheromone availability. We have isolated a novel gene named rcd1+ as a key factor required for nitrogen starvation-induced sexual development.rcd1 + encodes a 283-amino-acid protein with no particular motifs. However, genes highly homologous torcd1 + (encoding amino acids with >70% identity) are present at least in budding yeasts, plants, nematodes, and humans. Cells with rcd1 + deleted are sterile if sexual development is induced by nitrogen starvation but fertile if it is induced by glucose starvation. This results largely from a defect in nitrogen starvation-invoked induction ofste11 +, a key transcriptional factor gene required for the onset of sexual development. The striking conservation of the gene throughout eukaryotes may suggest the presence of an evolutionarily conserved differentiation controlling system.

The Novel Protein Complex with SMARCAD1/KIAA1122 Binds to the Vicinity of TSS

The SMARCAD1/KIAA1122 protein is structurally classified into the SWI2/SNF2 superfamily of DNA-dependent ATPases that are catalytic subunits of chromatin-remodeling complexes. Although the importance of other members of the SWR1-like subfamily in chromatin remodeling (EP400, INOC1, and SRCAP) has already been elucidated, the biological function of SMARCAD1/KIAA1122 in transcriptional regulation remains to be clarified. To gain insight into the role of this protein, we generated a specific antibody against SMARCAD1/KIAA1122 and used it for chromatin and protein immunoprecipitation assays. We employed high-resolution genome tiling microarrays in chromatin immunoprecipitation and found the binding sites of SMARCAD1/KIAA1122 in the vicinity of the transcriptional start site of 69 candidate target genes. In the protein immunoprecipitation assay, we found that endogenous SMARCAD1/KIAA1122 binds with TRIM28, a recently highlighted transcriptional regulator in the cancer field. From these findings, we propose a novel model for gene regulation via the SMARCAD1/KIAA1122 protein complex.