Sulfur, sterol and trehalose metabolism in the deep-sea hydrocarbon seep tubeworm Lamellibrachia luymesi.

BACKGROUND: Lamellibrachia luymesi dominates cold sulfide-hydrocarbon seeps and is known for its ability to consume bacteria for energy. The symbiotic relationship between tubeworms and bacteria with particular adaptations to chemosynthetic environments has received attention. However, metabolic studies have primarily focused on the mechanisms and pathways of the bacterial symbionts, while studies on the animal hosts are limited. RESULTS: Here, we sequenced the transcriptome of L. luymesi and generated a transcriptomic database containing 79,464 transcript sequences. Based on GO and KEGG annotations, we identified transcripts related to sulfur metabolism, sterol biosynthesis, trehalose synthesis, and hydrolysis. Our in-depth analysis identified sulfation pathways in L. luymesi, and sulfate activation might be an important detoxification pathway for promoting sulfur cycling, reducing byproducts of sulfide metabolism, and converting sulfur compounds to sulfur-containing organics, which are essential for symbiotic survival. Moreover, sulfide can serve directly as a sulfur source for cysteine synthesis in L. luymesi. The existence of two pathways for cysteine synthesis might ensure its participation in the formation of proteins, heavy metal detoxification, and the sulfide-binding function of haemoglobin. Furthermore, our data suggested that cold-seep tubeworm is capable of de novo sterol biosynthesis, as well as incorporation and transformation of cycloartenol and lanosterol into unconventional sterols, and the critical enzyme involved in this process might have properties similar to those in the enzymes from plants or fungi. Finally, trehalose synthesis in L. luymesi occurs via the trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) pathways. The TPP gene has not been identified, whereas the TPS gene encodes a protein harbouring conserved TPS/OtsA and TPP/OtsB domains. The presence of multiple trehalases that catalyse trehalose hydrolysis could indicate the different roles of trehalase in cold-seep tubeworms. CONCLUSIONS: We elucidated several molecular pathways of sulfate activation, cysteine and cholesterol synthesis, and trehalose metabolism. Contrary to the previous analysis, two pathways for cysteine synthesis and the cycloartenol-C-24-methyltransferase gene were identified in animals for the first time. The present study provides new insights into particular adaptations to chemosynthetic environments in L. luymesi and can serve as the basis for future molecular studies on host-symbiont interactions and biological evolution.

The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment.

BACKGROUND: Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in deep-sea hydrothermal vents, cold seeps, and organic falls. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to endemic environment. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, remain to be investigated. RESULT: We assembled a draft genome of R. piscesae collected at the Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis showed that vent-dwelling tubeworms with a higher growth rate had smaller genome sizes than seep-dwelling tubeworms that grew much slower. A strong positive correlation between repeat content and genome size but not intron size and the number of protein-coding genes was identified in these deep-sea tubeworm species. Evolutionary analysis revealed that Ridgeia pachyptila and R. piscesae, the two tubeworm species that are endemic to hydrothermal vents of the eastern Pacific, started to diverge between 28.5 and 35 million years ago. Four genes involved in cell proliferation were found to be subject to positive selection in the genome of R. piscesae. CONCLUSION: Ridgeia pachyptila and R. piscesae started to diverge after the formation of the Gorda/Juan de Fuca/Explorer ridge systems and the East Pacific Rise. The high growth rates of vent-dwelling tubeworms might be derived from their small genome sizes. Cell proliferation is important for regulating the growth rate in R. piscesae.

Molecular characterization and function of the lipid raft protein Lvflotillin-1A from Litopenaeus vannamei.

