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An assimilatory sulfite reductase, CysI, negatively regulates the dormancy of Microbulbifer aggregans CCB-MM1T

Diyana T, Furusawa G

J Basic Microbiol, 2021 Dec;61(12):1124-1132.
PMID: 34796964 DOI: 10.1002/jobm.202100198

Sulfur is one of the common and essential elements of all life. Sulfate, which is a major source of sulfur, plays an important role in synthesizing sulfur-containing amino acids, such as cysteine and methionine, organic compounds essential to all living organisms. Some investigations reported that the assimilatory sulfate reduction pathway (ASRP) involved in cysteine synthesis is crucial to entering bacterial dormancy in pathogens. Our previous investigation reported that the halophilic marine bacterium, Microbulbifer aggregans CCB-MM1T , possesses an ASRP and the dissimilatory sulfate reduction pathway (DSRP). The bacterium might use DSRP to generate energy required for entering its dormant. However, the role of the ASRP in the dormancy of M. aggregans CCB-MM1T was so far unknown. In this study, we found that genes involved in ASRP were downregulated in the dormancy. The disruption of the gene encoding an assimilatory sulfite reductase, cysI, suppressed a completely dormant state under low nutrient conditions. In addition, the cysI mutant showed cell aggregation at the middle-exponential phase under high nutrient conditions, indicating that the mutation might be stimulated to enter the dormancy. The wild-type phenotype of the bacterium was recovered by the addition of cysteine. These results suggested that cysteine concentration may play an important role in inducing the dormancy of M. aggregans.
Fulltext Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1

Furusawa G, Iwamoto K

PeerJ, 2022;10:e12867.
PMID: 35223202 DOI: 10.7717/peerj.12867

Inorganic and synthetic flocculants are widely investigated for removing harmful microalgae, such as Microcystis aeruginosa. However, their toxicity and non-biodegradability are shortcomings. Bioflocculants based on extracellular polysaccharides have attracted much attention as alternative flocculants. However, its high production cost is a limiting factor for applying bioflocculants. Here, we investigate the potential of the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1, as a novel flocculant on M. aeruginosa cells. The removal efficiency of M. aeruginosa cells by the dead cells was measured by mixing and shaking both components in a buffer with 5 mM CaCl2 in different incubation times and concentrations of the dead cells. After that, the minimum effective concentration of CaCl2 was determined. The combination effect of FeCl3 and the dead cells on the removal efficiency was tested. The structure of cell aggregates consisted of the dead cells and M. aeruginosa cells were also observed using a scanning electron microscope. The maximum removal efficiency (75.39%) was reached within 3 min in the presence of CaCl2 when 5 mg/ml of the dead cells (wet cells) were added. The optimal concentration of CaCl2 was 5 mM. The combination of the dead cells and a low concentration of FeCl3 (10 mg/L) with 5 mM of CaCl2 significantly improved the removal efficiency by about 1.2 times (P
Polysaccharide degradation in Cellvibrionaceae: Genomic insights of the novel chitin-degrading marine bacterium, strain KSP-S5-2, and its chitinolytic activity

Lau NS, Furusawa G

Sci Total Environ, 2024 Feb 20;912:169134.
PMID: 38070563 DOI: 10.1016/j.scitotenv.2023.169134

