Publications

If you don't have access to any of our papers, please email Crysten at cblaby@lbl.gov for a copy of the accepted manuscript.

2025

Rehman, Y., Kim, Y., Tong, M., Blaby, I.K., Blaby-Hass, C.E. and Beatty, J.T., 2025. Mining thermophile photosynthesis genes: a synthetic operon expressing Chloroflexota species reaction center genes in Rhodobacter sphaeroides. bioRxiv, pp.2025-09.

Shrestha, B., Romero, M.F., Villada, J.C., Plastid MAG Consortium, Blaby-Haas, C.E. and Schulz, F., 2025. Global metagenomics reveals plastid diversity and unexplored algal lineages. bioRxiv, pp.2025-03. https://doi.org/10.1101/2025.03.28.644651

Kivimaki, S. E., S. Dempsey, C. Camper, et al. 2025. Type IV Pili-Associated Secretion of a Biofilm Matrix Protein From Clostridium perfringens That Forms Intermolecular Isopeptide Bonds. Molecular Microbiology 1–18. https://doi.org/10.1111/mmi.70020.

Tadesse, D., Dai, Y., Li, G., Yang, L., Yang, Y., Dwivedi, N., Kumaran, D., Blaby‐Haas, C.E., Lipzen, A., Santiago, K. and Barry, K., 2025. Populus PtrbHLH011 Is a Transcriptional Co‐Regulator Involved in the Activation of Cell Wall Biosynthesis by Iron Deprivation. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.70275

Craig, R. J., Duenas, M. A., Camacho, D. J., Gallaher, S. D., Blaby-Haas, C. E., Moseley, J. L., & Merchant, S. S. (2025). Allodiploid hybridization, loss-of-heterozygosity and aneuploidy in the green alga Auxenochlorella, an emerging model for discovery research and bioengineering. bioRxiv, 2025-02. https://www.biorxiv.org/content/10.1101/2025.02.07.637104v1.abstract

2024

Tadesse D, Dai Y, Yang L, Yang Y, Dwivedi N, Kumaran D, Blaby-Haas CE, Lipzen A, Santiago K, Barry K, Liu CJ. (2024) Iron deprivation activates aboveground cell wall biosynthesis in Populus and the role of PtrbHLH011. bioRxiv. 2024 Jul 2:2024-06.

Verdejo-Torres, O., Klein, D. C., Novoa-Aponte, L., Carrazco-Carrillo, J., Bonilla-Pinto, D., Rivera, A., ... & Padilla-Benavides, T. (2024). Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis. PLoS Genetics, 20(12), e1011495. https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011495

Kivimaki, S. E., Dempsey, S., Tani, J. M., Camper, C., Hicklin, I. K., Blaby-Haas, C. E., ... & Melville, S. (2024). Type IV pili-associated secretion of a biofilm matrix protein from Clostridium perfringens that forms intermolecular isopeptide bonds. bioRxiv, 2024-11. https://www.biorxiv.org/content/10.1101/2024.11.04.621531v1.abstract

Grosjean, N., Zhang, L., Kumaran, D., Xie, M., Fahey, A., Santiago, K., ... & Blaby-Haas, C. E. (2024). Functional diversification within the heme-binding split-barrel family. Journal of Biological Chemistry, 300(11), 107888. https://www.sciencedirect.com/science/article/pii/S0021925824023901

Njenga, R. K., Boele, J., Drepper, F., Sinha, K., Marouda, E., Huesgen, P. F., ... & Koch, H. G. (2024). Ribosome-inactivation by a class of widely distributed C-tail anchored membrane proteins. Structure. https://www.cell.com/structure/fulltext/S0969-2126(24)00388-5

Liu, H. W., Urzica, E. I., Gallaher, S. D., Schmollinger, S., Blaby-Haas, C. E., Iwai, M., & Merchant, S. S. (2024). Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium. Photosynthesis Research, 161(3), 213-232. https://link.springer.com/article/10.1007/s11120-024-01103-8

Grosjean, N., Yee, E.F., Kumaran, D. ... & Blaby-Haas, C. E. (2024) A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nature Commun 15, 3167. https://doi.org/10.1038/s41467-024-47486-z

