Dr. Yan Liao is now a Postdoctoral Research Associate in the ithree institute, University of Technology Sydney. She was awarded her PhD degree in Microbiology in 2017 at University of New South Wales, Australia. From her PhD work, she developed, for the first time, a gene transfer system of a psychrophilic haloarchaea, which provided the means to study gene function and opened the way to probe molecular mechanisms of adaptation in psychrophilic archaea. She also established an integrative approach combining microscopy and quantitative proteomics to comprehensively investigate the ecologically relevant mechanisms of growth, survival, and speciation of the two psychrophilic haloarchaeal species isolated from Deep Lake, Antarctica.
In 2017, she accepted a postdoctoral research position in ARC Future Fellow A/Prof Iain Duggin’s group at UTS, working on cell structural dynamics and cytoskeleton of archaea. Her research is focusing on cell division and survival in archaea with the aim of understanding cytokinesis mechanisms in the Archaea domain, and early evolution of life on Earth, in which the ancestors of modern archaea played a central role. Currently her research involves characterising the function of cytoskeletal proteins and identifying genes associated with cell survival and cell division/morphological changes in Haloferax. volcanii, a model archaeal organism.
- Member of The Australian Society for Microbiology;
- Member of The Australian Microscopy & Microanalysis Society
Can supervise: YES
Genetic manipulation in archaea;
Cell growth and survival in archaea;
Adpatation and speciation of haloarchaea;
Cell structural dynamics and cytokeleton of archaea;
Liao, Y, Ithurbide, S, Löwe, J & Duggin, IG 2020, 'Two FtsZ proteins orchestrate archaeal cell division through distinct functions in ring assembly and constriction', BioRxiv.View/Download from: Publisher's site
AbstractThe tubulin homolog FtsZ assembles a ring in bacteria and plays a key role in the machinery that constricts to divide the cells. Many archaea encode two FtsZs from distinct families, FtsZ1 and FtsZ2, of previously unclear functions. We show that Haloferax volcanii cannot divide properly without either or both but proliferates in alternative ways via remarkable envelope plasticity. The FtsZs co-localize as a dynamic midcell division ring. FtsZ1 independently assembles and stabilizes FtsZ2 in the ring, and influences cell shape, whereas FtsZ2 functions in the constriction mechanism; their GTPase active sites are crucial for these activities. The two FtsZs are widespread in archaea with a single S-layer envelope, but those with a pseudomurein wall only have FtsZ1. FtsZ2 appears to be essential for constriction of the flexible membrane-S-layer, where an internal constriction force might dominate the division mechanism in contrast to bacteria and archaea that divide by wall ingrowth.
Williams, TJ, Allen, MA, Liao, Y, Raftery, MJ & Cavicchioli, R 2019, 'Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics', Applied and Environmental Microbiology, vol. 85, no. 6.View/Download from: Publisher's site
The canonical pathway for sucrose metabolism in haloarchaea utilizes a modified Embden-Meyerhof-Parnas pathway (EMP), in which ketohexokinase and 1-phosphofructokinase phosphorylate fructose released from sucrose hydrolysis. However, our survey of haloarchaeal genomes determined that ketohexokinase and 1-phosphofructokinase genes were not present in all species known to utilize fructose and sucrose, thereby indicating that alternative mechanisms exist for fructose metabolism. A fructokinase gene was identified in the majority of fructose- and sucrose-utilizing species, whereas only a small number possessed a ketohexokinase gene. Analysis of a range of hypersaline metagenomes revealed that haloarchaeal fructokinase genes were far more abundant (37 times) than haloarchaeal ketohexokinase genes. We used proteomic analysis of Halohasta litchfieldiae (which encodes fructokinase) and identified changes in protein abundance that relate to growth on sucrose. Proteins inferred to be involved in sucrose metabolism included fructokinase, a carbohydrate primary transporter, a putative sucrose hydrolase, and two uncharacterized carbohydrate-related proteins encoded in the same gene cluster as fructokinase and the transporter. Homologs of these proteins were present in the genomes of all haloarchaea that use sugars for growth. Enzymes involved in the semiphosphorylative Entner-Doudoroff pathway also had higher abundances in sucrose-grown H. litchfieldiae cells, consistent with this pathway functioning in the catabolism of the glucose moiety of sucrose. The study revises the current understanding of fundamental pathways for sugar utilization in haloarchaea and proposes alternatives to the modified EMP pathway used by haloarchaea for sucrose and fructose utilization.
Liao, Y, Ithurbide, S, de Silva, RT, Erdmann, S & Duggin, IG 2018, 'Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope', Emerging Topics in Life Sciences, vol. 2, no. 4, pp. 547-559.View/Download from: Publisher's site
Tang, Z, Jin, W, Sun, R, Liao, Y, Zhen, T, Chen, H, Wu, Q, Gou, L & Li, C 2018, 'Improved thermostability and enzyme activity of a recombinant phyA mutant phytase from Aspergillus niger N25 by directed evolution and site-directed mutagenesis', Enzyme and Microbial Technology, vol. 108, pp. 74-81.View/Download from: Publisher's site
© 2017 Elsevier Inc. We previously constructed three recombinant phyA mutant strains (PP-NPm-8, PP-NPep-6A and I44E/T252R-PhyA), showing improved catalytic efficiency or thermostability of Aspergillus niger N25 phytase, by error-prone PCR or site-directed mutagenesis. In this study, directed evolution and site-directed mutagenesis were further applied to improve the modified phytase properties. After one-round error-prone PCR for phytase gene of PP-NPep-6A, a single transformant, T195L/Q368E/F376Y, was obtained with the significant improvements in catalytic efficiency and thermostability. The phytase gene of T195L/Q368E/F376Y, combined with the previous mutant phytase genes of PP-NPep-6A, PP-NPm-8 and I44E/T252R-PhyA, was then sequentially modified by DNA shuffling. Three genetically engineered strains with desirable properties were then obtained, namedQ172R, Q172R/K432R andQ368E/K432R. Among them, Q172R/K432R showed the highest thermostability with the longest half-life and the greatest remaining phytase activity after heat treatment, while Q368E/K432R showed the highest catalytic activity. Five substitutions (Q172R, T195L, Q368E, F376Y, K432R) identified from random mutagenesis were added sequentially to the phytase gene of PP-NPep-6A to investigate how the mutant sites influence the properties of phytase. Characterization and structural analysis demonstrated that these mutations could produce cumulative or synergistic improvements in thermostability or catalytic efficiency of phytase.