In this study, we present the genome characterization of a novel chitin-degrading strain, KSP-S5-2, and comparative genomics of 33 strains of Cellvibrionaceae. Strain KSP-S5-2 was isolated from mangrove sediment collected in Balik Pulau, Penang, Malaysia, and its 16S rRNA gene sequence showed the highest similarity (95.09%) to Teredinibacter franksiae. Genome-wide analyses including 16S rRNA gene sequence similarity, average nucleotide identity, digital DNA-DNA hybridization, and phylogenomics, suggested that KSP-S5-2 represents a novel species in the family Cellvibrionaceae. The Cellvibrionaceae pan-genome exhibited high genomic variability, with only 1.7% representing the core genome, while the flexible genome showed a notable enrichment of genes related to carbohydrate metabolism and transport pathway. This observation sheds light on the genetic plasticity of the Cellvibrionaceae family and the gene pools that form the basis for the evolution of polysaccharide-degrading capabilities. Comparative analysis of the carbohydrate-active enzymes across Cellvibrionaceae strains revealed that the chitinolytic system is not universally present within the family, as only 18 of the 33 genomes encoded chitinases. Strain KSP-S5-2 displayed an expanded repertoire of chitinolytic enzymes (25 GH18, two GH19 chitinases, and five GH20 β-N-acetylhexosaminidases) but lacked genes for agar, xylan, and pectin degradation, indicating specialized enzymatic machinery focused primarily on chitin degradation. Further, the strain degraded 90% of chitin after 10 days of incubation. In summary, our findings provided insights into strain KSP-S5-2's genomic potential, the genetics of its chitinolytic system, genomic diversity within the Cellvibrionaceae family in terms of polysaccharide degradation, and its application for chitin degradation.
Crystal structure of a neoagarobiose-producing GH16 family β-agarase from Persicobacter sp. CCB-QB2

Teh AH, Fazli NH, Furusawa G

Appl Microbiol Biotechnol, 2020 Jan;104(2):633-641.
PMID: 31784792 DOI: 10.1007/s00253-019-10237-y

PdAgaC from the marine bacterium Persicobacter sp. CCB-QB2 is a β-agarase belonging to the glycoside hydrolase family 16 (GH16). It is one of only a handful of endo-acting GH16 β-agarases able to degrade agar completely to produce neoagarobiose (NA2). The crystal structure of PdAgaC's catalytic domain, which has one of the highest Vmax value at 2.9 × 103 U/mg, was determined in order to understand its unique mechanism. The catalytic domain is made up of a typical β-jelly roll fold with two additional insertions, and a well-conserved but wider substrate-binding cleft with some minor changes. Among the unique differences, two unconserved residues, Asn226 and Arg286, may potentially contribute additional hydrogen bonds to subsites -1 and +2, respectively, while a third, His185 from one of the additional insertions, may further contribute another bond to subsite +2. These additional hydrogen bonds may probably have enhanced PdAgaC's affinity for short agaro-oligosaccharides such as neoagarotetraose (NA4), rendering it capable of binding NA4 strongly enough for rapid degradation into NA2.
Multifaceted interactions between the pseudomonads and insects: mechanisms and prospects

Teoh MC, Furusawa G, Veera Singham G

Arch Microbiol, 2021 Jul;203(5):1891-1915.
PMID: 33634321 DOI: 10.1007/s00203-021-02230-9

Insects and bacteria are the most widespread groups of organisms found in nearly all habitats on earth, establishing diverse interactions that encompass the entire range of possible symbiotic associations from strict parasitism to obligate mutualism. The complexity of their interactions is instrumental in shaping the roles of insects in the environment, meanwhile ensuring the survival and persistence of the associated bacteria. This review aims to provide detailed insight on the multifaceted symbiosis between one of the most versatile bacterial genera, Pseudomonas (Gammaproteobacteria: Pseudomonadaceae) and a diverse group of insect species. The Pseudomonas engages with varied interactions with insects, being either a pathogen or beneficial endosymbiont, as well as using insects as vectors. In addition, this review also provides updates on existing and potential applications of Pseudomonas and their numerous insecticidal metabolites as biocontrol agents against pest insects for the improvement of integrated pest management strategies. Here, we have summarized several known modes of action and the virulence factors of entomopathogenic Pseudomonas strains essential for their pathogenicity against insects. Meanwhile, the beneficial interactions between pseudomonads and insects are currently limited to a few known insect taxa, despite numerous studies reporting identification of pseudomonads in the guts and haemocoel of various insect species. The vector-symbiont association between pseudomonads and insects can be diverse from strict phoresy to a role switch from commensalism to parasitism following a dose-dependent response. Overall, the pseudomonads appeared to have evolved independently to be either exclusively pathogenic or beneficial towards insects.
Calcium is required for ixotrophy of Aureispira sp. CCB-QB1