Strenkert, D., Schmollinger, S., Paruthiyil, S., Brown, B. C., Green, S., Shafer, C. M., ... & Merchant, S. S. (2024). Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization. Metallomics, 16(3), mfae013. https://academic.oup.com/metallomics/article-abstract/16/3/mfae013/7619135

Hammack, A. and Blaby-Haas, C. E. (2024) Machine learning sheds light on microbial dark proteins. Nature Reviews Microbiology. Available online https://rdcu.be/dsVBg

2023

Zhang, L., Braynen, J., Fahey, A., Chopra, K., Cifani, P., Tadesse, D., ... & Blaby-Haas, C. E. (2023) Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis. Frontiers in Plant Science, 14, 1237722. https://www.frontiersin.org/articles/10.3389/fpls.2023.1237722/full

Strenkert, D., Schmollinger, S., Paruthiyil, S., Brown, B. C., Green, S., Shafer, C. M., ... & Merchant, S. S. (2023). Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization. bioRxiv, 2023-10. https://www.biorxiv.org/content/10.1101/2023.10.19.563170v1.abstract

Khalfaoui-Hassani, B., Blaby-Haas, C. E., Verissimo, A., & Daldal, F. (2023). The Escherichia coli MFS-type transporter genes yhjE, ydiM, and yfcJ are required to produce an active bo3 quinol oxidase. PloS one, 18(10), e0293015. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0293015

Davidi L, et al. Pumping iron: A multi-omics analysis of two extremophilic algae reveals iron economy management. Proceedings of the National Academy of Sciences. 2023 Jul 25;120(30):e2305495120. https://www.pnas.org/doi/abs/10.1073/pnas.2305495120

Craig RJ, et al. The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory. The Plant Cell. 2023 Feb 1;35(2):644-72. https://academic.oup.com/plcell/article-abstract/35/2/644/6958632

Öztürk Y, Andrei A, Blaby-Haas CE, Daum N, Daldal F, Koch HG. Metabolic Sensing of Extracytoplasmic Copper Availability via Translational Control by a Nascent Exported Protein. Mbio. 2023 Feb 28;14(1):e03040-22. https://journals.asm.org/doi/abs/10.1128/mbio.03040-22

Blaby-Haas CE, Merchant SS. Trace metal nutrition and response to deficiency. InThe Chlamydomonas Sourcebook 2023 Jan 1 (pp. 167-203). Academic Press. https://www.sciencedirect.com/science/article/pii/B978012821430500002X

Blaby IK, Soto MJ, Blaby-Haas CE. Functional genomics of Chlamydomonas reinhardtii. InThe Chlamydomonas Sourcebook 2023 Jan 1 (pp. 65-84). Academic Press. https://www.sciencedirect.com/science/article/pii/B9780128224571000133

Y Öztürk, A Andrei, CE Blaby-Haas, N Daum, F Daldal, HG Koch. "Metabolic Sensing of Extracytoplasmic Copper Availability via Translational Control by a Nascent Exported Protein." Mbio, e03040-22 (2023) https://journals.asm.org/doi/full/10.1128/mbio.03040-22

Davidi, L, et al. "Pumping Iron: A Multi-omics Analysis of Two Extremophilic Algae Reveals Mechanisms of Iron Economy." bioRxiv 2023.02. 09.527888 https://www.biorxiv.org/content/10.1101/2023.02.09.527888v2.abstract

2022

de Crécy-Lagard V, et al. "A roadmap for the functional annotation of protein families: a community perspective." Database (Oxford). 2022 Aug 12;2022. doi: 10.1093/database/baac062. PubMed PMID: 35961013; PubMed Central PMCID: PMC9374478.

Pollo-Oliveira L, et al. "The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12." Metallomics 14.9 (2022). doi: 10.1093/mtomcs/mfac065. PubMed PMID: 36066904; PubMed Central PMCID: PMC9508795.