White spot syndrome virus (WSSV) can cause a contagious, high virulent and pandemic disease for crustaceans, especially shrimps. However, the molecular mechanism of WSSV pathogenesis remains unclear. Flotillins are lipid raft-associated proteins, which mainly include flotillin-1 and flotillin-2. They are involved in the formation of large heteromeric protein complexes engaged in diverse signalling pathways at the membrane-cytosol interface. They defined a clathrin-independent endocytic pathway in mammalian cells. Our previous studies suggested that shrimp flotillin-2 might mediate endocytosis involved in WSSV infection. To further explore the function of shrimp flotillin, a flotillin-1 homologous, Lvflotillin-1A was identified and characterized in Litopenaeus vanamei. The transcription of Lvflotillin-1A showed a significant decline at 12h post-infection, followed by complete recovery and a slight up-regulation after the WSSV challenge. Gene silencing revealed that inhibition of Lvflotillin-1A raised the virus infection, suggesting Lvflotillin-1A might play an important role in shrimp immunity. Furthermore, co-immunoprecipitation and immunofluorescence illustrated that Lvflotillin-1A and Lvflotillin-2 could form hetero-oligomers, and co-expression promoted the accumulation of intracellular vesicles. The study revealed that WSSV might up-regulate Lvflotillin-2 expression and alter the subcellular location of Lvflotillin-1 protein to facilitate virus infection. These results will provide information for understanding the interaction between WSSV and shrimp.

Identification of a Yorkie homolog from Litopenaeus vannamei as a negative regulator in anti-WSSV immune response.

Hippo signaling pathway is a serine threonine kinase cascade that is evolutionary conserved with well-established roles in organ size control, development, tumorigenesis and immunity. As its core molecule, Yorkie also plays an important role against pathogen. In this study, we cloned and characterized a Yorkie homolog from Litopenaeus vannamei, designed as LvYKI, which has a 1650 bp open reading frame. It has the characterized domains of Yokie family, and displayed to be close to the insects and crustacean. Quantitative Real-time PCR showed that LvYKI had different regulatory mechanisms in different tissues. The transcriptional level of Lvyki was down-regulated in gill, while up-regulated in hepatopancreas post white spot syndrome virus (WSSV) infection. Moreover, the expression and phosphorylation of LvYKI was reduced upon WSSV infection, which indicated that LvYKI was involved in WSSV infection. Furthermore, RNAi was performed to evaluate the role of LvYKI in shrimp immune responses. Knocking down of Lvyki resulted in inhibition of the transcription of WSSV gene ie1 and vp28, and delayed mortality of shrimp post WSSV infection. Meanwhile, the apoptosis of hemocyte was increased as well. All results suggested that shrimp can promote apoptosis to resist WSSV infection mediated by down-regulation of LvYKI. In addition, it was found that LvYKI could interact with Lvß-catenin, which cross-linked the Wnt and Hippo signaling pathway in innate immunity. Conclusively, our study provided clues that LvYKI plays an important role in the interaction between shrimp and virus. It will promote our understanding of the molecular mechanism in innate immunity.

The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity.

BACKGROUND: Horseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanisms underlying their abilities of distinguishing and defending against invading microbes are still unclear. RESULTS: Here, we describe the 2.06 Gbp genome assembly of Tachypleus tridentatus with 24,222 predicted protein-coding genes. Comparative genomics shows that T. tridentatus and the Atlantic horseshoe crab Limulus polyphemus have the most orthologues shared among two species, including genes involved in the immune-related JAK-STAT signalling pathway. Divergence time dating results show that the last common ancestor of Asian horseshoe crabs (including T. tridentatus and C. rotundicauda) and L. polyphemus appeared approximately 130 Mya (121-141), and the split of the two Asian horseshoe crabs was dated to approximately 63 Mya (57-69). Hox gene analysis suggests two clusters in both horseshoe crab assemblies. Surprisingly, selective analysis of immune-related gene families revealed the high expansion of conserved pattern recognition receptors. Genes involved in the IMD and JAK-STAT signal transduction pathways also exhibited a certain degree of expansion in both genomes. Intact coagulation cascade-related genes were present in the T. tridentatus genome with a higher number of coagulation factor genes. Moreover, most reported antibacterial peptides have been identified in T. tridentatus with their potentially effective antimicrobial sites. CONCLUSIONS: The draft genome of T. tridentatus would provide important evidence for further clarifying the taxonomy and evolutionary relationship of Chelicerata. The expansion of conserved immune signalling pathway genes, coagulation factors and intact antimicrobial peptides in T. tridentatus constitutes its robust and effective innate immunity for self-defence in marine environments with an enormous number of invading pathogens and may affect the quality of the adaptive properties with regard to complicated marine environments.

