Yasuhiro Anraku

Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts

VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of Saccharomyces cerevisiae. There have been two independent subfamilies of VDE, one from S. cerevisiae strain X2180‐1A and the other from Saccharomyces sp. DH1‐1A in the host VMA1 gene, and they share the identity of 96.3%. In order to search the occurrence, intra/interspecies transfer and molecular degeneration of VDE, complete sequences of VMA1 in 10 strains of S. cerevisiae, eight species of saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were determined. We found that six of 10 S. cerevisiae strains contain VDEs 99.7–100% identical to that of the strain X2180‐1A, one has no VDE, whereas the other three harbour VDEs 100% identical to that of the strain DH1‐1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that of the strain X2180‐1A with VDE 100% identical to that of the strain DH1‐1A and the other containing the same VMA1 in S. pastorianus with no VDE. This and other evidence indicates that intra/interspecies transmissions of VDEs have occurred among saccharomycete yeasts. Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs had branched earlier than other VDEs from an ancestral VDE and had invaded into the host loci as relatively late events. The two VDEs seemed to degenerate in individual host loci, retaining their splicing capacity intact. The degeneration of the endonuclease domains was distinct and, if compared, its apparent rate was much faster than that of the protein‐splicing domains. The VMA1 gene sequences determined in this study have been deposited in the GenBank data library under the Accession Nos shown in Table 1 . Copyright

Protein splicing: its discovery and structural insight into novel chemical mechanisms.

Protein splicing is a posttranslational cellular process, in which an intervening protein sequence (intein) is self‐catalytically excised out from a nascent protein precursor and the two flanking sequences (N‐ and C‐exteins) are ligated to produce two mature enzymes. This unique reaction was first discovered from studies of the structure and expression of the VMA1 gene in Saccharomyces cerevisiae. VMA1 consists of a single open reading frame and yet comprises two independent genetic information for Vma1p (a catalytic 70‐kDa subunit of the vacuolar H + ‐ATPase) and VDE (a 50‐kDa DNA endonuclease) as an in‐frame spliced insert in the gene. Subsequent studies have demonstrated that protein splicing is not unique for the VMA1 precursor and there are many operons in nature, which implement genetic information editing at protein level. To elucidate its precise reaction mechanisms from a viewpoint of structure‐directed chemistry, a series of crystal structural studies has been carried out with the use of splicing‐inactive and slowly spliceable precursors of VMA1 recombinants. One precursor structure revealed that the N‐terminal junction of the introduced extein polypeptide forms an intermediate containing a five‐membered thiazolidine ring. The other precursor structures showed spliced products with a linkage between the N‐ and C‐extein segments. This article summarizes biochemical and structural studies on a self‐catalytic mechanism for protein splicing that is triggered and terminated solely via thiazolidine intermediates with tetrahedral configurations formed within the splicing sites where proton ingress and egress are driven by balanced protonation and deprotonation. IUBMB Life, 57: 563‐574, 2005

Homing at an extragenic locus mediated by VDE (PI‐SceI) in Saccharomyces cerevisiae

PI‐SceI (VDE), a homing endonuclease with protein splicing activity, is a genomic parasite in the VMA1 gene of Saccharomyces cerevisiae. In a heterozygous diploid of the VDE‐less VMA1 allele and a VDE‐containing VMA1 allele, VDE specifically cleaves its recognition sequence (VRS) in the VDE‐less VMA1 allele at meiosis, followed by ‘homing’, i.e. a conversion to a VDE‐containing allele. We found that upon VDE expression, homing of a marker gene at an extragenic locus occurs only when a 45 bp element containing the VRS is inserted at its allelic site, while mutants of VDE with no endonuclease activity lack authentic extragenic homing activity. Thus, both the VRS and VDE are required for homing. Insertion of the VRS in a homozygous diploid significantly lowered the spore germination ability, indicating that a template for gene repair at its allelic locus is essential for efficient homing and survival of yeast cells. Copyright

Schizosaccharomyces pombe stt3+ is a functional homologue of Saccharomyces cerevisiae STT3 which regulates oligosaccharyltransferase activity

