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As an extreme and unique environment, microgravity presents a novel condition to study microorganisms at the molecular, physiological, and transcription levels.Application of simulated microgravity techniques in biochemical engineering such as recombinant protein production by microbial host and the mechanisms that microbes sense and respond to the environment of low shear modelled microgravity (LSSMG) will draw much more attention in further experimentation.Pichia pastoris is widely used as an expression system for production of recombinant proteins of prokaryotic and eukaryotic origin.In previous study, we reported that the recombinant P.pastoris grew faster under SMG than NG during methanol induction phase and the efficiencies of recombinant enzyme production and secretion were enhanced under LSSMG compared with normal gravity (NG) control.In this work, we focus on the gene expression profiling combined with proteomic analyses in the central carbon metabolism, protein chaperone, RNA polymerase, protein transportation or secretion, virulence factors and other functional categories.Four categories of 141 genes function as methanol utilization, protein chaperone, RNA polymerase and protein transportation or secretion classified according to Gene Ontology (GO) analysis.It was found that most genes of methanol metabolism (85% of 20genes) and protein transportation or secretion (82.2% of 45 genes) were significantly up-regulated under LSSMG.The quantity and fold change of up-regulated genes in exponential phase of each category were higher than those of stationary phase.Based on next-generation sequencing (NGS) technologies and data mining, we selected some key genes for co-expression in the P.pastoris strain already secreting a recombinant β-glucuronidase(PGUS) from Penicillium purpurogenum Li-3 to improve an improved recombinant protein yield.This work will provide an important platform for yeast engineering.