Characterization and function of GSK3ß from Litopenaeus vannamei in WSSV infection.

GSK3ß, a serine/threonine protein kinase, is a crucial regulator in several signaling pathway and plays a vital role in multiple cellular processes including cell proliferation, growth, apoptosis and immune response. In this study, a GSK3ß homolog from L. vannamei, designed as LvGSK3ß, was characterized. Sequence analysis showed that LvGSK3ß possessed a highly similarity with GSK3ß from other species, which contained a catalytic domain and serine/threonine phosphorylation sites. To analyze the role of LvGSK3ß in the process of white spot syndrome virus (WSSV) infection, real-time quantitative PCR and western blot assays were performed. The results showed that the transcription and expression levels of LvGSK3ß were inhibited upon WSSV challenge, accompanied with down-regulated phosphorylation levels. When LvGSK3ß was silenced, the transcription of WSSV gene ie1 was inhibited, and the apoptosis of hemocytes induced by WSSV was up-regulated remarkably as well. In addition, inactivation of LvGSK3ß could also depress virus infection that further validated the results. Conclusively, LvGSK3ß was an important protein for shrimp immunomodulation, and shrimp might promote the apoptosis to restrain WSSV infection by inhibition of LvGSK3ß. The study will be helpful for understanding the molecular mechanism of host-virus interaction.

Wnt5b regulates apoptosis in Litopenaeus vannamei against white spot syndrome virus.

The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. Wnt5b is one of the Wnt signaling molecules that initiate the cascade. In this study, we cloned and characterized a Wnt5b homolog from Litopenaeus vannamei designed as LvWnt5b. The full length of LvWnt5b transcript was 1726 bp with an 1107 bp open reading frame that encoded a 368 aa protein, which contained 24 discontinuous and highly conserved cysteine. Real-time quantitative PCR showed that the transcriptional level of LvWnt5b was down-regulated when infected with white spot syndrome virus (WSSV). Knock-down of LvWnt5b resulted in inhibition of the transcriptional level of WSSV gene ie1, indicating that LvWnt5b mediated signaling pathway may play an important role in defense against WSSV infection. When LvWnt5b was silenced, caspase3/7 activity in hemocytes was increased significantly, and the transcription of viral gene was decreased as well. Moreover, overexpression of LvWnt5b in HEK293T cells led to inhibition of caspase3/7 activity, which further proved the role of LvWnt5b in restraining apoptosis. The study showed that the shrimp may decrease the expression of LvWnt5b initiatively to act as an immune defense mechanism against WSSV infection via promoting apoptosis. It will be helpful for understanding the function of Wnt signaling pathway in virus invasion and host defense.

Cloning, identification and function analysis of a Chibby homolog from Litopenaeus vannamei.

Chibby, a vital inhibitor molecule of Wnt/ß-catenin signaling pathway, participates in development and stem cell differentiation through the regulation of ß-catenin. Our previous studies have demonstrated that Litopenaeus vannamei ß-catenin (Lv-ß-catenin) was involved in WSSV infection and could inhibit virus replication by modulating the host immune system. In the study, a Chibby homolog from L. vannamei (designed as Lv-Chibby) was isolated and its role in WSSV infection was investigated. Sequence analysis suggested that Lv-Chibby was a novel homolog of Chibby family. It could transcript in all examined tissues, including hemocyte, gill, intestine, hepatopancreas, muscle and heart. Real-time quantitative PCR demonstrated that Lv-Chibby could take part in WSSV infection and be down-regulated by WSSV. Further studies confirmed that Lv-Chibby was able to interact with Lv-ß-catenin. Moreover, the relationship of Lv-ß-catenin, Lv-Chibby and WSSV069 was investigated. It was shown that Lv-Chibby enhanced the interaction between Lv-ß-catenin and WSSV069. Interestingly, WSSV069 promoted the interaction between Lv-ß-catenin and Lv-Chibby under high concentration, while low concentration of WSSV069 inhibited their interaction. A subsequent immunofluorescence assay revealed that WSSV069 appeared to reduce the nuclear entry of Lv-ß-catenin. In sum, these results implied that Wnt/ß-catenin signal pathway plays an important role in the defense against virus, and Chibby could be modulated by WSSV to regulate the signal pathway.