Pasquini, Miriam, et al. "Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase." Cell Reports 39.7 (2022): 110834. https://www.sciencedirect.com/science/article/pii/S2211124722006076

Schwechheimer, Claus, Peter Michael Schröder, and Crysten E. Blaby-Haas. "Plant GATA Factors: Their Biology, Phylogeny, and Phylogenomics." Annual Review of Plant Biology 73 (2022). https://www.annualreviews.org/doi/full/10.1146/annurev-arplant-072221-092913

Blaby-Haas, Crysten E. "Polar algae flaunt their zinc assets." Nature Ecology & Evolution (2022): 1-2. https://www.nature.com/articles/s41559-022-01721-2

Blaby-Haas, Crysten E. "The Mosaic Landscape of Algal Metal Transport and Usage." Microbial Metabolism of Metals and Metalloids. Springer, Cham, 2022. 55-75. https://link.springer.com/chapter/10.1007/978-3-030-97185-4_3

Craig, Rory J., et al. "The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory." bioRxiv (2022). https://www.biorxiv.org/content/10.1101/2022.06.16.496473v1.abstract

2021

Cole, Benjamin, et al. "Plant single-cell solutions for energy and the environment." Communications biology 4.1 (2021): 1-12. https://www.nature.com/articles/s42003-021-02477-4

Gallaher, Sean D., et al. "Widespread polycistronic gene expression in green algae." Proceedings of the National Academy of Sciences 118.7 (2021): e2017714118. https://www.pnas.org/doi/abs/10.1073/pnas.2017714118

Foflonker, Fatima, and Crysten E. Blaby-Haas. "Colocality to cofunctionality: eukaryotic gene neighborhoods as a resource for function discovery." Molecular biology and evolution 38.2 (2021): 650-662. https://academic.oup.com/mbe/article/38/2/650/5901547

Blaby-Haas, Crysten E. "Cyanobacteria provide a new paradigm in the regulation of cofactor dependence." Proceedings of the National Academy of Sciences 118.7 (2021): e2100281118. https://www.pnas.org/doi/abs/10.1073/pnas.2100281118

Öztürk, Yavuz, et al. "Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product." Frontiers in microbiology 12 (2021). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8456105/

2020

Merchant, Sabeeha S., et al. "From economy to luxury: Copper homeostasis in Chlamydomonas and other algae." Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 1867.11 (2020): 118822. https://www.sciencedirect.com/science/article/pii/S0167488920301804

Grosjean, Nicolas, and Crysten E. Blaby-Haas. "Leveraging computational genomics to understand the molecular basis of metal homeostasis." New Phytologist 228.5 (2020): 1472-1489. https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.16820

Selamoglu, Nur, et al. "Comparative differential cuproproteomes of Rhodobacter capsulatus reveal novel copper homeostasis related proteins." Metallomics 12.4 (2020): 572-591. https://academic.oup.com/metallomics/article/12/4/572/5961803

2016 - 2019

Marckmann D, Trasnea P, Schimpf J, Winterstein C, Andrei A, Schmollinger S, Blaby-Haas CE, Friedrich T, Daldal F, Koch H. (2019) The cbb3-type cytochrome oxidase assembly factor CcoG is a widely distributed novel cupric reductase. Proc Natl Acad Sci USA 116(42): 21166-21175. PMID: 31570589

Tsui HS, Pham NV, Amer BR, Bradley MC, Gosschalk JE, Gallagher-Jones M, Ibarra H, Clubb RT, Blaby-Haas CE, Clarke CF. (2019) Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function. J Lipid Res 60(7): 1293-1310. PMID: 31048406

Blaby-Haas CE and Merchant SS. (2019) Comparative and Functional Algal Genomics. Ann Rev Plant Biol 70: 605-638. PMID: 30822111

Roth MS, Gallaher SD, Westcott DJ, Iwai M, Louie KB, Mueller M, Walter A, Foflonker F, Bowen BP, Ataii NN, Song J, Chen J, Blaby-Haas CE, Larabell C, Auer M, Northen TR, Merchant SM, Niyogi KK. (2019) A molecular switch for oxygenic photosynthesis and metabolism in a green alga. Plant Cell 31(3): 579-601. PMID: 30787178