Furusawa G, Hartzell PL, Navaratnam V

Microbiology (Reading), 2015 Oct;161(10):1933-1941.
PMID: 26306656 DOI: 10.1099/mic.0.000158

Ixotrophy is a process that enables certain microbes to prey on other cells. The ability of cells to aggregate or adhere is thought to be a significant initial step in ixotrophy. The gliding, multicellular filamentous bacterium Aureispira sp. CCB-QB1 belongs to the family Saprospiraceae and preys on bacteria such as Vibrio sp. in seawater. Adhesion and cell aggregation were coincident with preying and were hypothesized to play an important role in the ixotrophy in this bacterium. To test this hypothesis, experiments to elucidate the mechanisms of aggregation or adhesion in this bacterium were performed. The ability of Aureispira QB1 to adhere and aggregate to prey bacterium, Vibrio sp., required divalent cations, especially calcium ions. In the presence of calcium, Aureispira QB1 cells captured 99 % of Vibrio sp. cells after 60 min of incubation. Toluidine blue O, which binds acidic polysaccharides, bound to Aureispira QB1 and inhibited adhesion of Aureispira QB1. These results suggest that acidic polysaccharides are needed for aggregation or adhesion of Aureispira and that calcium ions play a significant role in these phenomena.
Mangrovimonas xylaniphaga sp. nov. isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia

Dinesh B, Furusawa G, Amirul AA

Arch Microbiol, 2017 Jan;199(1):63-67.
PMID: 27506901 DOI: 10.1007/s00203-016-1275-8

A Gram-staining-negative, aerobic, rod-shaped, yellow-orange-pigmented, gliding bacterium, designated as strain ST2L12(T), was isolated from estuarine mangrove sediment from Matang Mangrove Forest, Perak, Malaysia. Strain ST2L12(T) grew at 15-39 °C, pH 6-8 and in 1-6 % (w/v) NaCl. This strain was able to degrade xylan and casein. 16S rRNA gene sequence analysis showed 95.3-92.8 % similarity to members of the genera Mangrovimonas, Meridianimaribacter, Sediminibacter, Gaetbulibacter and Hoppeia. Phylogenetic analysis indicated that it belonged to the family Flavobacteriaceae. Respiratory quinone present was menaquinone-6 (MK-6), and the DNA G+C content was 38.3 mol%. The predominant fatty acids were iso-C15:0, iso-C15:1, C15:0 and iso-C17:0 3-OH. Moreover, previous genome comparison study showed that the genome of ST2L12(T) is 1.4 times larger compared to its closest relative, Mangrovimonas yunxiaonensis LYYY01(T). Phenotypic, fatty acid, 16S rRNA gene sequence and previous genome data indicate that strain ST2L12(T) represents a novel species of the genus Mangrovimonas in the family Flavobacteriaceae, for which the name Mangrovimonas xylaniphaga sp. nov. is proposed. The type strain of Mangrovimonas xylaniphaga is ST2L12(T) (=LMG 28914(T)=JCM 30880(T)).
Biochemical Characterization of Thermostable and Detergent-Tolerant β-Agarase, PdAgaC, from Persicobacter sp. CCB-QB2

Hafizah NF, Teh AH, Furusawa G

Appl Biochem Biotechnol, 2019 Mar;187(3):770-781.
PMID: 30073451 DOI: 10.1007/s12010-018-2849-5