Characterization of a novel non-receptor tyrosine kinase Src from Litopenaeus vannamei and its response to white spot syndrome virus infection.

Src family kinases (SFKs), a class of non-receptor tyrosine kinases, mediate a wide aspect of cellular signaling pathways that regulate cell proliferation, differentiation, motility and survival. In this study, we identified and characterized for the first time a novel SFK homologue from Litopenaeus vannamei (designated as LvSrc). Sequence analysis showed that LvSrc had a high homology with the identified SFKs, especially those from invertebrates. LvSrc contained the conserved SH3, SH2 and tyrosine kinase domains, as well as the potential phosphorylation and lipid modification sites. Immunofluorescence analysis demonstrated that LvSrc was mostly localized at the plasma membrane and partly resided in the perinuclear vesicle and nucleus or whole cell. Infection with white spot syndrome virus (WSSV) could up-regulate the transcription and expression levels of LvSrc and further induced its phosphorylation, suggesting that LvSrc was implicated in WSSV infection. Furthermore, our co-immunoprecipitation result confirmed the interaction between Src and focal adhesion kinase (FAK) in shrimp, while the phosphorylation of FAK was markedly enhanced by co-expression with LvSrc. In sum, our studies suggested that LvSrc might act in the FAK-regulated signaling pathway during WSSV infection, which would give us a better insight in understanding the role of SKFs in host-virus interactions in crustaceans.

Shrimp STAT was hijacked by white spot syndrome virus immediate-early protein IE1 involved in modulation of viral genes.

STATs are a family of transcription factors that regulate a cascade of cellular processes including cell growth, differentiation, apoptosis and immune responses. However, they are usually targeted by viruses to assist infection. In this study, we identified that white spot syndrome virus (WSSV) immediate-early protein IE1 interacted with Litopenaeus vannamei STAT (LvSTAT) and thereby led to its phosphorylation activation. In addition, we demonstrated that LvSTAT could bind to the promoters of the viral immediate-early genes wsv051 and ie1 through STAT-binding motifs in vitro and vivo, allowing the enhancement of their promoters' activities. Moreover, IE1 could promote the transcriptional activation activity of LvSTAT to augment the transcription of wsv051 and ie1. In conclusion, our findings revealed a novel linkage between WSSV IE1 and shrimp STAT, which was a clue to well understand how WSSV adopted the active strategies to modulate the shrimp signaling pathway.

Membrane associated protein flotillin-2 in Litopenaeus vannamei plays a role in WSSV infection.

Flotillin-2, an important protein of vesicular endocytosis, plays an essential role in a large number of cellular processes, including viruses and pathogen infection. In the present study, a flotillin-2 homolog in Litopenaeus vannamei, designed as Lvflotillin-2, was cloned and characterized. To analyze the putative role of Lvflotillin-2 during white spot syndrome virus (WSSV) infection, real-time quantitative PCR was performed. The result showed that the transcriptional level of Lvflotillin-2 was up-regulated significantly after virus challenge. Furthermore, upon WSSV stimulation, Lvflotillin-2 in shrimp cells could translocate from the plasma membrane to intracellular compartments, and unexpectedly, also into nucleus. Additionally, depletion of Lvflotillin-2 inhibited WSSV gene ie1 transcription. It suggested that Lvflotillin-2 could be hijacked by WSSV. These observations indicated that Lvflotillin-2 was involved in WSSV infection, and presented here should be useful for gaining insight into shrimp immunity and WSSV pathogenesis.

eIF2α of Litopenaeus vannamei involved in shrimp immune response to WSSV infection.

