Publications

[3] Miichi S, Shimamura D, Yasuda J, Tokutsu R, Yamano T^＊

A CO₂-limitation-induced cytosolic repressor enables shutdown of the algal CO₂-concentrating mechanism.

bioRxiv

We discovered that the cytosolic factor HCR1 is a second repressor that shuts down the algal CO₂-concentrating mechanism. This study follows Shimamura et al., PNAS 2026.

[2] Matsuo K and Yamano T^＊

Unsupervised machine-learning identifies latent pyrenoid states linked to mitotic remodeling defects and CO₂-dependent growth.

bioRxiv

We combined machine learning with live imaging to study links between subtle shape abnormalities in a phase-separated organelle, its remodeling during cell division, and CO₂-dependent growth.

[1] Kanazawa H, Takusagawa M, Shimamura D, Kinoshita Y, Nishiyama T, Tokutsu R, Onishi M, Shikanai T, Yamano T, Nishimura Y^＊ Collaboration

MITH1 promotes biased positioning of chloroplast nucleoids linked to localized rbcL expression and pyrenoid biogenesis in Chlamydomonas reinhardtii.

SSRN

[4] Shin S, Choi BY, Song J, Je S, Roh Y, Kim E, Yamano T, Li-Beisson Y, Shim D, Yamaoka Y^＊ Collaboration

Medium acidification and redox imbalance drive triacylglycerol hyperaccumulation in Chlorella sorokiniana.

Bioresour Technol. in press

[3] Shimamura D and Yamano T^＊ Method paper

Routine Isolation of Random Insertion Mutants in Cell-Walled Chlamydomonas reinhardtii by Electroporation of an AphVII Hygromycin-Resistance Cassette.

Methods Mol Biol. in press

We describe how to transform green algae with intact cell walls using square-wave pulse electroporation.

[2] Shimamura D and Yamano T^＊ Open access Review paper

Regulatory Logic of the Chlamydomonas CO₂-Concentrating Mechanism: Coupling Carbon Flux, Energy Supply, and Pyrenoid Architecture.

Front Plant Sci. 2026 July 8;17:1882169.

DOI PubMed Zenodo

We reviewed the CO₂-concentrating mechanism in the green alga Chlamydomonas, bringing together carbon flow, energy supply, pyrenoid structure, and regulatory networks.

[1] Shimamura D, Yasuda J, Yamahara Y, Nakano H, Ozawa S, Tokutsu R, Yamagami A, Matsushita T, Takahashi Y, Nakano T, Fukuzawa H, Yamano T^＊ Open access

A nuclear CobW/WW-domain factor represses the CO₂-concentrating mechanism in the green alga Chlamydomonas reinhardtii.

Proc Natl Acad Sci USA.2026 Feb 10;123(6):e2518136123.

DOI PubMed bioRxiv Press release Kyoto University repository

We discovered CBP1, a nuclear repressor that helps cells save energy by controlling the CO₂-concentrating mechanism in aquatic photosynthesis.

[4] Opinion

Japan can be a science heavyweight once more — if it rethinks funding

Nature 2025 Feb;638(8050):318-320.

DOI PubMed

An opinion article co-signed by 138 Japanese researchers that identifies problems in Japan's science and technology policy and proposes solutions.

[3] Yamano T^＊ Open access Review paper

Algal Pyrenoids in Global Carbon Cycling: Frontier Research on Structure, Function, and Convergent Evolution

Algal Science and Technology 18(1):13-25

DOI

We reviewed the molecular basis and evolutionary significance of the pyrenoid, an algal CO₂-concentrating organelle involved in about one-third of global carbon cycling.

[2] Yamaoka Y^＊, Petroutsos D, Je S, Yamano T, Li-Beisson Y Review paper

Light, CO₂, and carbon storage in microalgae

Curr Opin Plant Biol. 2025 Feb 20:84:102696.

DOI PubMed

A review of how interactions between light and CO₂ affect carbon metabolism in microalgae.

[1] Shimamura D, Matsuda A, Yamano T^＊ Review in Japanese

Extracellular carbonic anhydrase enhances CO₂ uptake in green algae

Bioscience and Industry (B&I) 2025 83(2):1320133

A commentary on Shimamura et al., Plant Physiol. 2024, which clarified the role of extracellular carbonic anhydrase.

[3] Shimamura D, Ikeuchi T, Matsuda A, Tsuji Y, Fukuzawa H, K Mochida, Yamano T^＊ Open access

Periplasmic carbonic anhydrase CAH1 contributes to high inorganic carbon affinity in Chlamydomonas reinhardtii

Plant Physiol. 2024 Dec 2;196(4):2395-2404.