Williams, TJ, Liao, Y, Ye, J, Kuchel, RP, Poljak, A, Raftery, MJ & Cavicchioli, R 2017, 'Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi', Environmental Microbiology, vol. 19, no. 6, pp. 2210-2227.View/Download from: Publisher's site
Halohasta litchfieldiae represents ∼ 44% and Halorubrum lacusprofundi ∼ 10% of the hypersaline, perennially cold (≥ −20°C) Deep Lake community in Antarctica. We used proteomics and microscopy to define physiological responses of these haloarchaea to growth at high (30°C) and low (10 and 4°C) temperatures. The proteomic data indicate that both species responded to low temperature by modifying their cell envelope including protein N‐glycosylation, maintaining osmotic balance and translation initiation, and modifying RNA turnover and tRNA modification. Distinctions between the two species included DNA protection and repair strategies (e.g. roles of UspA and Rad50), and metabolism of glycerol and pyruvate. For Hrr. lacusprofundi, low temperature led to the formation of polyhydroxyalkanoate‐like granules, with granule formation occurring by an unknown mechanism. Hrr. lacusprofundi also formed biofilms and synthesized high levels of Hsp20 chaperones. Hht. litchfieldiae was characterized by an active CRISPR system, and elevated levels of the core gene expression machinery, which contrasted markedly to the decreased levels of Hrr. lacusprofundi. These findings greatly expand the understanding of cellular mechanisms of cold adaptation in psychrophilic archaea, and provide insight into how Hht. litchfieldiae gains dominance in Deep Lake.
Liao, Y, Williams, TJ, Walsh, JC, Ji, M, Poljak, A, Curmi, PMG, Duggin, IG & Cavicchioli, R 2016, 'Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function.', Scientific Reports, vol. 6, pp. 1-15.View/Download from: Publisher's site
No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
Liao, Y, Williams, TJ, Ye, J, Charlesworth, J, Burns, BP, Poljak, A, Raftery, MJ & Cavicchioli, R 2016, 'Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi', Scientific Reports, vol. 6, no. 1, pp. 1-17.View/Download from: Publisher's site
Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.
Liao, Y, Li, C-M, Chen, H, Wu, Q, Shan, Z & Han, X-Y 2013, 'Site-Directed Mutagenesis Improves the Thermostability and Catalytic Efficiency of Aspergillus niger N25 Phytase Mutated by I44E and T252R', APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY, vol. 171, no. 4, pp. 900-915.View/Download from: Publisher's site
Liao, Y, Zeng, M, Wu, Z-F, Chen, H, Wang, H-N, Wu, Q, Shan, Z & Han, X-Y 2012, 'Improving Phytase Enzyme Activity in a Recombinant phyA Mutant Phytase from Aspergillus niger N25 by Error-Prone PCR', APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY, vol. 166, no. 3, pp. 549-562.View/Download from: Publisher's site
Yao, Y, Hou, S, Li, C, Chen, H & Liao, Y 2011, 'Directed Evolution of Neutral Endoglucanase Gene by Error-prone PCR', Chinese Journal of Agricultural Biotechnology, vol. 19, no. 6, pp. 1136-1143.View/Download from: Publisher's site
Low enzymatic activity and high cost are the two main problems that limit the industrial applications of
cellulose. In order to enhance the enzymatic activity of neutral endoglucanase activity, error-prone PCR was
conducted to engineer the Bacillus subtilis C-36 endoglucanase gene. Two optimum mutants, b-15 and b-28 were
obtained, with an endoglucanase activity 2.1 folds and 3.6 folds increased, respectively. The sequence of b-15
endoglucanase gene showed six nucleotide substitutions leading to four mutated amino acids; and b-28
endoglucanase gene showed one nucleotide substitution leading to one mutated amino acid. According to the 3D
structure of endoglucanase mimicked by SWISS-MODEL, the four mutated amino acids of b-15 were either
located at the corner between the fourth and fifth α-helix in the catalytic domain or at the fifth β-fold or the corner
between the ninth and tenth β-fold in the carbohydrate-binding domain. And the mutation of b-28 was located at
the fourth β-fold in the carbohydrate-binding domain. Following the orthogonal experiment, the mutant b-15 and
b-28 could reach to an endoglucanase activity of 4.542 U/mL and 5.136 U/mL through fermentation, respectively,
both of which were much higher than the wild-type control. These results have provided a base for further research
Prof. Anita Marchfelder (Ulm University, Germany)
Dr. Tanmay Bharat (Univeristy of Oxford, United Kingdom)
Dr. Susanne Erdmann (Max Planck Institute for Marine Microbiology, Germany)
Dr. Timothy Williams (UNSW, Australia)