Research

I am interested in understanding how genetic entities called species are maintained or change in unicellular organisms by studying population evolution and the survival strategy of bacteria. My research addresses fundamental questions regarding sexual reproduction in prokaryotes and molecular mechanisms that support the persistence of prokaryotic mobile DNA elements. 

Local diversification of Mycobacterium avium complex (MAC)

MAC is a group of opportunistic human pathogens belonging to the genus Mycobacteria. MAC is known to reside in nature, for example, rivers, soil, and even in shower rooms. Comparative genomics studies have revealed that MAC conducts chromosomal recombination frequently in the evolutionary time scale unlike human-adapted Mycobacterium tuberculosis, which is thought to have spread over the world largely through clonal expansion. The evolutionary pattern of free-living environmental bacterial species has been largely unknown. Using MAC population as a model of free-living bacterial species, I address how bacterial lineage emerges (bacteria speciate), and how chromosomal recombination contributes to local adaptation. I also aim to identify chromosomal loci responsible for its virulence, antibiotic resistance, and niche adaption using the bioinformatic approach to provide clues for the prevention of MAC-associated infectious diseases.

Persistence of mobile DNA

Mobile genetic elements (MGE) such as plasmids and transposons are known as major players in the spread of antibiotic resistance to human pathogens.  My current research put emphasis on clarifying the DNA strand-exchange pathway used in the transposition of a recently discovered mobile DNA group, SE (Strand-biased circularizing integrative Elements), and tracing the evolution of SEs in clinical and environmental bacterial populations.

Publications

1. Yano H, Hayashi W, Kawakami S, Aoki S, Anzai E, Zuo H, Kitamura N, Hirabayashi A, Kajihara T, Kayama S, Sugawara Y, Yahara K, and Sugai M. Nationwide genome surveillance of carbapenem resistant Pseudomonas aeruginosa in Japan.  Antimicrob Agents Chemother 68(5):e01669-23 (2024) [Full Text] 

2. Kitamura N, Kajihara T, Volpiano CG, Naung M, Guillaume Méric G, Hirabayashi A, Yano H, Yamamoto M, Yoshida F, Kobayashi T, Yamanashi S, Kawamura T,  Matsunaga N, Okochi J, Sugai M, and Yahara K. Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing.  Microb. Genom. 10(2):001180 (2024). [Full Text]

3. Yano H, Suzuki M, and Nonaka L. Mobile classA beta-lactamase gene blaGMA-1. Microbiol. Spectr. 12:1. e02589-23 (2024)  [Full Text]

4. Idola D, Mori H, Nagata Y, Nonaka L, and Yano H. Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria. Mobile DNA 14: 7 (2023) [Full Text]

5. Komatsu T, Ohya K, Ota A, Nishiuchi Y, Yano H, Matsuo K, Odoi JO, Suganuma S, Sawai K, Hasebe A, Asai T, Yanai T, Fukushi H, Wada T, Yoshida S, Ito T, Arikawa K, Kawai M, Ato M, Baughn AD, Maruyama F. Unique genomic sequences in a novel Mycobacterium avium subsp. hominissuislineage enable fine scale transmission route tracing during pig movement. One Health 16. 100559 (2023)[Full Text]

6. Nonaka L, Masuda M, and Yano H. Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis. PLoS ONE 17(8): e0271627(2022) [Full Text]

7. Komatsu T, Ohya K, Ota A, Nishiuchi Y, Yano H, Matsuo K, Odoi JO, Suganuma S, Sawai K, Hasebe A, Asai T, Tokuma Yanai T, Fukushi H, Wada T, Yoshida S, Ito T, Arikawa K, Kawai M, Ato M, Baughn AD, Iwamoto T, and Maruyama F. Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan. Gigabyte. 1. (2021) [Full Text]

8. Tuan VP, Yahara K, Dung HDQ, Binh TT, Huu Tung P, Tri TD, Thuan NPM, Khien VV, Trang TTH, Phuc BH, Tshibangu-Kabamba E, Matsumoto T, Akada J, Suzuki R, Okimoto T, Kodama M, Murakami K, Yano H, Fukuyo M, Takahashi N, Kato M, Nishiumi S, Azuma T, Ogura Y, Hayashi T, Toyoda A, Kobayashi I, and Yamaoka Y. Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates. Microb. Genom. 7: 000680 (2021) [Full Text]

