Area of Interest

My research interest is to understand the physiology and biochemistry of methanogenic archaea, which are obligate anaerobes that form methane as a major product of their energy metabolism. They play a fundamental role in the global carbon cycle and produce most of the atmospheric methane (~ 1 billion tons per year), a highly potent greenhouse gas. Methanogens are also frequently employed in bioreactors to convert organic wastes to methane, a renewable, carbon neutral fuel in common use. Using the methanogenic archaeon Methanococcus maripaludis as a model organism, the overall goal of our laboratory is to (i) discover novel metabolic enzymes, pathways, and regulatory networks in methanogens that will broaden our view of the microbial metabolic diversity; (ii) understand the molecular mechanisms of anaerobic lifestyle that will imply evolutionary processes on the early anoxic Earth; and (iii) engineer the metabolism of methanogens to gain insights into synthetic biology solutions to energy storage and production. We are currently combining biochemical, genetic, and physiological approaches to investigate sulfur metabolism, an essential but poorly understood process in methanogens, at the molecular and the systems levels.

 

Complete publication list is available at
https://scholar.google.com/citations?user=JzEycd4AAAAJ&hl=en&oi=ao

Selected Publications

Čavužić M & Liu Y (2017) Biosynthesis of sulfur-containing tRNA modifications: A comparison of bacterial, archaeal, and eukaryotic pathways. Biomolecules 7: E27.

Pikuta EV, Lyu Z, Williams MD, Patel NB, Liu Y, Hoover RB, Busse HJ, Lawson PA & Whitman WB (2017) Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions for the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S. soli and S. suarezii. Int J Syst Evol Microbiol 67:1442-50.

Pikuta EV, Menes RJ, Bruce AM, Lyu Z, Patel NB, Liu Y, Hoover RB, Busse HJ, Lawson PA & Whitman WB (2016) Raineyella antarctica gen. nov., sp. nov., a psychrotolerant, d-amino-acid-utilizing anaerobe isolated from two geographic locations of the Southern Hemisphere. Int J Syst Evol Microbiol 66:5529-36.

Liu Y, Vinyard DJ, Reesbeck ME, Suzuki T, Manakongtreecheep K, Holland PL, Brudvig GW & Söll D (2016) A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc Natl Acad Sci USA 113: 12703-8.

Haruna KI, Alkazemi MH, Liu Y, Söll D, & Englert M (2014) Engineering the elongation factor Tu for efficient selenoprotein synthesis. Nucleic Acids Res 42:9976-83.

Liu Y, Nakamura A, Nakazawa Y, Asano N, Ford KA, Hohn MJ, Tanaka I, Yao M, & Söll D (2014) Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea. Proc Natl Acad Sci USA 111:10520-5.

Liu Y, Long F, Wang L, Söll D, & Whitman WB (2014) The putative tRNA 2-thiouridine synthetase Ncs6 is an essential sulfur carrier in Methanococcus maripaludis. FEBS Lett 588:873-7.

Steinfeld JB, Aerni HR, Rogulina S, Liu Y, & Rinehart J (2014) Expanded cellular amino acid pools containing phosphoserine, phosphothreonine, and phosphotyrosine. ACS Chem Biol 9:1104-12.

Mandal D, Köhrer C, Su D, Babu IR, Chan CT, Liu Y, Söll D, Blum P, Kuwahara M, Dedon PC, & Rajbhandary UL (2014) Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs. RNA 20:177-88.

Liu Y, Zhu X, Nakamura A, Orlando R, Söll D, & Whitman WB (2012) Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis. J Biol Chem 287: 36683-92.

Liu Y, Beer LL, & Whitman WB (2012) Sulfur metabolism in archaea reveals novel processes. Environ Microbiol 14:2632-44.

Liu Y, Beer LL, & Whitman WB (2012) Methanogens: a window into ancient sulfur metabolism.Trends Microbiol 20:251-8.

Liu Y, Dos Santos PC, Zhu X, Orlando R, Dean DR, Söll D, & Yuan J (2012) Catalytic mechanism of Sep-tRNA:Cys-tRNA synthase: sulfur transfer is mediated by disulfide and persulfide. J Biol Chem 287:5426-33.

Liu Y, Sieprawska-Lupa M, Whitman WB, & White RH (2010) Cysteine is not the sulfur source for iron-sulfur cluster and methionine biosynthesis in the methanogenic archaeon Methanococcus maripaludisJ Biol Chem 285:31923-9.

Major TA, Liu Y, & Whitman WB (2010) Characterization of energy conserving hydrogenase B in Methanococcus maripaludis. J Bacteriol 192:4022-30.

Liu Y, White RH, & Whitman WB (2010) Methanococci use diaminopimelate aminotransferase (DapL) for lysine biosynthesis. J Bacteriol 192:3304-10.

Liu Y, Guo L, Guo R, Wong RL, Hernandez H, Hu J, Chu Y, Amster IJ, Whitman WB, & Huang L (2009) The Sac10b homolog in Methanococcus maripaludis binds DNA at specific sites. J Bacteriol 191:2315-29.

Hendrickson EL, Liu Y, Rosas-Sandoval G, Porat I, Sӧll D, Whitman WB, & Leigh JA (2008) Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J Bacteriol 190:2198-205.

Liu Y & Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann NY Acad Sci 1125:171-89.