DOI PubMed bioRxiv Press release

We clarified the role of carbonic anhydrase CAH1 in the CO₂-concentrating mechanism, resolving a debate that had lasted for 40 years.

[2] Matsuo K, Yamano T^＊ Review in Japanese

The molecular basis of a CO₂-concentrating organelle involved in the function and regulation of aquatic photosynthesis

Agri-Bio, July 2024 Special Issue

[1] Yamano T^＊ Review in Japanese

Pyrenoids and the CO₂-concentrating mechanism in green algae

In "Current Status and Future Prospects of Microalgal Bioproduction", Agri-Bio, February 2024 Issue

[5] Yamano T^＊ Review in Japanese

The CO₂-concentrating mechanism in cyanobacteria

In "Technologies for CO₂ Utilization by Autotrophic Bacteria", Part II, Chapter 18, pp.227-232. CMC Publishing, published December 13, 2023

[4] Yoshizawa S^＊, Azuma T, Kojima K, Inomura K, Hasegawa M, Nishimura Y, Kikuchi M, Armin G, Tsukamoto Y, Miyashita H, Ifuku K, Yamano T, Marchetti A, Fukuzawa H, Sudo Y, Kamikawa R Award Collaboration

Light-driven proton pumps as a potential regulator for carbon fixation in marine diatoms

Microbes Environ. 2023;38(2):ME23015.

DOI PubMed

In collaboration with the Yoshizawa lab at the University of Tokyo, we proposed a theoretical model in which local acidic pools generated by light-driven H⁺ transport through microbial rhodopsins promote CO₂ fixation. This paper received the 2023 M&E Paper Award.

[3] Yamano T^＊ Review in Japanese

Understanding the green algal pyrenoid as a phase-separated CO₂-concentrating organelle

Plant Morphology 35: 3-8 (2023)

DOI

A review of the molecular mechanisms of the CCM, focusing on the model green alga Chlamydomonas.

[2] Yamano T^＊, Hirakawa Y, Matsuzaki R Review in Japanese

Pyrenoids: The Cutting Edge of Plant Phase-Separated Organelles

Plant Morphology 35: 1-2 (2023)

DOI

An overview of the symposium "Pyrenoids: The Cutting Edge of Plant Phase-Separated Organelles" at the 86th Annual Meeting of the Botanical Society of Japan.

[1] Shimamura D, Yamano T^＊, Niikawa Y, Donghui H, Fukuzawa H

A pyrenoid-localized protein SAGA1 is necessary for Ca²⁺-binding protein CAS-dependent expression of nuclear genes encoding inorganic carbon transporters in Chlamydomonas reinhardtii

Photosynth Res. 2023 May;156(2):181-192.

DOI PubMed

Based on analyses of pyrenoid-deficient mutants, we proposed that the pyrenoid is one source of retrograde signals from the chloroplast to the nucleus.

[5] Gururaj M, Ohmura A, Ozawa M, Yamano T, Fukuzawa H, Matsuo T^＊ Open access Collaboration

A potential EARLY FLOWERING 3 homolog in Chlamydomonas is involved in the red/violet and blue light signaling pathways for the degradation of RHYTHM OF CHLOROPLAST 15

PLoS Genet. 2022 Oct 17;18(10):e1010449.

DOI PubMed

[4] Tsuji Y^＊, Kinoshita A, Tsukahara M, Ishikawa T, Shinkawa H, Yamano T, Fukuzawa H^＊

A YAK1-type protein kinase, triacylglycerol accumulation regulator 1, in the green alga Chlamydomonas reinhardtii is a potential regulator of cell division and differentiation into gametes during photoautotrophic nitrogen deficiency

J Gen Appl Microbiol. 2023 Jun 22;69(1):1-10.

DOI PubMed

We showed that the well-known role of DYRK in promoting differentiation through cell division control is conserved in green algae under photoautotrophic, nitrogen-deficient conditions.

[3] Mei NL, Komaki S, Takahashi H, Yamano T, Fukuzawa H, Hashimoto T^＊ Open access Collaboration

Hyperosmotic stress-induced microtubule disassembly in Chlamydomonas reinhardtii

BMC Plant Biol. 2022 Jan 22;22(1):46.

DOI PubMed

[2] Choi BY, Kim H, Shim D, Jang S, Yamaoka Y, Shin S, Yamano T, Kajikawa M, Jin E, Fukuzawa H^＊, Lee Y^＊ Collaboration

The Chlamydomonas bZIP transcription factor BLZ8 confers oxidative stress tolerance by inducing the carbon-concentrating mechanism

Plant Cell 2022 Feb 3;34(2):910-926.

