NAIST Division of Biological Science

Laboratories and faculty

Microbial Molecular Genetics


Prof. Shiozaki Assoc prof. Akiyama
Adjunct Professor
Associate Professor
AKIYAMA Masahiro

Outline of Research and Education

At our research group, we have been studying how genetic information is precisely transmitted from parent cells to daughter cells and, conversely, how mutation and abnormal chromosome are produced by blockage of replication progression. To approach these questions, we study molecular mechanisms of DNA replication dynamics and genomic instability. We also put strong emphasis on the international education of young students who are highly interested in basic issues related to DNA transaction (DNA replication, repair and recombination). We want to assist our laboratory members in becoming globally active individuals who act and think independently.

Major Research Topics

Replication fork movement on chromosomal DNA is intrinsically impeded by numerous natural obstacles that are the sources of cellular stress called replication stress. The chromosomal obstacles to replication include spontaneous DNA lesions, unusual DNA structures, DNA-binding proteins, RNA polymerases and depletion of nucleotide pools. Because stalled and collapsed replication forks potentially cause genomic instability, characteristics of most cancer, replication blockage is resolved by various repair mechanisms such as recombination repair, bypass DNA synthesis and template-switching (inaccurate template choice in replication). (Fig.1)

Replication fork movement on chromosomal DNA (Fig.2)

It has not been well elucidated where and how fork movement is affected globally by the natural fork barriers. To approach these questions, it is important to understand molecular dynamics of DNA replication fork on chromosome. As described in biology textbooks, basic molecular mechanisms of replication enzymes is well known. However, an overall picture of replication fork dynamics on chromosomal DNA has not been fully understood yet in any organisms. Using Escherichia coli, we study how replication fork travels on chromosome and how it copes with the replication barriers. We have recently succeeded in determining distribution of replication forks on the E. coli genome.

Genomic instability during nucleotide starvation (Fig.3)

When cells are starved for the DNA precursor dTTP, they quickly lose viability, a phenomenon named thymine-less death (TLD). Although TLD has been exploited by popular anti-cancer and bactericidal drugs such as 5-fluorouracil and trimethoprim, respectively, the precise mechanisms of genomic instability and cell lethality in TLD have not been unknown since its discovery more than 60 years ago. We study how replication inhibition by nucleotide starvation induces genomic instability and cell lethality of E. coli. We have recently found that replication fork is arrested at discreate regions near the replication origin by low levels of thymidine and thereby provoke abnormal DNA synthesis leading to genetic instability.

Fig. 1
Fig. 1 Generation and suppression of genomic instability.
Replication fork movement is inhibited by many kinds of obstacles on chromosomal DNA. Because blocked fork results in DNA damage leading to genomic instability, cells deal with replication inhibition by various repair mechanisms.
Fig. 2
Fig. 2 Distribution of replication fork on the E. coli genome.
Circles show the relative abundance of replication fork on the E. coli genome.Replication fork movement is impeded at the genomic location where the relative abundance is high. The slow replication occurs at rrn genes (blue arrows) and the regions (corresponding to red circles) proximal to the replication origin oriC (a green triangle).
Fig. 3
Fig. 3 A model for regulating replication fork movement on the E. coli genome.
We presume that the E. coli genome is programmed to pause replication near the replication origin under low levels of nucleotides and to induce genome instability when cells are starved for nucleotides.


  1. K. Uchida et al., Mol. Microbiology, 70, 608-622, 2008
  2. T.M. Pham et al., Mol. Microbiology, 90, 584-596, 2013
  3. M. Ikeda et al., Nucleic. Acid Res., 42, 8461-8472, 2014
  4. K.W. Tan et al., Nucleic. Acid Res., 43, 1714-25, 2015
  5. M.T. Akiyama et al., Genes Cells, 21, 907-914, 2016