Adaptive evolution of microorganisms based on industrial environmental perturbations / 生物工程学报

The development of synthetic biology has greatly promoted the construction of microbial cell factories, providing an important strategy for green and efficient chemical production. However, the bottleneck of poor tolerance to harsh industrial environments has become the key factor hampering the productivity of microbial cells. Adaptive evolution is an important method to domesticate microorganisms for a certain period by applying targeted selection pressure to obtain desired phenotypic or physiological properties that are adapted to a specific environment. Recently, with the development of technologies such as microfluidics, biosensors, and omics analysis, adaptive evolution has laid the foundation for efficient productivity of microbial cell factories. Herein, we discuss the key technologies of adaptive evolution and their important applications in improvement of environmental tolerance and production efficiency of microbial cell factories. Moreover, we looked forward to the prospects of adaptive evolution to realize industrial production by microbial cell factories.

The adaptation of SARS-CoV-2 to humans

The process of adaptation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to humans probably had started decades ago, when its ancestor diverged from the bat coronavirus. The adaptive process comprises strategies the virus uses to overcome the respiratory tract defense barriers and replicate and shed in the host cells. These strategies include the impairment of interferon production, hiding immunogenic motifs, avoiding viral RNA detection, manipulating cell autophagy, triggering host cell death, inducing lymphocyte exhaustion and depletion, and finally, mutation and escape from immunity. In addition, SARS-CoV-2 employs strategies to take advantage of host cell resources for its benefits, such as inhibiting the ubiquitin-proteasome system, hijacking mitochondria functions, and usage of enhancing antibodies. It may be anticipated that as the tradeoffs of adaptation progress, the virus destructive burden will gradually subside. Some evidence suggests that SARS-CoV-2 will become part of the human respiratory virome, as had occurred with other coronaviruses, and coevolve with its host.

Adaptive evolution analysis of squalene synthase in medicinal plants of Araliaceae / 中草药

Objective: To analyze the adaptive evolution of squalene synthase (SS) in the medicinal plants of Araliaceae. Methods: The adaptive evolutionary analysis of 23 SS genes of seven medicinal plants of Araliaceae was carried out by using the branch model, site model, branch-site model, MEC model, SLAC, FEL, and REL of PAML software. Results: In the analysis of PAML and MEC models, most of the branches and loci were found to be under strong negative selection, and no positive selection sites were found. The analysis by SLAC, FEL, and REL also showed that there were a large number of negative selection sites, only 412P, 413N, and 415K were positive selection sites. Conclusion: This indicates that negative selection plays a leading role in SS gene of Araliaceae. The 412P, 413N, and 415K sites found may be involved in the activity of SS.

Fitness analysis between the L-sorbosone dehydrogenase modules and Ketogulonigenium vulgare chassis / 生物工程学报

Ketogulonigenium vulgare is an acid-producing strain in the process of two-step vitamin C fermentation. L-sorbosone dehydrogenase (SNDH) is one of the key enzymes during the biosynthesis of 2-keto-L-gulonic acid (2-KGA), the precursor of vitamin C. However, the catalytic mechanism of SNDH is unclear. According to the whole genome sequencing of K. vulgare, two genes encoding sorbosone dehydrogenases, one derived from the chromosome (named as sndhg) and one from plasmid (named as sndhp), were introduced into an industrial strain K. vulgare. The overexpression of gene sndhg had hardly effect on 2-KGA production, and the overexpression of gene sndhp produced an obvious byproduct in the fermentation broth. Combinational expression of sndhg/sndhp with pqqA (obtaining sndhg-pqqA and sndhp-pqqA modules) in K. vulgare resulted in the similar fermentation phenotype to two previous strains. After serial sub-cultivation of co-cultured Bacillus endophyticus with each engineered K. vulgare for 50 d, the conversion rate of 2-KGA increased by 15.4%, 179%, 0.65% and 125% compared with that of the parental K. vulgare with B. endophyticus. This study shows that adaptive evolution of microbial consortium is an effective strategy to increase the fitness between functional modules and chassis, thus quickly getting better strains for production of 2-KGA.

Signatures of positive selection at hemopexin (PEX) domain of matrix metalloproteinase-9 (MMP-9) gene.

Matrix metalloproteinases-9 (MMP-9) is an important cancer-associated, zinc-dependent endopeptidase. To investigate the natural selection hypothesis of MMP-9, the orthologous sequences from 12 vertebrates were compared and a molecular evolution analysis was performed. Results suggest that amino acid residues present in the middle region of the protein are more selectively constrained, whereas amino acid residues in the C-terminal region of the MMP-9 protein including exon 13 showed lowest conservation level in non-primate species, suggesting that it is an exon with fast evolving rate compared to the others analyzed. InterProScan analysis shows that exon 13 was located in hemopexin (PEX) domain of MMP-9. Positive selection was detected in PEX domain of MMP-9 protein between human and other species, which indicates that selective pressure may play a role in shaping the function of MMP-9 in the course of evolution.

Adaptive evolution in the S gene of hepatitis B virus from patients with occult HBV infection / 中华微生物学和免疫学杂志

Objective To detect the positively selected sites in the surface ( S) gene of hepatitis B viruses ( HBVs) from patients with occult HBV infection and to study the molecular mechanism of occult HBV infection.Methods The sequence of S gene from patients with occult HBV infection and reference strains of eight HBV genotypes ( A through H) were downloaded from GenBank and then alignment analysis were performed by using Clustal W software .Phylogenetic trees were constructed by using MEGA 5.05 soft-ware package.PAML4.7 was used to analyze positively selected sites .Results A total of 1286 HBV se-quences from patients with occult infection were searched in GenBank .One hundred and seventy-four com-plete gene sequences encoding surface S protein were screened after alignment analysis and confirmation , of which 13 sequences with nonsense mutation were removed .The likelihood ratio test showed that for both the 161 remained sequences and the 31 reference sequences , the selection models of M2, M3 and M8 were sig-nificantly better than the neutral models of M0, M1 and M7 (2△lnL<55.12, P<0.001).By using Bayes Empirical Bayes (BEB) analysis, 14 positively selected sites (including codon 3, 8, 40, 45, 46, 47, 49, 68, 126, 127, 164, 184, 207 and 210) were detected in the surface gene of HBVs from patients with occult HBV infection, eight of which were located at the immune epitope of HBsAg .However, only 2 positively se-lected sites were identified in reference sequences .Conclusion The long-lasting persistence of HBV in pa-tients with occult HBV infection might be caused by the adaptive evolution of their surface gene in a form of escape mutant under immune suppressive condition .