The Analysis Of Rhizopus Chinensis Genome Sequence And Its Preliminary Application

Rhizopus chinensis CCTCCM201021，as an important fungus isolated from Daqu, a kindof traditional leaven for the production of Chinese liquor, can be widely used in manyindustries such as traditional fermentation, food, enzyme and so on. Moreover, themembrane-bound lipase obtained from R. chinensis catalyzing the reaction of esterificationand transesterification is attractive for its great applied potential in bio-energy and chiralcatalysis. However, the researches about genus Rhizopus, even Zygomycetes, are only ininfancy. The genomic information provide multiple insights into the physiologicalcharacteristics of R. chinensis for further exploration of the metabolisms, regulatorymechanisms and giving better guidances on the industrial application. It is also applied to datamining for the function in solid-state fermentation, exploitation for the discovery of newresources and investigation about safety. This work analyses the R. chinensis genomesequence and discusses some enzymatic and microorganic characteristics based on thegenomic information. The results in details are as follows:(1) The annotation of Rhizopus chinensis genome and comparative analyses with otherZygomycetes. The genomic DNA of this strain is de novo sequenced using Solexa paired-endand mate paired sequencing technology. The genome is assembled by SOAPdenovo whichgenerated3,281contigs with a total size of45,666,236bp and a GC content of36.99%.Subsequent gene prediction analysis yields a total of17,676predicted protein-coding geneswith74.92%(13243) genes successfully annotated, but only about50%genes are indentifiedfunctionally. The comparative genomic analyses indicate that the highest coverage is11.04%and the homology genes account for about65%among the Zygomycetes. The results ofclassification and pathway mapping by searching against the COG and KEGG database showthat R. chinensis possesses complex metabolisms for application in traditional fermentation.Further analysis of the glycoside hydrolases in R. chinensis based on the CAZydatabase indicates its excellent properties for starch degradation. The large amount ofenzymes involved organic acid synthesis are consistent with the function of this strain as wellas ester formation and amino acid metabolism which make contributions to flavor formationduring Chinese liquor production.(2) Through the analysis of multiple sequences alignment, molecular phylogeneticanalysis, the hydrophobicity analysis and the comparative analysis of gene clusters, it is foundthat there are2and3lipases existed in R. chinensis and R. oryzae respectively. Although theypossessed different properties in solubility and location, the sequences are of high similarity.The analyses indicate that the differences are depended on the hydrophobicity and the geneclusters influenced by position effect mainly. The gene cluster, the membrane-boundinglipases located in, encodes membrane-bounding proteins related to protein prenylation. Thelipases may be the catalyst for combination of G-protien and plasma membrane. The changesin conformation and composition of plasma membrane may promote the capacity of bindingsites for membrane-bounding lipases.(3) From the perspective of the biosynthetic pathway of mycotoxins and antibiotics, the safety of R. chinensis CCTCCM201021is investigated based on the bioinformations of thewhole genomic sequences. The key synthetic pathways and genes of rhizoxin and rhizonin, aswell as mycotoxins metabolism are analyzed, including PKS, NRPS and PKS-NRPS hybridmetabolic pathways, terpenoid metabolism and other metabolic pathways. The results showthat R. chinensis does not have the abilities in production of mycotoxins, and its products aregenerally considered as safe.