9. Yano H, Alam MZ, Rimbara E, Shibata TF, Fukuyo M, Furuta Y, Nishiyama T, Shigenobu S, Hasebe M, Toyoda A, Suzuki Y, Sugano S, Shibayama K, and Kobayashi I. Networking and specificity-changing DNA methyltransferease in Helicobacter pylori. Front. Microbiol. 11:1628 (2020) [Full Text]

10. Stalder T, Cornwell B, Lacroix J, Kohler B, Dixon S, Yano H, Kerr B, Forney LJ, and Top EM. Evolving populations in biofilms contain more persistent plasmids.  Mol. Biol. Evol.  37: 1563-1576 (2020) [Full text]  

11. Inaba S, Sakai H, Kato H, Horiuchi T, Yano H, Ohtsubo Y, Tsuda M, and Nagata Y. Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions . Microbiology. 166:531-545 (2020)   [Full Text]

12. Yano H, Suzuki H, Maruyama F, and Iwamoto T. The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium. BMC Genomics. 20:752. (2019)   [Full text]

13. Arikawa K, Ichijo T, Nakajima S, Nishiuchi Y, Yano H, Tamaru A, Yoshida S, Maruyama F, Ota A, Nasu M, Starkova DA, Mokrousov I, Narvskaya OV, and Iwamoto T.  Genetic relatedness of Mycobacterium avium subsp. hominissuis isolates from bathrooms of healthy volunteers, rivers, and soils in Japan with human clinical isolates from different geographical areas. Infect. Genet. Evol. 73: 103923 (2019). [Full text]

14. Yano H, Shintani M, Tomita M, Suzuki H, and Oshima T. Reconsidering plasmid maintenance factors for computational plasmid design. Comput. Struct. Biotechnol. J. 17: 70-81 (2019) [Full text]

15. Nonaka L, Yamamoto T,  Maruyama F, Hirose Y, Onishi Y, Kobayashi T, Suzuki S, Nomura N, Masuda M, and Yano H. Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate. PLoS ONE 13: e0198613 (2018)  [Full text]

16. Miyazaki R*, Yano H*, Sentchilo V, and Van der Meer JR. Physiological and transcriptome changes induced by Pseudomonas putida acquisition of an integrative and conjugative element. Scientific Rep. 8: 5550 (2018) [Full Text] *Equal contribution

17. Yano H, Iwamoto T, Nishiuchi Y, Nakajima C, Starkova DA, Mokrousov I, Narvskaya O, Yoshida S, Arikawa K, Nakanishi N, Osaki K, Nakagawa I, Ato M, Suzuki Y, and Maruyama F. Population structure and local adaptation of MAC lung disease agent Mycobacterium avium subsp. hominissuis. Genome Biol. Evol. 9: 2403-2417 (2017) [Full Text]

18. Stalder T, Rogers LM, Renfrow C, Yano H, Smith Z. and Top EM. Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance. Scientific Rep. 7: 4588 (2017) [Full Text]

19. Zhang Y, Matsuzaka T, Yano H, Furuta Y, Nakano T, Ishikawa K, Fukuyo M, Takahashi N, Suzuki Y, Sugano S, Ide H, and Kobayashi I. Restriction glycosylases: involvement of endonuclease activities in the restriction process.  Nucleic Acids Res. 45: 1392-1403 (2017). [Full Text]

20. Yano H, Wegrzyn K, Loftie-Eaton W, Johnson J, Deckert GE, Rogers LM, Konieczny I, and Top EM. Evolved plasmid-host interactions reduce plasmid interference cost. Mol. Microbiol. 101:743- 756 (2016). [Full Text]

21. Loftie-Eaton W, Yano H, Burleigh S, Simmons RS,  Hughes JM, Rogers LM, Hunter SS., Settles LM, Forney LJ,  Ponciano JM, and Top  EM. Evolutionary paths that expand plasmid host-range: implications for spread of antibiotic resistance. Mol. Biol. Evol. 33: 885-897 (2016). [Full Text]

22. Fukuyo M, Nakano T, Zhang Y, Furuta Y, Ishikawa K, Watanabe-Matsui M, Yano H, Hamakawa T, Ide H, and Kobayashi I. Restriction-modification system with methyl-inhibited base excision and abasic- site cleavage activities. Nucleic Acids Res. 43: 2841-2852 (2015). [Full Text]

23. Hunter SS, Yano H, Loftie-Eaton W, Hughes J, De Gelder L, Stragier P, De Vos P, Settles ML, and Top EM. Draft Genome Sequence of Pseudomonas moraviensis R28-S. Genome Announc. 2: e00035- 14 (2014). 

