Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 23;13(1):10.
doi: 10.1186/s13568-023-01510-5.

Comparative genomic and transcriptome analysis of Bacillus velezensis CL-4 fermented corn germ meal

Long Chen  1 , Zihui Qu  1 , Wei Yu  1 , Lin Zheng  1 , Haixin Qiao  2 , Dan Wang  1 , Bingdong Wei  3 , Zijian Zhao  4
Affiliations

Comparative genomic and transcriptome analysis of Bacillus velezensis CL-4 fermented corn germ meal

Long Chen et al. AMB Express. .

Abstract

Bacillus, an excellent organic-degrading agent, can degrade lignocellulose. Notably, some B. velezensis strains encode lignocellulases. However, their ability to degrade lignocellulose in fermented feed is not much appreciated. This study performed a comparative genomic analysis of twenty-three B. velezensis strains to find common carbohydrate-active enzymes (CAZymes) encoding genes and evaluated their potential to degrade lignocellulose. The comparative genomic and CAZyme database-based analyses identified several potential CAZymes genes that degrade cellulose (GH1, GH4, GH5, GH13, GH16, GH32, PL1, and PL9), hemicellulose (GH11, GH26, GH43, GH51, and CE3) and lignin (AA4, AA6, AA7, and AA10). Furthermore, Illumina RNA-seq transcriptome analysis revealed the expression of more than 1794 genes in B. velezensis CL-4 fermented corn germ meal at 48 h (FCGM 48 h). Gene ontology analysis of expressed genes revealed their enrichment in hydrolase activity (breaking the glycosyl bonds during carbohydrate metabolism), indicating the upregulation of CAZymes. In total, 58 differentially upregulated CAZymes-encoding genes were identified in FCGM 48 h compared to FCGM 0 h. The upregulated CAZymes-encoding genes were related to cellulose (6-phospho-β-galactosidase and 6-phospho-α-glucosidase), starch (α-glucosidase and α-amylase), pectin (pectin lyase), and hemicellulose (arabinan endo-1,5-α-L-arabinosidase, xylan 1,4-beta-xylosidase, α-N-arabinofuranosidase, and acetyl xylan esterase). Importantly, arabinoxylan degradation mainly occurred in FCGM 48 h, followed by partial degradation of cellulose, pectin, and starch. This study can support the development of enzymatic cocktails for the solid-state fermented feed (SFF).

Keywords: B. velezensis CL-4; Comparative genomics; Corn germ meal; Lignocellulose-degrading enzymes; Transcriptome.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no confict of interest.

Figures

Fig. 1
Fig. 1
The total number of genes in each species and genes/gene family were obtained by comparative CAZyme analysis of the twenty-three B. velezensis strains. Side circles represent the total number of genes in a species, and the center circle represents the number of gene families shared by the B. velezensis strains. The total number of genes/gene families shared by a B. velezensis strain is shown in parenthesis
Fig. 2
Fig. 2
Gene ontology (GO) enrichment analysis of differentially expressed genes in B. velezensis CL-4 between the FCGM-0 h and FCGM-48 h groups. A A bubble diagram and B bar chart show the results of the GO enrichment analysis. MF stands for molecular function, BP for biological processes, and CC for cellular components
Fig. 2
Fig. 2
Gene ontology (GO) enrichment analysis of differentially expressed genes in B. velezensis CL-4 between the FCGM-0 h and FCGM-48 h groups. A A bubble diagram and B bar chart show the results of the GO enrichment analysis. MF stands for molecular function, BP for biological processes, and CC for cellular components
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Adeniji AA, Loots DT, Babalola OO. Bacillus velezensis: phylogeny, useful applications, and avenues for exploitation. Appl Microbiol Biot. 2019;103(9):3669–3682. doi: 10.1007/s00253-019-09710-5. - DOI - PubMed
    1. Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high throughput sequencing data. Bioinformatics. 2015;31(2):166–169. doi: 10.1093/bioinformatics/btu638. - DOI - PMC - PubMed
    1. Bai W, Xue Y, Zhou C, Ma Y. Cloning, expression, and characterization of a novel alkali-tolerant xylanase from alkaliphilic Bacillus. sp SN5. Biotechnol Appl Bioc. 2015;62(2):208–217. doi: 10.1002/bab.1265. - DOI - PubMed
    1. Bandounas L, Wierckx NJ, de Winde JH, Ruijssenaars HJ. Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential. BMC Biotechnol. 2011;11:94. doi: 10.1186/1472-6750-11-94. - DOI - PMC - PubMed
    1. Barker IJ, Petersen L, Reilly PJ. Mechanism of xylobiose hydrolysis by GH43 β-xylosidase. J Phys Chem B. 2010;114(46):15389–15393. doi: 10.1021/jp107886e. - DOI - PubMed

LinkOut - more resources