DOI PubMed Press release

We showed that a bZIP transcription factor provides resistance to oxidative stress by regulating the expression of inorganic carbon transporters and carbonic anhydrases involved in the CCM.

[1] Yamano T^＊, Toyokawa C, Shimamura D, Matsuoka T, Fukuzawa H Open access

CO₂-dependent migration and relocation of LCIB, a pyrenoid-peripheral protein in Chlamydomonas reinhardtii

Plant Physiol. 2022 Feb 4;188(2):1081-1094.

DOI PubMed Press release

We revealed how changes in chloroplast protein localization help maintain aquatic photosynthesis under changing conditions. This work was featured in Nikkei Sangyo Shimbun.

[1] Tsuji Y, Kusi-Appiah G, Kozai N, Fukuda Y, Yamano T, Fukuzawa H^＊

Characterization of a CO₂-Concentrating Mechanism with Low Sodium Dependency in the Centric Diatom Chaetoceros gracilis.

Mar Biotechnol (NY). 2021 Jun;23(3):456-462.

DOI PubMed

We showed that the CCM of the commercially useful diatom Chaetoceros gracilis has a low dependence on sodium and can function even in a medium without sodium salts.

[6] Kato-Minoura T^＊, Ogiwara Y, Yamano T, Fukuzawa H, Kamiya R Open access Collaboration

Chlamydomonas reinhardtii tubulin-gene disruptants for efficient isolation of strains bearing tubulin mutations.

PLoS One. 2020 Nov 23;15(11):e0242694.

DOI PubMed

[5] Yamano T Review in Japanese

Pyrenoids: CO₂-concentrating structures in photosynthesis

In The Full Picture of Phase Separation Biology, edited by Shiraki K. Tokyo Kagaku Dojin

[4] Nitta N, Iino T, Isozaki A, Yamagishi M, Kitahama Y, Sakuma S, Suzuki Y, Tezuka H, Oikawa M, Arai F, Asai T, Deng D, Fukuzawa H, Hase M, Hasunuma T, Hayakawa T, Hiraki K, Hiramatsu K, Hoshino Y, Inaba M, Inoue Y, Ito T, Kajikawa M, Karakawa H, Kasai Y, Kato Y, Kobayashi H, Lei C, Matsusaka S, Mikami H, Nakagawa A, Numata K, Ota T, Sekiya T, Shiba K, Shirasaki Y, Suzuki N, Tanaka S, Ueno S, Watarai H, Yamano T, Yazawa M, Yonamine Y, Di Carlo D, Hosokawa Y, Uemura S, Sugimura T, Ozeki Y, Goda K^＊ Open access Collaboration

Raman image-activated cell sorting

Nat Commun. 2020 Jul 10;11(1):3452.

DOI PubMed

[3] Toyokawa C, Yamano T, Fukuzawa H^＊ Open access

Pyrenoid Starch Sheath Is Required for LCIB Localization and the CO₂-Concentrating Mechanism in Green Algae.

Plant Physiol. 2020 Apr;182(4):1883-1893.

DOI PubMed Press release Press release

We established the importance of the starch sheath surrounding the pyrenoid for the CCM.

[2] Yamano T, Fukuzawa H^＊

Transformation of the Model Microalga Chlamydomonas reinhardtii Without Cell-Wall Removal.

Methods Mol Biol. 2020;2050:155-161.

DOI PubMed Kyoto University repository

[1] Jang S, Kong F, Lee J, Choi BY, Wang P, Gao P, Yamano T, Fukuzawa H, Kang BH, Lee Y^＊ Open access Collaboration

CrABCA2 Facilitates Triacylglycerol Accumulation in Chlamydomonas reinhardtii under Nitrogen Starvation.

Mol Cells. 2020 Jan 31;43(1):48-57.

DOI PubMed

[6] Hidayati NA, Yamada-Oshima Y, Iwai M, Yamano T, Kajikawa M, Sakurai N, Suda K, Sesoko K, Hori K, Obayashi T, Shimojima M, Fukuzawa H, Ohta H^＊ Open access Collaboration

LIPID REMODELING REGULATOR 1 (LRL1) Is Differently Involved in the Phosphorus-depletion Response from PSR1 in Chlamydomonas reinhardtii.

Plant J. 2019 Nov;100(3):610-626.

DOI PubMed Press release

We identified an algal regulator that controls lipid accumulation during nutrient deficiency.