Zhang Y, Blaby-Haas CE, Steimle S, Verissimo AF, Garcia-Angulo VA, Koch H, Daldal F and Khalfaoui-Hassani B. (2019) Cu transport by the extended family of CcoA-like Transporters (CalT) in Proteobacteria. Sci Reps 9(1): 1208. PMID: 30718766

Luxmi R, Blaby-Haas CE, Kumar D, Rauniyar N, King SK, Mains RE, Eipper BA. (2018) Proteases shape the Chlamydomonas secretome: Comparison to classical neuropeptide processing machinery. Proteomes 6(4): 36. PMID: 30249063

Mains RE, Blaby-Haas C, Rheaume BA, Eipper BA. (2018) Changes in corticotrope gene expression upon increased expression of peptidylglycine α-amidating monooxygenase. Endocrinology 159(7): 2621-39. PMID: 29788427

Khalfaoui-Hassani B, Wu H, Blaby-Haas CE, Zhang Y, Sandri F, Verissimo AF, Koch H, Daldal F. (2018) Widespread Distribution and Functional Specificity of the Copper Importer CcoA: Distinct Cu Uptake Routes for Bacterial Cytochrome c Oxidases. mBio 9(1): pp.e00065-18. PMID: 29487231

Blaby-Haas CE, Page M and Merchant SS. (2018) Using YFP as a reporter of gene expression in the green alga Chlamydomonas reinhardtii. In Reporter Gene Assays (pp. 135-148). Humana Press, New York, NY. PMID: 29671268

Blaby IK and Blaby-Haas CE. (2018) Gene expression analysis by arylsulfatase assays in the green alga Chlamydomonas reinhardtii. In Reporter Gene Assays (pp. 149-161). Humana Press, New York, NY. PMID: 29671269

Blaby IK and Blaby-Haas CE. (2017) Genomics and functional genomics in Chlamydomonas reinhardtii. In Chlamydomonas: Molecular Genetics and Physiology, pp. 1-26. Springer, Cham.

Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, ... and Prochnik S. (2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA 17: 201703088. PMC5547612

Blaby-Haas CE and Merchant SS. (2017) Regulating cellular trace metal economy in algae. Curr Opin Plant Bio 39: 88-96. PMC5595633

Blaby-Haas CE, Castruita M, Kropat J, Fitz-Gibbon S and Merchant SS. (2016) Ni induces the CRR1- dependent regulon revealing overlap and distinction between hypoxia and Cu-deficiency responses in Chlamydomonas reinhardtii. Metallomics 8(7): 679-691. PMC4945368

Publications from Crysten's postdoc work

Lojek LJ, Farrand AJ, Wisecaver JH, Blaby-Haas CE, Merchant SS, Rokas A and Skaar E. (2017) Chlamydomonas reinhardtii LFO1 is an IsdG family heme oxygenase. mSphere 2.4: e00176-17. PMC5557675

Kumar D, Blaby-Haas CE, Merchant SS, Mains RE, King SM and Eipper BA. (2016) Early eukaryotic origins for cilia-associated bioactive peptide-amidating activity. J Cell Sci 129(5): 943-956. PMC4813317

Blaby IK, Blaby-Haas CE, Pérez-Pérez ME, Schmollinger S, Fitz-Gibbon S, Lemaire SD, and Merchant SS. (2015) Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes. Plant J 84(5): 974-988. PMC4715741

Pérez-Martín M, Blaby-Haas CE, Pérez-Pérez ME, Andrés-Garrido A, Blaby IK, Merchant SS and Crespo JL. (2015) Activation of autophagy by metals in Chlamydomonas reinhardtii. Eukaryot Cell 14(9): 964-73. PMC4551596

Fristedt R, Herdean A, Blaby-Haas CE, Mamedov F, Merchant SS, Last RL and Lundin B. (2015) PHOTOSYSTEM II PROTEIN33, a protein conserved in the plastid lineage, is associated with the chloroplast thylakoid membrane and provides stability to photosystem II supercomplexes in Arabidopsis. Plant Physiol 167(2): 481-92. PMC4326745

