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The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.

Qin QL, Zhang XY, Wang XM, Liu GM, Chen XL, Xie BB, Dang HY, Zhou BC, Yu J, Zhang YZ - BMC Genomics (2010)

Bottom Line: There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases.SM-A87 is a moderate halophile.SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China.

ABSTRACT

Background: Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes.

Results: The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins.

Conclusion: Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

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The MEROPS category of the extracellular peptidases from Z. profunda SM-A87, G. forsetii KT0803 and S. piezotolerans WP3.
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Figure 2: The MEROPS category of the extracellular peptidases from Z. profunda SM-A87, G. forsetii KT0803 and S. piezotolerans WP3.

Mentions: Fifty-two of the SM-A87 peptidases with signal peptides can be assigned to different families in the MEROPS peptidase database [38]. As shown in Figure 2, the peptidases mainly belong to families of metallopeptidases and serine peptidases, consistent with our previous study that the extracellular peptidases of marine sedimentary bacteria are mainly serine proteases and metalloproteases [9]. Compared to G. forsetii KT0803, deep-sea bacteria SM-A87 and S. piezotolerans WP3 have more peptidases in families S09 and S41, but fewer in family M14 (Figure 2). The variety of extracellular peptidases suggests that SM-A87 has the capacity to decompose diverse peptides and proteins from its surroundings. For instance, SM-A87 has six exported family M01 peptidases, which are aminopeptidases. It has been reported that when marine bacteria grow on HMW dissolved organic nitrogen (DON) as the sole nitrogen source, aminopeptidase activity is greatly enhanced [39]. Aminopeptidase activity in the deep-sea sediment is higher than that in the surface seawater; however, this is not the case for other hydrolysis enzymes [40]. The large number of aminopeptidases secreted by SM-A87 may contribute to the high aminopeptidase activity in the deep-sea sediment, and suggests that SM-A87 may be able to respond to HMW DON and decompose it. SM-A87 secretes seven S09 peptidases, which are prolyl oligopeptidases that cannot degrade peptides of more than 30 residues in length [41]. Therefore, the S09 peptidases specifically hydrolyze oligopeptides. Notably, there are six exported peptidases that contain a PDZ domain, which is known to be involved in peptide binding [42]. The large number of PDZ domain-containing peptidases secreted by SM-A87 suggests a strategy for binding and degrading proteins, similar to the PKD domains of exported proteins in G. forsetii KT0803 [19]. In the deep-sea sedimentary nitrogen cycle, the process by which particulate organic nitrogen is converted to NH4+ is known to be dominated by bacteria but is poorly characterized [1,14]. The secreted peptidases of SM-A87 may play an important role in this process.


The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation.

Qin QL, Zhang XY, Wang XM, Liu GM, Chen XL, Xie BB, Dang HY, Zhou BC, Yu J, Zhang YZ - BMC Genomics (2010)

The MEROPS category of the extracellular peptidases from Z. profunda SM-A87, G. forsetii KT0803 and S. piezotolerans WP3.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864250&req=5

Figure 2: The MEROPS category of the extracellular peptidases from Z. profunda SM-A87, G. forsetii KT0803 and S. piezotolerans WP3.
Mentions: Fifty-two of the SM-A87 peptidases with signal peptides can be assigned to different families in the MEROPS peptidase database [38]. As shown in Figure 2, the peptidases mainly belong to families of metallopeptidases and serine peptidases, consistent with our previous study that the extracellular peptidases of marine sedimentary bacteria are mainly serine proteases and metalloproteases [9]. Compared to G. forsetii KT0803, deep-sea bacteria SM-A87 and S. piezotolerans WP3 have more peptidases in families S09 and S41, but fewer in family M14 (Figure 2). The variety of extracellular peptidases suggests that SM-A87 has the capacity to decompose diverse peptides and proteins from its surroundings. For instance, SM-A87 has six exported family M01 peptidases, which are aminopeptidases. It has been reported that when marine bacteria grow on HMW dissolved organic nitrogen (DON) as the sole nitrogen source, aminopeptidase activity is greatly enhanced [39]. Aminopeptidase activity in the deep-sea sediment is higher than that in the surface seawater; however, this is not the case for other hydrolysis enzymes [40]. The large number of aminopeptidases secreted by SM-A87 may contribute to the high aminopeptidase activity in the deep-sea sediment, and suggests that SM-A87 may be able to respond to HMW DON and decompose it. SM-A87 secretes seven S09 peptidases, which are prolyl oligopeptidases that cannot degrade peptides of more than 30 residues in length [41]. Therefore, the S09 peptidases specifically hydrolyze oligopeptides. Notably, there are six exported peptidases that contain a PDZ domain, which is known to be involved in peptide binding [42]. The large number of PDZ domain-containing peptidases secreted by SM-A87 suggests a strategy for binding and degrading proteins, similar to the PKD domains of exported proteins in G. forsetii KT0803 [19]. In the deep-sea sedimentary nitrogen cycle, the process by which particulate organic nitrogen is converted to NH4+ is known to be dominated by bacteria but is poorly characterized [1,14]. The secreted peptidases of SM-A87 may play an important role in this process.

Bottom Line: There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases.SM-A87 is a moderate halophile.SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China.

ABSTRACT

Background: Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes.

Results: The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins.

Conclusion: Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

Show MeSH