scholarly journals Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales

2021 ◽  
Vol 12 ◽  
Author(s):  
Ashley Isaac ◽  
Ben Francis ◽  
Rudolf I. Amann ◽  
Shady A. Amin
Keyword(s):  
Relative Abundance ◽  
Molecular Mechanisms ◽  
Phytoplankton Bloom ◽  
Gene Clusters ◽  
Niche Differentiation ◽  
Bacterial Attachment ◽  
Vitamin B ◽  
The North ◽  
Significant Enrichment ◽  
Diatom Blooms

The multiple interactions of phytoplankton and bacterioplankton are central for our understanding of aquatic environments. A prominent example of those is the consistent association of diatoms with Alphaproteobacteria of the order Rhodobacterales. These photoheterotrophic bacteria have traditionally been described as generalists that scavenge dissolved organic matter. Many observations suggest that members of this clade are specialized in colonizing the microenvironment of diatom cells, known as the phycosphere. However, the molecular mechanisms that differentiate Rhodobacterales generalists and phycosphere colonizers are poorly understood. We investigated Rhodobacterales in the North Sea during the 2010–2012 spring blooms using a time series of 38 deeply sequenced metagenomes and 10 metaproteomes collected throughout these events. Rhodobacterales metagenome assembled genomes (MAGs) were recurrently abundant. They exhibited the highest gene enrichment and protein expression of small-molecule transporters, such as monosaccharides, thiamine and polyamine transporters, and anaplerotic pathways, such as ethylmalonyl and propanoyl-CoA metabolic pathways, all suggestive of a generalist lifestyle. Metaproteomes indicated that the species represented by these MAGs were the dominant suppliers of vitamin B12 during the blooms, concomitant with a significant enrichment of genes related to vitamin B12 biosynthesis suggestive of association with diatom phycospheres. A closer examination of putative generalists and colonizers showed that putative generalists had persistently higher relative abundance throughout the blooms and thus produced more than 80% of Rhodobacterales transport proteins, suggesting rapid growth. In contrast, putative phycosphere colonizers exhibited large fluctuation in relative abundance across the different blooms and correlated strongly with particular diatom species that were dominant during the blooms each year. The defining feature of putative phycosphere colonizers is the presence of the tight adherence (tad) gene cluster, which is responsible for the assembly of adhesive pili that presumably enable attachment to diatom hosts. In addition, putative phycosphere colonizers possessed higher prevalence of secondary metabolite biosynthetic gene clusters, particularly homoserine lactones, which can regulate bacterial attachment through quorum sensing. Altogether, these findings suggest that while many members of Rhodobacterales are competitive during diatom blooms, only a subset form close associations with diatoms by colonizing their phycospheres.

scholarly journals Impact of Shifting Subpolar Front on Phytoplankton Dynamics in the Western Margin of East/Japan Sea

2021 ◽  
Vol 8 ◽  
Author(s):  
Dongyoung Kim ◽  
Rubao Ji ◽  
Hyun Je Park ◽  
Zhixuan Feng ◽  
Jaebin Jang ◽  
...  
Keyword(s):  
Algal Blooms ◽  
Frontal Zone ◽  
Phytoplankton Bloom ◽  
Japan Sea ◽  
Early Spring ◽  
Nutrient Concentrations ◽  
Western Margin ◽  
The North ◽  
Water Column Stratification ◽  
Diatom Blooms

A subpolar front (SPF) generated between the East Korea Warm Current (EKWC) and the North Korea Cold Current (NKCC) in the western margin of the East/Japan Sea has shifted northward in recent decades. This study investigated the biomass and composition of the phytoplankton assemblage in relation to hydrological and biogeochemical features in the shallow shelf and slope off the Korean coast from January to June in 2016 and 2017, to determine the mechanistic effects of SPF on spring–summer phytoplankton bloom dynamics. Monthly average depth-integrated chlorophyll a (Chl a) levels and the contribution of phytoplankton classes revealed bimodal diatom blooms in early spring and summer in the frontal zone. Canonical correspondence analysis showed that the distribution of high Chl a was associated with cold, low-salinity NKCC water in March 2016. No Chl a peak was observed in March 2017 when the warm saline EKWC water mass invaded. These results suggest that the NKCC intrusion acts as a forcing mechanism leading to enhanced phytoplankton biomass in the frontal zone. In contrast, positive correlations of Chl a concentration with water density and nutrient concentrations suggest that summer blooms were fed by the subsurface chlorophyll maximum (SCM) driven by shoaling of the pycnocline and nitracline. Varying water-column stratification determined the thickness of the SCM layer, driving year-to-year variability in the magnitude of diatom blooms. These findings further suggest that seasonal/interannual variability in the timing of algal blooms affects regional trophodynamics and hence could be an important factor in explaining ecosystem changes in this region.