Persicobacter sp. CCB-QB2 belonging to the family Flammeovirga is an agarolytic bacterium and exhibits a diauxic growth in the presence of tryptone and agarose. A glycoside hydrolase (GH) 16 β-agarase, PdAgaC, was identified in the genome of the bacterium and was highly expressed during the second growth phase, indicating the agarase may play an important role in the diauxic growth. In this study, the catalytic domain of PdAgaC (PdAgaCgh) was cloned and characterized. PdAgaCgh showed thermostability at 50 °C and tolerance towards several detergents. In addition, the activity of PdAgaCgh after incubation with 0.1% of SDS and Triton X-100 increased approximately 1.2-fold. On the other hand, PdAgaCgh was sensitive to Fe2+, Ni2+, and Cu2+. The Km and Vmax of PdAgaCgh were 5.15 mg/ml and 2.9 × 103 U/mg, respectively. Interestingly, although the major hydrolytic product was neoagarobiose (NA2), monomeric sugar was also detected by thin-layer chromatographic analysis.
Fulltext Metabolic strategies of dormancy of a marine bacterium Microbulbifer aggregans CCB-MM1: Its alternative electron transfer chain and sulfate-reducing pathway

Furusawa G, Diyana T, Lau NS

Genomics, 2022 01;114(1):443-455.
PMID: 33689784 DOI: 10.1016/j.ygeno.2021.02.024

Bacterial dormancy plays a crucial role in maintaining the functioning and diversity of microbial communities in natural environments. However, the metabolic regulations of the dormancy of bacteria in natural habitats, especially marine habitats, have remained largely unknown. A marine bacterium, Microbulbifer aggregans CCB-MM1 exhibits rod-to-coccus cell shape change during the dormant state. Therefore, to clarify the metabolic regulation of the dormancy, differential gene expression analysis based on RNA-Seq was performed between rod- (vegetative), intermediate, and coccus-shaped cells (dormancy). The RNA-Seq data revealed that one of two distinct electron transfer chains was upregulated in the dormancy. Dissimilatory sulfite reductase and soluble hydrogenase were also highly upregulated in the dormancy. In addition, induction of the dormancy of MM1 in the absence of MgSO4 was slower than that in the presence of MgSO4. These results indicate that the sulfate-reducing pathway plays an important role in entering the dormancy of MM1.
Fulltext Genome sequence data of Bacillus sp. CCB-MMP212 isolated from Malaysian mangrove: A potential strain in arsenic resistance with ArsI, C•As lyase

Azami NA, Lau NS, Furusawa G

Data Brief, 2022 Dec;45:108597.
PMID: 36164294 DOI: 10.1016/j.dib.2022.108597

Bacillus sp. CCB-MMP212 is a Gram-positive bacterium isolated from mangrove sediment in Matang Perak, Malaysia (4.85496°E, 100.73495°N). Genome sequencing was performed using the Oxford Nanopore and Illumina platforms. The assembled genome was annotated using the rapid annotation subsystem technology server (RAST) (rast.nmpdr.org). The genome size of the Bacillus sp. CCB-MMP212 was 6,151,644 base pairs (bp) with a G+C content of 34.75%. The genome includes 6,311 coding sequences and 58 RNAs. The sequence has been deposited at Genbank with the accession number of JALDQE000000000. Interestingly, an arsenic resistance (ars) operon consisted of arsenic resistance operon repressor (arsR), ACR3 family arsenite efflux transporter (arsB), and arsenate reductase (arsC) genes were found in the genome. In addition, the arsenic inducible gene (arsI), which encoded a dioxygenase with C•As lyase activity, was also found in the ars operon. The enzyme is crucial for the methylation of methylarsonous acid [MAs(III)] and trivalent roxarsone [Rox(III)]. This dataset reveals the genetic ability of this strain in arsenic resistance. To the best of our knowledge, the arsI encoding C•As lyase is rarely reported within the genus Bacillus. Therefore, the dataset presented in this manuscript provides further insight into the arsenic resistance mechanisms of the genus Bacillus.
Saccharobesus litoralis gen. nov., sp. nov., a novel alginate-degrading bacterium isolated from the surface of intertidal algal turf