The alpha subunit of Eukaryotic Initiation Factor 2 (eIF2α) is a key translation regulator that plays an important role in cellular stress responses, which including virus infection. To investigate whether WSSV infection can activate the PERK-eIF2α pathway, the eIF2α in shrimp Litopenaeus vannamei, designed as LveIF2α, was analyzed. The LveIF2α, a 332-amino acid polypeptide, shares a high degree of similarity with eIF2α from other species, having two eIF2α protein signatures at the 13-88 aa and 192-243 aa. The WSSV challenge experiment showed that the protein level of the total LveIF2α was decreased after infection, while the phosphorylation of LveIF2α has no significant change, which indicated that the phosphorylation ratio of LveIF2α was increased after infection. Furthermore, inhibitor treatment led to a significant decrease of WSSV loads. Moreover, the Binding immunoglobulin protein (BiP), an endoplasmic reticulum (ER) stress sensor, and PERK were also investigated during virus infection and it was shown that they were both up-regulated. Taken together, these results suggested that WSSV infection can induce ER stress and activated the unfolded protein response (UPR), and the PERK-eIF2α pathway is important for innate immune during WSSV infection in shrimp.

Enrichment and characterization of an anaerobic cellulolytic microbial consortium SQD-1.1 from mangrove soil.

Enrichment of microbial consortia provides an approach to simulate and investigate microbial communities in natural environments. In this study, a cellulolytic microbial consortium SQD-1.1 was enriched from mangrove soil of Qinglan port (Hainan, China) by 27 times continuous subcultivation under anaerobic static conditions. The consortium could completely degrade 0.2% (w/v) filter paper within 3 days and utilized it as the sole carbon source. PCR-denaturing gradient gel electrophoresis analysis revealed a stable microbial community structure in the incubation process of 10 days and in the procedure of subcultivation. Twenty-four operational taxonomic units belonging to seven phyla were obtained from the full-length 16S rRNA gene library. Five clones, closest related to the genera Alkaliflexus, Clostridium, Alistipes, Spirochaeta, and Trichococcus, were the predominant ones. Among them, M117, phylogeneticly showing high similarity (16S rRNA gene identity, 95.3%) with the cellulolytic anaerobic bacterium Clostridium straminisolvens CSK1(T), was the potential key cellulolytic bacterium. Using the plate cultivation method, 12 strains, including one potential new species and four potential new species of new genera, were isolated. The strain P2, corresponding to the most frequently detected clone (M05) in the 16S rRNA gene library, showed both CMCase and xylanase activity and may be another important cellulolytic bacterium. The findings of cellulase activity in cell pellet and cohesion and dockerin domains in metagenome data further suggested the potential of utilization of cellulosomes by the consortium to degrade cellulose. Consortium SQD-1.1 provides a candidate for investigating the mechanism of cellulose degradation under anoxic conditions in natural environments.

Thermophagus xiamenensis gen. nov., sp. nov., a moderately thermophilic and strictly anaerobic bacterium isolated from hot spring sediment.

A moderately thermophilic and strictly anaerobic bacterium, designated HS1(T), was isolated from offshore hot spring sediment in Xiamen, China. Cells were Gram-negative, catalase-positive, oxidase-negative, slender and flexible rods without flagella. The strain could grow at 35-55 °C (optimum at 50 °C) and in 1-8 % NaCl (w/v; optimum 2-4 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HS1(T) was affiliated with the family Marinilabiliaceae and shared a distant relationship with the previously described genera. The isolate was most closely related to Anaerophaga thermohalophila Fru22(T) with 16S rRNA gene sequence similarity of 92.4 %, followed by the other members of the family Marinilabiliaceae with 88.7-91.1 % similarity. The dominant cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The predominant quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE) and an unknown polar lipid. The genomic DNA G+C content was 38.7 mol%. Besides the phylogenetically distant relationship, strain HS1(T) was obviously distinguished from the most closely related genera in several phenotypic properties including colony colour and pigment production, optimal temperature, optimal NaCl, relation to O(2), bicarbonate/carbonate requirement, catalase activity, nitrate reduction, fermentation products and cellular fatty acid profile. Based on the phenotypic and phylogenetic data, strain HS1(T) represents a novel species of a new genus, for which the name Thermophagus xiamenensis gen. nov., sp. nov. is proposed. The type strain of the type species is HS1(T) (= DSM 19012(T) = CGMCCC 1.5071(T)).