The Saccharomyces cerevisiae STT3 (ScSTT3) gene encodes a protein which is involved in protein glycosylation via the regulation of oligosaccharyltransferase activity. We have cloned and isolated the Schizosaccharomyces pombe STT3 homologous gene (Spstt3+). The Spstt3+ gene encodes a protein consisting of 749 amino acid residues which has significant homology with ScStt3p and the mouse Stt3p‐homologue Itm1p. Disruption of the Spstt3+ gene shows that this gene is essential for growth. Like Itm1, Spstt3+ partially suppressed the temperature sensitivity of the stt3‐1 mutation of S. cerevisiae, indicating that Spstt3+ is a functional and structural homologue of the ScSTT3 gene. The nucleotide sequence data reported in this paper appears in the DDBJ/EMBL/GenBank nucleotide sequence database with Accession No. AB015232. Copyright

Thirty‐Three Years of The Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) (1972 ‐ 2005)

My official duty as a member (1997 – 2003) of the IUBMB Executive Committee (EC) was to act as a liaison with ICSU (International Council for Science) and to establish bridges with other International Scientific Unions for joint activities and interdisciplinary cooperation (1). This portfolio was established in 1982 and abolished in 2003. I was also the liaison member for the EC to the Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB). On the occasion of commemorating the jubilee of the IUBMB, I would like to write with pleasure a brief history of the FAOBMB. The FAOBMB is one of the Associated Organizations of the IUBMB and was the first regional association in biochemistry to focus on its promotion and development in the Asian and Oceanian regions. The brief history says that it was in mid July, 1972 when three biochemists, Professors Edwin C. Webb, N. R. Mougdal, and Takashi Murachi as delegates of the Australian Biochemical Society, the Indian Society of Biological Chemists, and the Japanese Biochemical Society, respectively, conferred in Adelaide, Australia with Professor W. H. Elliot in attendance. They deliberated on the matter of founding a Federation of Asian and Oceanian Biochemists (FAOB) and decided that the FAOB was jointly founded by the three members on 1 August 1972. The membership grew rapidly and there are now 20 adhering societies, from Australia, Bangladesh, China, Hawaii, Hong Kong, India, Indonesia, Iran, Japan, Korea, Malaysia, Myanmar, Nepal, New Zealand, Pakistan, Philippines, Singapore, Taipei China, Thailand, and Viet Nam. On 8 December 1992, the Federation became officially incorporated as a non-profit, tax-exempt association (FAOB, Inc.) in Melbourne, Australia and undertook a change in name to the Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB, Inc.). The Federation’s logo, adopted in 1989 and modified in 1993 to include the change in name, reflects the dynamic nature of FAOBMB and the continual flow of information in biochemistry and molecular biology among the member societies. The motto of FAOBMB is ‘a Federation that exists for and exists through the cooperation of its Constituent Members’. The governance of the Federation is conducted by a FAOBMB Council represented by one delegate from each Constituent Member and four Executive Officers. The Officers are President, Secretary-General, Treasurer and President-Elect or Immediate Past President. Two delegates, elected by the Council, serve as the Chairpersons of the Education Committee and of the Travel Fellowships Committee. Since its founding 33 years ago, the FAOBMB has developed steadily, playing an important catalytic role in stimulating life sciences in countries of the region and working in close association with the IUBMB in support of their common goals (see Table 1). Presently, the Federation’s 20 Constituent Members represent in excess of 20,000 active scientists with some 20 Special Members and three distinguished Honorary Members. The member societies are heterogeneous in respect of their history and academic capability, yet share equal partnership and responsibility in governance and the decision-making process. For example, the Japanese Biochemical Society has 11,000 biochemists and 80 years of history in 2005, while the smallest groups such as Nepal andMyanmar have only 20 – 40 members and have been in existence for less than 20 years. Only 10 of the FAOBMB Constituent Members are Adhering Bodies to the IUBMB and five are Associate Adhering Bodies. The organization and the activities of the other five societies/groups are immature at present, but the FAOBMB Council is encouraging them to apply for the IUBMB Membership in the near future. The FAOBMB began sponsoring its own scientific meetings in 1977. FAOBMB Congresses, organized triennially, and FAOBMB Symposia, held in intervening years, are major scientific activities, which are co-hosted by a local society or group and sponsored by the IUBMB (Table 2). A Congress, 1,000 – 2,000 participants in size, is a gathering for discussing and presenting major topics in biochemistry and molecular biology and has become a main event in the biochemical calendar of the region. A Symposium, with 100 – 300 Received 13 December 2004; accepted 9 March 2005 Address correspondence to: Yasuhiro Anraku, Department of Biosciences, Teikyo University of Science and Technology, Uenohara, Yamanashi 409-0193, Japan. E-mail: anraku@ntu.ac.jp IUBMBLife, 57(4/5): 231 – 233, April/May 2005