Amrina RA, Furusawa G, Lau NS

Int J Syst Evol Microbiol, 2021 Nov;71(11).
PMID: 34752210 DOI: 10.1099/ijsem.0.005087

A novel rod-shaped, Gram-stain-negative, strictly aerobic and alginate-degrading marine bacterium, designated CCB-QB4T, was isolated from a surface of algal turf collected from a coastal area of Penang, Malaysia. The cells showed motility by a lateral flagellum. The rod-shaped cells formed long chains end-to-end. Phylogenetic analysis based on the 16S rRNA gene sequence of strain CCB-QB4T showed 94.07, 92.69, 91.52 and 90.90 % sequence similarity to Algibacillus agarilyticus RQJ05T, Catenovulum maritimum Q1T, Catenovulum agarivorans YM01T and Catenovulum sediminis D2T, respectively. Strain CCB-QB4T formed a cluster with A. agarilyticus RQJ05T. Strain CCB-QB4T was catalase-negative, oxidase-positive, and degraded agar, alginate, and starch. Cell growth was observed at 15-40 °C, at pH 7.0-10.0 and in the presence of 1-6 % (w/v) NaCl and glucose. The major fatty acids were summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH), C16 : 0 and C18 : 1 ω7c. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified glycolipids, an unidentified phospholipid and unidentified lipid. The major respiratory quinone was ubiquinone-8. The genomic DNA G+C content was 46.7 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain CCB-BQ4T represents a novel species in a new genus, for which the name Saccharobesus litoralis gen. nov., sp. nov. is proposed. The type strain is CCB-QB4T (=JCM 33513T=CCB-MBL 5008T).
Fulltext Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2

Sim PF, Furusawa G, Teh AH

Sci Rep, 2017 10 20;7(1):13656.
PMID: 29057942 DOI: 10.1038/s41598-017-13288-1

AlyQ from Persicobacter sp. CCB-QB2 is an alginate lyase with three domains - a carbohydrate-binding domain modestly resembling family 16 carbohydrate-binding module (CBM16), a family 32 CBM (CBM32) domain, and an alginate lyase domain belonging to polysaccharide lyase family 7 (PL7). Although AlyQ can also act on polyguluronate (poly-G) and polymannuronate (poly-M), it is most active on alginate. Studies with truncated AlyQ showed that the CBM32 domain did not contribute to enhancing AlyQ's activity under the assayed conditions. Nevertheless, it could bind to cleaved but not intact alginate, indicating that the CBM32 domain recognises alginate termini. The crystal structure containing both CBM32 and catalytic domains show that they do not interact with one another. The CBM32 domain contains a conserved Arg that may bind to the carboxyl group of alginate. The catalytic domain, meanwhile, shares a conserved substrate-binding groove, and the presence of two negatively charged Asp residues may dictate substrate specificity especially at subsite +1. As Persicobacter sp. CCB-QB2 was unable to utilise alginate, AlyQ may function to help the bacterium degrade cell walls more efficiently.
Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest

Moh TH, Furusawa G, Amirul AA

Int J Syst Evol Microbiol, 2017 Oct;67(10):4089-4094.
PMID: 28905698 DOI: 10.1099/ijsem.0.002258