[5] Isozaki A, Mikami H, Hiramatsu K, Sakuma S, Kasai Y, Iino T, Yamano T, Yasumoto A, Oguchi Y, Suzuki N, Shirasaki Y, Endo T, Ito T, Hiraki K, Yamada M, Matsusaka S, Hayakawa T, Fukuzawa H, Yatomi Y, Arai F, Di Carlo D, Nakagawa A, Hoshino Y, Hosokawa Y, Uemura S, Sugimura T, Ozeki Y, Nitta N, Goda K^＊ Collaboration

A practical guide to intelligent image-activated cell sorting.

Nature Protoc. 2019 Aug;14(8):2370-2415.

DOI PubMed

[4] Yamano T, Fukuzawa H^＊ Review in Japanese

How the photosynthetic turbo engine works and is controlled in the green alga Chlamydomonas

Kougousei Kenkyu 29(1):14-28 (2019)

Kyoto University repository

[3] Yamaoka Y, Shin S, Choi BY, Kim H, Jang S, Kajikawa M, Yamano T, Kong F, Legeret B, Fukuzawa H, Li-Beisson Y, Lee Y^＊ Open access Collaboration

The bZIP1 Transcription Factor Regulates Lipid Remodeling and Contributes to ER Stress Management in Chlamydomonas reinhardtii.

Plant Cell May;31(5):1127-1140.

DOI PubMed

[2] Owa M, Uchihashi T, Yanagisawa H, Yamano T, Iguchi H, Fukuzawa H, Wakabayashi K, Ando T, Kikkawa M^＊ Open access Collaboration

Inner lumen proteins stabilize doublet microtubules in cilia and flagella.

Nature Commun. 2019 Mar 8;10(1):1143. doi: 10.1038/s41467-019-09051-x.

DOI PubMed Kyoto University repository

We reported new proteins that bind to the inside of ciliary microtubules and reinforce their structure.

[1] Shinkawa H, Kajikawa M, Nomura Y, Ogura M, Sawaragi Y, Yamano T, Nakagami H, Sugiyama N, Ishihama Y, Kanesaki Y, Yoshikawa H, Fukuzawa H^＊ Open access

Algal Protein Kinase, Triacylglycerol Accumulation Regulator1, Modulates Cell Viability and Gametogenesis in Carbon/Nitrogen Imbalanced Conditions.

Plant Cell Physiol. 2019 Apr 1;60(4):916-930. doi: 10.1093/pcp/pcz010.

DOI PubMed Kyoto University repository

[3] Nitta N, Sugimura T, Isozaki A, Mikami H, Hiraki K, Sakuma S, Iino T, Arai F, Endo T, Fujiwaki Y, Fukuzawa H,Hase M,Hayakawa T, Hiramatsu K,Hoshino Y, Inaba M, Ito T, Karakawa H, Kasai Y, Koizumi K, Lee S, Lei C,Li M, Maeno T, Matsusaka S, Murakami D, Nakagawa A, Oguchi Y, Oikawa M, Ota T, Shiba K, Shintaku H, Shirasaki Y, Suga K, Suzuki Y, Suzuki N, Tanaka Y, Tezuka H, Toyokawa C, Yalikun Y, Yamada M, Yamagishi M, Yamano T, Yasumoto A, Yatomi Y, Yazawa M, Di Carlo D, Hosokawa Y, Uemura S, Ozeki Y, Goda K^＊ Open access Collaboration

Intelligent Image-Activated Cell Sorting

Cell 2018 Sep 20;175(1):266-276.e13. doi: 10.1016/j.cell.2018.08.028.

DOI PubMed Kyoto University repository Press release

We developed an image-activated cell sorter that reduced the time needed to select rare cells by about 6,500-fold, demonstrating its potential to enable unexpected discoveries through serendipity.

[2] Yamano T Textbook

Chapter 18, "Reading the Blueprint of the Body: Genome Information and Evolution"

In Frontiers in Life Science from Kyoto University, edited by the Graduate School of Biostudies, Kyoto University. Kodansha

[1] Yamano T, Toyokawa C, Fukuzawa H^＊

High-resolution suborganellar localization of Ca²⁺-binding protein CAS, a novel regulator of CO₂-concentrating mechanism.

Protoplasma. 2018 Jul;255(4):1015-1022. doi: 10.1007/s00709-018-1208-2.

DOI PubMed Press release Kyoto University repository

We tracked how the localization of CAS, a calcium-binding protein important for CCM induction, changes with CO2 levels.

[1] Kinoshita A, Niwa Y, Onai K, Yamano T, Fukuzawa H, Ishiura M, Matsuo T^＊ Open access Collaboration

CSL encodes a leucine-rich-repeat protein implicated in red/violet light signaling to the circadian clock in Chlamydomonas.