24. Yano H, Rogers LM, Molly K, Heuer H, Smalla K, Brown CJ, and Top EM. Diversification of host range within the IncP-1 plasmid group. Microbiology. 159: 2303-2315 (2013). [Full Text]

25. Brown CJ, Sen D., Yano H, Bauer ML, Rogers LM, Van der Auwera GA, and Top EM. Diverse broad-host-range plasmids from freshwater carry few accessory genes. Appl. Environ. Microbiol. 79: 7684-7695 (2013). [PubMed]

26. Yano H, Genka H, Ohtsubo Y, Nagata Y, Top EM, and Tsuda M. Cointegrate-resolution of toluene-catabolic transposon Tn4651: determination of crossover site and the segment required for full resolution activity. Plasmid 69, 24-35 (2013). [PubMed]

27. Król JE, Penrod JT, McCaslin H, Rogers LM, Yano H, Stancik A, Dejonghe W, Brown CJ, Parales RE, Wuertz S, and Top EM. Genomic and functional analysis of the IncP-1β plasmids pWDL7::rfp and pNB8c explains their role in chloroaniline catabolism. Appl. Environ. Microbiol. 78, 828-838 (2012). [PubMed]

28. Yano H, Deckert GE, Rogers LM, and Top EM. Roles of long and short replication initiation proteins in the fate of broad host range IncP-1 plasmids. J. Bacteriol. 194, 1533-1543 (2012). [PubMed]

29. Suzuki H, Yano H, Brown CJ, and Top EM. Predicting plasmid promiscuity based on genomic signature. J. Bacteriol. 192, 6045-6055 (2010). [PubMed]

30. Sen D, Yano H, Suzuki H, Król JE, Rogers LM, Brown CJ, and Top EM. Comparative genomics of pAKD4, the prototype IncP-1δ plasmid with a complete backbone. Plasmid 63, 98-107 (2010). [PubMed]

31. Sota M*, Yano H*, Hughes JM, Daughdrill GW, Abdo Z, Forney LJ, and Top EM. Shifts in host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J. 4, 1568- 1580 (2010). * Equal contribution. [PubMed]

32. Yano H, Miyakoshi M, Ohshima K, Tabata M, Nagata Y, Hattori M, and Tsuda M. Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J. Bacteriol. 192, 4337-4347 (2010). 

33. Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H, Sota M, Ohtsubo Y, Tsuda M, and Miyazaki K. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J. 12, 1335-1348 (2009). 

34. Yano H, Garruto CE, Sota M, Ohtsubo Y, Nagata Y, Zylstra GJ, Williams PA, and Tsuda M. Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elements. J. Mol. Biol. 369, 11-26 (2007). 

35. Sota M, Tsuda M, Yano H, Forney LJ, and Top EM. Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids. J. Bacteriol. 189, 3091-3098 (2007).

36. Sota M, Yano H, Ono A, Miyazaki R, Ishii H, Genka H, Top EM, and Tsuda M. Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J. Bacteriol. 188, 4057-4067 (2006). 

37. Shintani M, Yano H, Habe H, Omori T, Yamane H, Tsuda M, and Nojiri H. Characterization of the replication, maintenance, and transfer features of the IncP-7 plasmid pCAR1, which carries genes involved in carbazole and dioxin degradation. Appl. Environ. Microbiol. 72, 3206-3216 (2006).

38. Sota M, Yano H, Nagata Y, Ohtsubo Y, Genka H, Anbutsu H, Kawasaki H, and Tsuda M. Functional analysis of unique class II insertion sequence IS1071. Appl. Environ. Microbiol. 72, 291-297 (2006).