Whole genome sequencing and comparative genomics analysis of a new pyrroloquinoline quinone-producing methylotroph

Abstract:

[Background] Due to the short time of discovery of methylotrophs, only a few genomes of methylobacterium strains that can produce PQQ were sequenced. It increases the difficulty of study the genomics and biological metabolic pathways of methylobacterium. [Objective] The PQQ-producing bacteria was screened and treated with various mutagenesis methods to improve the yield of PQQ. Whole genome analysis of high-yield mutant strains was performed to provide sequence background information for studying the molecular mechanism of PQQ synthesis and subsequent molecular breeding of methylobacterium. [Methods] The wild-type PQQ production strains were subjected to ultraviolet rays mutagenesis, nitroso-guanidin mutagenesis, ethylmethylsulfone mutagenesis, diethyl sulfate mutagenesis, and ultraviolet rays-lithium chloride compound mutagenesis. The whole genome sequence of the mutant strain obtained by mutagenesis was sequenced using the PromethION sequencing platform and the MGISEQ-2000 sequencing platform. The assembled whole genome sequence was compared with the model strain Methylobacterium extorquens AM1. [Results] A mutant strain NI91 was obtained after 11 rounds of mutagenesis with PQQ yield 19.49 mg/L, which was 44.91% higher than the original strain. The genome of the mutant strain NI91 consists of a chromosome of 5 409 262 bp, encoding 4 957 proteins. Compared with the model strain M. extorquens AM1, it was found that the pqqF and pqqG genes that relate to shear processing during PQQ biosynthesis were deleted. Meanwhile, the pqqL was first discovered in methylotrophic bacteria which has a similar function to the pqqF, and the sequences of pqqC/D between the two strains were quite different. [Conclusion] This study provides basic data for functional genomics research of the methylotrophic bacterium and the study of PQQ synthesis mechanism. Comparative genomics between NI91 and the model strain M. extorquens AM1 provides a molecular basis for revealing different mechanisms of PQQ synthesis.