PLOS Genet. 2017 Mar 23;13(3):e1006645.

DOI PubMed Kyoto University repository Press release Press release

[4] Wang L, Yamano T, Takane T, Niikawa Y, Toyokawa C, Ozawa S, Tokutsu R, Takahashi Y, Minagawa J, Kanesaki Y, Yoshikawa H, Fukuzawa H^＊ Open access

Chloroplast-mediated regulation of CO₂-concentrating mechanism by Ca²⁺-binding protein CAS in the green alga Chlamydomonas reinhardtii.

Proc Natl Acad Sci USA. 2016 Nov 1;113(44):12586-12591.

DOI PubMed Kyoto University repository Press release

We showed that the algal calcium-binding protein CAS controls the CO₂-concentrating mechanism by regulating bicarbonate transporter expression.

[3] Yamano T, Fukuzawa H Review in Japanese

Bicarbonate transport supports photosynthesis in microalgae: discovery of bicarbonate transporters in the plasma membrane and chloroplast envelope

Kagaku to Seibutsu 54(7):459-460 (2016)

[2] Yamano T, Fukuzawa H^＊ Method paper

Indirect Immunofluorescence Assay in Chlamydomonas reinhardtii.

Bio-protocol: 6(13):e1864 (2016)

DOI Kyoto University repository

A detailed protocol for indirect immunofluorescence staining to examine where proteins are located inside cells.

[1] Fukuzawa H, Yamano T, Ifuku K, Hayakawa Y Patent

Method of transferring gene into algal cell involving utilizing multiple square-wave pulses in three steps. US Patent No. 9255276

A US patent was granted for our transformation technology, including the method reported in J Biosci Bioeng in 2013. The patent certificate is available here.

[3] Yamano T, Sato E, Iguchi H, Fukuda Y, Fukuzawa H^＊ Open access

Characterization of Cooperative Bicarbonate Uptake into Chloroplast Stroma in the Green Alga Chlamydomonas reinhardtii.

Proc. Natl. Acad. Sci. USA. 2015 Jun 9;112(23):7315-20.

DOI PubMed Kyoto University repository Press release

We identified the two-step bicarbonate transport pathway across the plasma membrane and chloroplast envelope, the HLA3/LCIA system, that supports the CCM.

[2] Kajikawa M, Sawaragi Y, Shinkawa H, Yamano T, Ando A, Kato M, Hirono M, Sato N, Fukuzawa H^＊ Open access

Algal Dual-specificity Tyrosine-phosphorylation-regulated Kinase TAR1 Regulates Accumulation of Triacylglycerol in Nitrogen- or Sulfur-deficiency.

Plant Physiol. 2015 Jun;168(2):752-64.

DOI PubMed

By analyzing the Chlamydomonas mutant tar1-1, which shows abnormal TAG accumulation, we identified TAR1 as the protein kinase gene involved in this regulation.

[1] Fukuzawa H, Yamano T, Ifuku K, Hayakawa Y Patent

Invention: "Method of transferring genes into algal cells using multiple square-wave pulses in three steps." Japanese Patent No. 5721191

A Japanese patent was granted for our transformation technology, including the method reported in J Biosci Bioeng in 2013. The patent certificate is available here.

[2] Wang L, Yamano T, Kajikawa M, Hirono M, Fukuzawa H^＊

Isolation and characterization of novel high-CO₂ requiring mutants of Chlamydomonas reinhardtii.

Photosynth Res. 2014 Sep;121(2-3):175-84.

DOI PubMed Kyoto University repository

We isolated and characterized three high-CO₂-requiring mutants from about 20,000 transformants generated by DNA tagging.

[1] Yamano T, Asada A, Sato E, Fukuzawa H^＊

Isolation and characterization of mutants defective in the localization of LCIB, an essential factor for the carbon-concentrating mechanism in Chlamydomonas reinhardtii.

Photosynth Res 2014 Sep;121(2-3):193-200. doi: 10.1007/s11120-013-9963-6.

DOI PubMed Kyoto University repository

We isolated and characterized 12 mutants with aberrant LCIB localization (abl mutants) from about 13,000 transformants generated by DNA tagging.

[1] Yamano T, Iguchi H, Fukuzawa H^＊

Rapid transformation of Chlamydomonas reinhardtii without cell-wall removal.

J Biosci Bioeng. 2013 Jun;115(6):691-4.

DOI PubMed Kyoto University repository

We developed a rapid and highly efficient Chlamydomonas transformation method using three-step, multiple square-wave pulse electroporation.