Mangroviflexus xiamenensis gen. nov., sp. nov., a member of the family Marinilabiliaceae isolated from mangrove sediment.

A Gram-negative, obligately anaerobic, non-spore-forming, long rod-shaped bacterium strain P2(T) was isolated from the offshore mangrove sediment of the South China Sea. Growth was observed at between 22 and 39 °C, with an optimum at 35 °C. The pH range for growth was 5.0-8.5, with an optimum around pH 7.0-7.5. Salt tolerance was determined between 0.2 and 3.5% (w/v), optimum at 0.5-1.0%. Catalase and oxidase activities were negative. Strain P2(T) utilized cysteine, lactate, pyruvate, yeast extract or H(2)/CO(2)+acetate as electron donors, and sulfate or sulfite as electron acceptors. Metabolism was strictly fermentative. The main organic fermentation products were propionate, acetate and succinate. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P2(T) formed a distinct evolutionary lineage within the family Marinilabiliaceae. Strain P2(T) was most closely related to members of the genera Alkaliflexus (92.0% 16S rRNA gene sequence similarity), Marinilabilia (91.7%) and Anaerophaga (89.9%) of the family Marinilabiliaceae. The DNA G+C content of the novel strain was 44.2 ± 1.0 mol%. The dominant fatty acids of strain P2(T) were iso-C(15:0) (33.5%), anteiso-C(15:0) (18.9%), C(16:0) (5.4%), C(16:0) 3-OH (7.7%) and iso-C(17:0) 3-OH (13.3%). The respiratory quinone was menaquinone 7 (100% of total quinone) and the major polar lipid was phosphatidylethanolamine. Strain P2(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of phylogenetic, phenotypic and physiological evidence, a novel genus, Mangroviflexus, is proposed to harbour strain P2(T) ( = CGMCC 1.5167(T) = DSM 24214(T)) which is described as the type strain of a novel species, Mangroviflexus xiamenensis gen. nov., sp. nov.

Desulfobaculum xiamenensis gen. nov., sp. nov., a member of the family Desulfovibrionaceae isolated from marine mangrove sediment.

A taxonomic study was carried out on strain P1(T), which was isolated from mangrove sediment samples collected from Qinglan Port (Hainan, China). Cells were curved rods, that were motile, with a single polar flagellum. The strain was non-spore-forming with a cell size of 0.6×1.5-2.2 µm. Catalase and oxidase activities were not detected. Growth was observed in the temperature range 22-44 °C (optimum, 35-40 °C) and pH range 5.5-8.5 (optimum, pH 7.0). NaCl was required for growth and tolerated at up to 3.5% (w/v) (optimum, 0.5%). Strain P1(T) utilized hydrogen, succinate, L-malate, citrate, oxalate, DL-lactate, pyruvate, or cysteine as electron donors, and sulfate or sulfite as electron acceptors. Fermentation products from pyruvate were acetate, H(2) and CO(2). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P1(T) formed a distinct evolutionary lineage within the family Desulfovibrionaceae. Strain P1(T) was most closely related to members of the genera Desulfovibrio (92.0-94.3% 16S rRNA gene sequence similarity), Desulfocurvus (91.1%), Bilophila (87.9%) and Lawsonia (86.0%) of the family Desulfovibrionaceae. The DNA G+C content of strain P1(T) was 64.5 mol% and the major cellular fatty acids were iso-C(15:0) (18.8%), anteiso-C(15:0) (5.0%), C(16:0) (14.2%) and iso-C(17:1)ω9c (24.4%). The predominant menaquinone was MK-7 (97%). Major polar lipids were phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. Strain P1(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain P1(T) represents a novel species of a new genus, for which the name Desulfobaculum xiamenensis gen. nov., sp. nov. is proposed. The type strain of Desulfobaculum xiamenensis is P1(T) (=CGMCC 1.5166(T)=DSM 24233(T)).

Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil.

A taxonomic study was carried out on a cellulase-producing bacterium, strain G21(T), isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15-40 °C and in 0.5-10% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21(T) belonged to the genus Vibrio and formed a clade with Vibrio furnissii ATCC 350116(T) (97.4% sequence similarity), V. fluvialis LMG 7894(T) (97.1%) and V. ponticus CECT 5869(T) (96.1%). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA-DNA hybridization experiments indicated that the strain was distinct from the closest related Vibrio species. Additionally, strain G21(T) could be differentiated from them phenotypically by the ability to grow in 10% NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA-DNA hybridization analysis, it is concluded that strain G21(T) represents a novel species of the genus Vibrio, for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21(T) ( = DSM 22851(T)  = CGMCC 1.10228(T)).

Molecular cloning and characterization of a cDNA encoding extracellular signal-regulated kinase from Litopenaeus vannamei.

Extracellular signal-regulated kinase (ERK) is a serine/threonine-specific kinase, which is activated by downstream signaling molecules of cellular activation, cytokine and chemokine stimulation and various other stimuli. Here we cloned an ERK gene from Litopenaeus vannamei and designated it as lverk. The lverk cDNA contained an open reading frame of 1098 bp encoding 365 amino acids. LVERK had a conserved TEY motif and serine/threonine protein kinase (S_TKc) domain, and close phylogenetic relationship to Penaeus monodon and Marsupenaeus japonicus ERK. Immunofluorescence staining analysis showed that following serum stimulation LVERK was located in cytoplasm and nucleus, but phospho-LVERK was prominently in nucleus, suggesting conserved ERK signaling module occurred in shrimp cells. Then during the white spot syndrome virus (WSSV) infection, LVERK and phospho-LVERK increased at the early stage of infection. Once silencing of lverk in vivo, the replication of WSSV was obviously inhibited. Moreover, treatment of mitogen-activated protein kinase kinase inhibitor in vitro could result in reduction of WSSV proliferation and delay of viral early gene transcription. Our results indicated a role of LVERK involved in WSSV infection. Understanding how WSSV influences ERK signaling pathway to dismantle an effective immune response may lead to insight into pathogenic progression and possible disease control.

The genome of a hadal sea cucumber reveals novel adaptive strategies to deep-sea environments.

How organisms cope with coldness and high pressure in the hadal zone remains poorly understood. Here, we sequenced and assembled the genome of hadal sea cucumber Paelopatides sp. Yap with high quality and explored its potential mechanisms for deep-sea adaptation. First, the expansion of ACOX1 for rate-limiting enzyme in the DHA synthesis pathway, increased DHA content in the phospholipid bilayer, and positive selection of EPT1 may maintain cell membrane fluidity. Second, three genes for translation initiation factors and two for ribosomal proteins underwent expansion, and three ribosomal protein genes were positively selected, which may ameliorate the protein synthesis inhibition or ribosome dissociation in the hadal zone. Third, expansion and positive selection of genes associated with stalled replication fork recovery and DNA repair suggest improvements in DNA protection. This is the first genome sequence of a hadal invertebrate. Our results provide insights into the genetic adaptations used by invertebrate in deep oceans.

Genome sequence of Pseudomonas sp. Strain S9, an extracellular arylsulfatase-producing bacterium isolated from Mangrove Soil.

Pseudomonas sp. strain S9 was originally isolated from mangrove soil in Xiamen, China. It is an aerobic bacterium which shows extracellular arylsulfatase activity. Here, we describe the 4.8-Mb draft genome sequence of Pseudomonas sp. S9, which exhibits novel cysteine-type sulfatases.