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. 2016 Nov 30;6:38248.
doi: 10.1038/srep38248.

Complete Genome Sequence and Transcriptomic Analysis of a Novel Marine Strain Bacillus Weihaiensis Reveals the Mechanism of Brown Algae Degradation

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Free PMC article

Complete Genome Sequence and Transcriptomic Analysis of a Novel Marine Strain Bacillus Weihaiensis Reveals the Mechanism of Brown Algae Degradation

Yueming Zhu et al. Sci Rep. .
Free PMC article

Abstract

A novel marine strain representing efficient degradation ability toward brown algae was isolated, identified, and assigned to Bacillus weihaiensis Alg07. The alga-associated marine bacteria promote the nutrient cycle and perform important functions in the marine ecosystem. The de novo sequencing of the B. weihaiensis Alg07 genome was carried out. Results of gene annotation and carbohydrate-active enzyme analysis showed that the strain harbored enzymes that can completely degrade alginate and laminarin, which are the specific polysaccharides of brown algae. We also found genes for the utilization of mannitol, the major storage monosaccharide in the cell of brown algae. To understand the process of brown algae decomposition by B. weihaiensis Alg07, RNA-seq transcriptome analysis and qRT-PCR were performed. The genes involved in alginate metabolism were all up-regulated in the initial stage of kelp degradation, suggesting that the strain Alg07 first degrades alginate to destruct the cell wall so that the laminarin and mannitol are released and subsequently decomposed. The key genes involved in alginate and laminarin degradation were expressed in Escherichia coli and characterized. Overall, the model of brown algae degradation by the marine strain Alg07 was established, and novel alginate lyases and laminarinase were discovered.

Figures

Figure 1
Figure 1. Phylogenetic tree of 16 S rRNA sequences from B. weihaiensis Alg07 and other known Bacillus species.
The trees containing the same species were collapsed and indicated with triangles. Several well-studied Bacillus species are highlighted in blue frame.
Figure 2
Figure 2. Circular representation of the genome map of B. weihaiensis Alg07.
The circles from the innermost to the outermost: Circle 1 for GC skew (G−C)/(G+C); Circle 2 for GC content; Circle 3 for rRNA and tRNA; Circles 4 and 5 for protein coding genes in the reverse and forward strands respectively; Circles 6 and 7 for N4-methylcytosine (m4C) and N6-methyladenosine (m6A) sites in CDS/rRNA/tRNA in the reverse and forward strands respectively; and Circle 8 for m4C and m6A sites in intergene regions.
Figure 3
Figure 3. Expression levels of key genes in Alg07 cells after 12, 24 and 48 h incubation identified by qRT-PCR analysis.
The 12 h incubation sample was set as the reference (RQ value was 1). RQ: Relative Quantification.
Figure 4
Figure 4. Loci for alginate, laminarin, and mannitol utilization of B. weihaiensis Alg07.
AlgL, alginate lyase; ABC, ABC transporter components; TCS, two-component system; DehR, DEH reductase; OlaL, oligoalginate lyase; KdgK, KDG kinase; KdpgA, KDPG aldolase; HP, hypothetical protein; Lam1, β-glucosidase; Lam2, laminarinase; mannitol PTS, mannitol specific PTS system; MPDH, mannitol-1-phosphate 5-dehydrogenase.
Figure 5
Figure 5. Model of brown algae degradation by B. weihaiensis Alg07.
Figure 6
Figure 6. Domain architectures of the high-molecular-weight enzymes in B. weihaiensis Alg07.
Hepar_II_III, heparinase II/III-like protein; CLAL, calcium-activated chloride channel; F5_F8_type_C, F5/8 type C domain; Gram_pos_anchor, Gram-positive anchor; Beta_helix, right-handed beta helix region; AMPK1_CBM, glycogen recognition site of AMP-activated protein kinase; CBM48, carbohydrate-binding module 48; Alpha-amylase, α-amylase catalytic domain; Big_2, bacterial Ig-like domain (group 2); PUD, bacterial pullanase-associated domain.

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