Allan CM, Awad AM, Johnson JS, Shirasaki DI, Wang C, Blaby-Haas CE, Merchant SS, Loo JA and Clarke CF. (2015) Identification of Coq11, a new coenzyme Q biosynthetic protein in the CoQ-synthome in Saccharomyces cerevisiae. J Biol Chem 290.12: 7517-7534. PMC4367260

Blaby IK, Blaby-Haas CE, Tourasse N, Hom EF, Lopez D, Aksoy M, ... and Prochnik S. (2014) The Chlamydomonas genome project: a decade on. Trends Plant Sci 19: 672-680. PMC4185214

Blaby-Haas CE, Padilla-Benavides T, Stübe R, Argüello JM and Merchant SS. (2014) Evolution of a plant- specific copper chaperone family for chloroplast copper homeostasis. Proc Natl Acad Sci USA 111(50): E5480-E5487. PMC4273408

Blaby-Haas CE and Merchant SS. (2014) Lysosome-related organelles as mediators of metal homeostasis. J Biol Chem 289: 28129-28136. PMC4192468

Glaesener AG, Merchant SS and Blaby-Haas CE. (2013) Iron economy in Chlamydomonas reinhardtii. Front Plant Sci 4:337. PMC3759009

Blaby-Haas CE and Merchant SS. (2013) Iron sparing and recycling in a compartmentalized cell. Curr Opin Microbiol 16(6): 677-85. PMC3842415

Ming R, Vanburen R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, ... and Shen-Miller J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol 14(5): R41. PMC4053705

Blaby-Haas CE and Merchant SS. (2013) Sparing and salvaging metals in chloroplasts in Metals in Cells. V. Culotta and R.A. Scott eds. Encyclopedia of Inorganic and Bioinorganic Chemistry (EIBC), EIC Books

Urzica EI, Casero D, Yamasaki H, Hsieh SI, Adler LN, Karpowicz SJ, Blaby-Haas CE, Clarke SG, Loo JA, Pellegrini M, and Merchant SS. (2012) Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell 24(10): 3921-48. PMC3517228

Blaby-Haas CE and Merchant SS. (2012) The ins and outs of algal metal transport. BBA Mol Cell Res 1823(9): 1531-52. PMC3408858

Publications from Crysten's PhD work

Blaby-Haas CE, Flood JA, de Crécy-Lagard V, and Zamble DB. (2012) YeiR: a metal-binding GTPase from Escherichia coli involved in metal homeostasis. Metallomics 4(5): 488-97. PMC3574555

Phillips G, Grochowski LL, Bonnett S, Xu H, Bailly M, Blaby-Haas C, El Yacoubi B, Iwata-Reuyl D, White RH, and de Crécy-Lagard V. (2012) Functional promiscuity of the COG0720 family. ACS Chem Biol 7(1): 197209. PMC3262898

Blaby-Haas CE, Furman R, Rodionov DA, Artsimovitch I, and de Crécy-Lagard V. (2011) Role of a Zn- independent DksA in Zn homeostasis and stringent response. Mol Micro 79(3): 700–715. PMC3076637

Gerdes S, El Yacoubi B, Bailly M*, Blaby IK *, Blaby-Haas CE*, Jeanguenin L*, Lara-Núñez A*, Pribat A*, Waller JC*, Wilke, A *, Overbeek R, Hanson AD, and de Crécy-Lagard V. (2011) Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics 12 Suppl 1: S2. PMC3223725

Blaby-Haas CE and de Crécy-Lagard V. (2011) Mining high-throughput experimental data to link gene and function. Trends in Biotech, 29(4): 174-182. PMC3073767

Blaby IK, Phillips G, Blaby-Haas C, Gulig K, El Yacoubi B, and de Crécy-Lagard, V. (2010) Towards a systems approach in the genetic analysis of Archaea: accelerating mutant construction and phenotypic analysis in Haloferax volcanii. Archaea 2010: 426239. PMC3017900

El Yacoubi B, Phillips G, Blaby IK, Haas CE, Cruz Y, Greenberg J, and de Crécy-Lagard, V. (2009) A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes. Archaea 2(4): 211-9. PMC2686393

Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS and de Crécy-Lagard V. (2009) A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics 10:470. PMC2770081

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