Sequence analysis of a beta-agarase gene (pjaA) from Pseudomonas sp. isolated from marine environment

Diversity of Culturable Bacteria from the Coral Reef Areas in the South China Sea and Their Agar-Degrading Abilities

The South China Sea (SCS) is abundant in marine microbial resources with high primary productivity, which is crucial for sustaining the coral reef ecosystem and the carbon cycle. Currently, research on the diversity of culturable bacteria in the SCS is relatively extensive, yet the culturable bacteria in coral reefs has been poorly understood. In this study, we analyzed the bacterial community structure of seawater samples among Daya Bay (Fujian Province), Qionghai (Hainan Province), Xisha Islands, and the southern South China Sea based on culturable methods and detected their abilities for agar degradation. There were 441 bacterial strains, belonging to three phyla, five classes, 43 genera, and 101 species, which were isolated by marine agar 2216E (MA; Becton Dickinson). Strains within Gammaproteobacteria were the dominant group, accounting for 89.6% of the total bacterial isolates. To investigate vibrios, which usually correlated with coral health, 348 isolates were obtained from TCBS agar, and all isolates were identified into three phylum, three classes, 14 orders, 25 families, and 48 genera. Strains belonging to the genus Vibrio had the greatest number (294 strains), indicating the high selectivity of TCBS agar for vibrios. Furthermore, nineteen strains were identified as potentially novel species according to the low 16S rRNA gene similarity (<98.65%), and 28 strains (15 species) had agar-degrading ability. These results indicate a high diversity of culturable bacteria in the SCS and a huge possibility to find novel and agar-degrading species. Our study provides valuable microbial resources to maintain the stability of coral ecosystems and investigate their roles in the marine carbon cycle.

Thermostability mechanisms of β-agarase by analyzing its structure through molecular dynamics simulation

Agarase is a natural catalyst with a good prospect in the industry. However, most of the currently discovered β-agarases are unsuitable for relatively high-temperature and high-pressure conditions required by industrial production. In this study, molecular dynamics simulations were first used to investigate the dynamic changes of folding and unfolding of mesophile and thermophile β-agarases (i.e., 1URX and 3WZ1) to explore the thermostability mechanism at three high temperatures (300 K, 400 K, and 500 K). Results showed that the sequence identity of 3WZ1 and 1URX reaches 48.8%. 1URX has a higher thermal sensitivity and less thermostability than 3WZ1 as more thermostable regions and hydrogen bonds exist in 3WZ1 compared with 1URX. The structures of 1URX and 3WZ1 become unstable with increasing temperatures up to 500 K. The strategies to increase the thermostability of 1URX and 3WZ1 are discussed. This study could provide insights into the design and modification of β-agarases at a high temperature.

Molecular cloning, characterization and enzymatic properties of a novel βeta-agarase from a marine isolate Psudoalteromonas SP. AG52

An agar-degrading Pseudoalteromonas sp. AG52 bacterial strain was identified from the red seaweed Gelidium amansii collected from Jeju Island, Korea. A β-agarase gene which has 96.8% nucleotide identity to Aeromonas β-agarase was cloned from this strain, and was designated as agaA. The coding region is 870 bp, encoding 290 amino acids and possesses characteristic features of the glycoside hydrolase family (GHF)-16. The predicted molecular mass of the mature protein was 32 kDa. The recombinant β-agarase (rAgaA) was overexpressed in Escherichia coli and purified as a fusion protein. The optimal temperature and pH for activity were 55 °C and 5.5, respectively. The enzyme had a specific activity of 105.1 and 79.5 unit/mg toward agar and agarose, respectively. The pattern of agar hydrolysis demonstrated that the enzyme is an endo-type β-agarase, producing neoagarohexaose and neoagarotetraose as the final main products. Since, Pseudoalteromonas sp. AG52 encodes an agaA gene, which has greater identity to Aeromonas β-agarase, the enzyme could be considered as novel, with its unique bio chemical characteristics. Altogether, the purified rAgaA has potential for use in industrial applications such as development of cosmetics and pharmaceuticals.

Cloning, purification and biochemical characterization of beta agarase from the marine bacterium Pseudoalteromonas sp. AG4

A gene (agrP) encoding a beta-agarase from Pseudoalteromonas sp. AG4 was cloned and expressed in Escherichia coli. The agrP primary structure consists of an 870-bp open reading frame (ORF) encoding 290 amino acids (aa). The predicted molecular mass and isoelectric point were determined at 33 kDa and 5.9, respectively. The signal peptide was predicted to be 21 aa. The deduced aa sequence showed 98.6% identity to beta-agarase from Pseudoalteromonas atlantica. The recombinant protein was purified as a fusion protein and biochemically characterized. The purified beta-agarase (AgaP) had specific activity of 204.4 and 207.5 units/mg towards agar and agarose, respectively. The enzyme showed maximum activity at 55 degrees C and pH 5.5. It was stable at pH 4.5 to 8.0 and below 55 degrees C for 1 h. The enzyme produced neoagarohexaose and neoagarotetraose from agar and in addition to that neoagarobiose from the agarose. The neoagarooligosaccharides were biologically active. Hence, AgaP is a useful enzyme source for use by cosmetic and pharmaceutical industries.

Investigation of the role of a β(1–4) agarase produced by Pseudoalteromonas gracilis B9 in eliciting disease symptoms in the red alga Gracilaria gracilis

Gracilariaspecies are an important source of agar. The South AfricanGracilariaindustry has experienced a number of setbacks over the last decade in the form of complete or partial die-offs of the agarophyte growing in Saldanha Bay, which may be attributed to bacterial infection. Since a positive correlation was observed between the presence of agarolytic epiphytes and bacterial pathogenicity, we investigated the role of an agarase in the virulence mechanism employed by a bacterium that elicits disease inGracilaria gracilis. The recombinant plasmid pDA1, isolated from aPseudoalteromonas gracilisB9 genomic library, was responsible for the agarolytic activity exhibited byEscherichia colitransformants when grown on solid medium. Ablastsearch of the GenBank database showed that an 873 bp ORF (aagA) located on pDA1 had 85 % identity to theβ-agarase (dagA) fromPseudoalteromonas atlanticaATCC 19262T(or IAM 12927T) at the amino acid level. AagA was purified from the extracellular medium of anE. colitransformant harbouring pDA1 by using a combination of gel filtration and ion-exchange chromatography. AagA has anMrof 30 000 on SDS-PAGE. TLC of the digestion products of AagA showed that the enzyme cleaves theβ-(1,4) linkages of agarose to yield predominately neoagarotetraose. Western hybridization confirmed that the cloned agarase was in fact the extracellularβ-agarase ofP. gracilisB9. The observed relationship between disease symptoms ofG. gracilisand the agarolytic phenotype ofP. gracilisB9 was confirmed. Transmission electron microscope examination of cross sections of both healthyG. gracilisandG. gracilisinfected withP. gracilis, revealed a weakening of the cell structure in the latter plants. Immunogold-labelled antibodies localized the agarasein situto the cell walls of bleachedG. gracilis. Thus, the weakening observed in the cell structure ofG. gracilisinfected withP. graciliscan be attributed to degradation of the mucilaginous component of the cell wall of the bleached thalli.