A novel, rod-shaped, Gram-stain-negative, halophilic and non-motile bacterium, designated CCB-MM1T, was isolated from a sample of estuarine sediment collected from Matang Mangrove Forest, Malaysia. The cells possessed a rod-coccus cell cycle in association with growth phase and formed aggregates. Strain CCB-MM1T was both catalase and oxidase positive, and able to degrade starch. Optimum growth occurred at 30 °C and pH 7.0 in the presence of 2-3 % (w/v) NaCl. The 16S rRNA gene sequence of strain CCB-MM1T showed 98.12, 97.46 and 97.33 % sequence similarity with Microbulbifer rhizosphaerae Cs16bT, Microbulbifer maritimus TF-17T and Microbulbifergwangyangensis GY2T respectively. Strain CCB-MM1T and M. rhizosphaerae Cs16bT formed a cluster in the phylogenetic tree. The major cellular fatty acids were iso-C17 : 1 ω9c and iso-C15 : 0, and the total polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphoaminolipid, two unidentified lipids, an unidentified glycolipid and an unidentified aminolipid. The major respiratory quinone was ubiquinone Q-8 and the genomic DNA G+C content of the strain was 58.9 mol%. On the basis of the phylogenetic, phenotypic and genotypic data presented here, strain CCB-MM1T represents a novel species of the genus Microbulbifer, for which the name Microbulbiferaggregans sp. nov. is proposed. The type strain is CCB-MM1T (=LMG 29920T=JCM 31875T).
Fulltext Complete genome sequence of marine filamentous bacterium, Saprospira grandis strain WHT

Heng WL, Lau NS, Furusawa G

Microbiol Resour Announc, 2023 Sep 19;12(9):e0044123.
PMID: 37589468 DOI: 10.1128/MRA.00441-23

Here, we report the complete genome sequence of a type strain of the genus Saprospira, Saprospira grandis strain WHT. The genome consists of one circular chromosome and plasmid comprising 4,250,550 bp and 53,161 bp with GC content of 46.6% and 46.8%, respectively.
Trigalacturonate-producing pectate lyase PelQ1 from Saccharobesus litoralis with unique exolytic activity

Lian MQ, Furusawa G, Teh AH

Carbohydr Res, 2024 Feb;536:109045.
PMID: 38340525 DOI: 10.1016/j.carres.2024.109045

PelQ1 from Saccharobesus litoralis is a Ca2+-dependent pectate lyase belonging to the polysaccharide lyase family 1 (PL1). Although being an endolytic enzyme, it degraded polygalacturonate into predominantly unsaturated trimer in an exolytic manner with delayed production of dimer, tetramer and pentamer. The enzyme harbours a C-terminal domain from the carbohydrate-binding module family 13 (CBM13), whose presence facilitated the production of dimer. PelQ1's homology model showed that it possessed a well-conserved catalytic cleft, with R232 acting as the general base and R203 as the general acid. Structural comparison with DcPelC, a similar trimer-generating pectate lyase from Dickeya chrysanthemi EC16, implied that both enzymes' catalytic clefts encompassed at least eight subsites, i.e. -5 to +3. The unequal distribution of the subsites between the reducing and non-reducing ends of the cleavage site might be responsible for the exolytic generation of the trimer. As all but the -1, +1 and + 2 subsites could accommodate methylated galacturonate, this subclass of PL1 pectate lyases may function to help break up methylated pectin.
Fulltext Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4

Furusawa G, Azami NA, Teh AH

PeerJ, 2021;9:e10929.
PMID: 33732545 DOI: 10.7717/peerj.10929

BACKGROUND: Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides.
METHODS: To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis.
RESULTS: The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in the QB4 genome based on the CAZy database. Eleven polysaccharide lyases and 16 glycoside hydrolases contained lipobox motif, indicating that these enzymes play an important role in degrading the polysaccharides. Fourteen of 28 polysaccharide lyases were classified into ulvan lyase, and the QB4 genome possessed the most abundant ulvan lyase genes in the CAZy database. Besides, genes involved in uronic acid metabolisms were also present in the genome. These results were consistent with the cell growth. In the pectin metabolic pathway, the strain had genes for three different pathways. However, the growth experiment using saturated galacturonate exhibited that the strain can only use the pathway related to unsaturated galacturonate.
Fulltext Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway

Furusawa G, Lau NS, Suganthi A, Amirul AA

Microbiologyopen, 2017 02;6(1).
PMID: 27987272 DOI: 10.1002/mbo3.405

The agarolytic bacterium Persicobacter sp. CCB-QB2 was isolated from seaweed (genus Ulva) collected from a coastal area of Malaysia. Here, we report a high-quality draft genome sequence for QB2. The Rapid Annotation using Subsystem Technology (RAST) annotation server identified four β-agarases (PdAgaA, PdAgaB, PdAgaC, and PdAgaD) as well as galK, galE, and phosphoglucomutase, which are related to the Leloir pathway. Interestingly, QB2 exhibited a diauxic growth in the presence of two kinds of nutrients, such as tryptone and agar. In cells grown with agar, the profiles of agarase activity and growth rate were very similar. galK, galE, and phosphoglucomutase genes were highly expressed in the second growth phase of diauxic growth, indicating that QB2 cells use galactose hydrolyzed from agar by its agarases and exhibit nutrient prioritization. This is the first report describing diauxic growth for agarolytic bacteria. QB2 is a potential novel model organism for studying diauxic growth in environmental bacteria.
Fulltext Draft Genome Sequence of the Halophilic Pararhodobacter-Like Strain CCB-MM2, Which Has Polyhydroxyalkanoate-Synthesizing Potential

Sam KK, Lau NS, Furusawa G, Amirul AA

Microbiol Resour Announc, 2019 Nov 14;8(46).
PMID: 31727719 DOI: 10.1128/MRA.01248-19

Pararhodobacter-like strain CCB-MM2 is a halophilic alphaproteobacterium isolated from estuarine sediment collected from Matang Mangrove Forest in Malaysia. Here, we present the draft genome sequence of CCB-MM2 and provide insights into its physiological roles and metabolic potential.
Modelling of polyhydroxyalkanoate synthase from Aquitalea sp. USM4 suggests a novel mechanism for polymer elongation

Teh AH, Chiam NC, Furusawa G, Sudesh K

Int J Biol Macromol, 2018 Nov;119:438-445.
PMID: 30048726 DOI: 10.1016/j.ijbiomac.2018.07.147

Polyhydroxyalkanoate (PHA) synthase, PhaC, is a key enzyme in the biosynthesis of PHA, a type of bioplastics with huge potential to replace petroleum-based plastics. While two structures have been determined, the exact mechanism remains unclear partly due to the absence of a tunnel for product passage. A model of the class I PhaC from Aquitalea sp. USM4, characterised with Km of 394 μM and kcat of 476 s-1 on 3-(R)-hydroxybutyryl-CoA, revealed a three-branched channel at the dimeric interface. Two of them are opened to the solvent and are expected to serve as the putative routes for substrate entrance and product exit, while the third is elongated in the class II PhaC1 model from Pseudomonas aeruginosa, indicating a role in accommodating the hydroxyalkanoate (HA) moiety of a HA-CoA substrate. Docking of the two tetrahedral intermediates, formed during the transfer of the growing PHA chain from the catalytic Cys to a new molecule of substrate and back to Cys, suggests a common elongation mechanism requiring the HA moiety of the ligand to rotate ~180°. Substrate specificity is determined in part by a bulky Phe/Tyr/Trp residue in the third branch in class I, which is conserved as Ala in class II to create room for longer substrates.
Fulltext Draft Genome Sequence of Halophilic Hahella sp. Strain CCB-MM4, Isolated from Matang Mangrove Forest in Perak, Malaysia

Sam KK, Lau NS, Furusawa G, Amirul AA

Genome Announc, 2017 Oct 19;5(42).
PMID: 29051257 DOI: 10.1128/genomeA.01147-17

Hahella sp. strain CCB-MM4 is a halophilic bacterium isolated from estuarine mangrove sediment. The genome sequence of Hahella sp. CCB-MM4 provides insights into exopolysaccharide biosynthesis and the lifestyle of the bacterium thriving in a saline mangrove environment.

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