scholarly journals Widespread alteration of protein autoinhibition in human cancers

2018 ◽  
Author(s):  
Ashwani Jha ◽  
Jennifer M. Bui ◽  
Dokyun Na ◽  
Jörg Gsponer
Keyword(s):  
Cancer Cells ◽  
Molecular Mechanisms ◽  
Signal Propagation ◽  
Genetic Alterations ◽  
Missense Mutations ◽  
Pathway Activation ◽  
Tumorigenic Potential ◽  
Significant Enrichment ◽  
Cancer Types ◽  
Cancer Drivers

ABSTRACTAutoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins as it prevents spurious pathway activation and primes for signal propagation only under appropriate inputs. Altered functioning of inhibitory allosteric switches underlies the tumorigenic potential of numerous cancer drivers. However, whether protein autoinhibition is altered generically in cancer cells remains elusive. Here, we reveal that cancer-associated missense mutations and fusion breakpoints are found with significant enrichment within inhibitory allosteric switches across all cancer types, which in the case of the fusion breakpoints is specific to cancer and not present in other diseases. Recurrently disrupted or mutated allosteric switches identify established and new cancer drivers. Cancer-specific mutations in allosteric switches are associated with distinct changes in signaling, and suggest molecular mechanisms for altered protein regulation, which in the case of ASK1, DAPK2 and EIF4G1 were supported by biophysical simulations. Our results demonstrate that autoinhibition-modulating genetic alterations are positively selected for by cancer cells, and that their study provides valuable insights into molecular mechanisms of cancer misregulation.

scholarly journals Niche differentiation and regeneration in the seasonally flooded Melaleuca forests of northern Australia

2007 ◽  
Vol 23 (4) ◽  
pp. 457-467 ◽  
Author(s):  
Donald C. Franklin ◽  
Peter S. Brocklehurst ◽  
Dominique Lynch ◽  
David M. J. S. Bowman
Keyword(s):  
Basal Area ◽  
Niche Differentiation ◽  
Floodplain Forests ◽  
Northern Australia ◽  
Closely Related Species ◽  
The North ◽  
Wide Range ◽  
Using Data ◽  
Seasonally Flooded ◽  
Burnt Areas

Gallery and floodplain forests in monsoonal northern Australia are mostly sclerophyllous and dominated by five closely related species of Melaleuca (Myrtaceae) amongst which niche differentiation is unclear. We present a floristic and environmental analysis of ‘the flooded forest’ using data from 340 plots distributed across 450 000 km2 of the Top End of the Northern Territory. Melaleuca argentea was confined to streams and occurred on sandier substrates, whereas M. cajuputi mostly occurred in the near-coastal lowlands on clay soils. The greater basal area of M. cajuputi suggests an association with productive sites. Melaleuca dealbata, M. viridiflora and M. leucadendra occurred on a wide range of soils. More deeply floodprone sites were occupied by M. argentea and M. leucadendra along streams and by M. leucadendra and M. cajuputi on floodplains and in swamps. A general deficiency but occasional abundance of Melaleuca seedlings suggests that regeneration is episodic. Seedlings were more frequent in recently burnt areas and especially where fires had been severe. We propose that Melaleuca forests occur where disturbance by fire and/or floodwater is too great for rain forest to persist, rendering them the wetland analogue to the eucalypts that dominate well-drained portions of the north Australian environment.

scholarly journals A Short Investigation into the Habits, Abundance, and Species of Seals on the North Cornwall Coast

1934 ◽  
Vol 19 (2) ◽  
pp. 189-501 ◽  
Author(s):  
G. A. Steven
Keyword(s):  
Relative Abundance ◽  
Direct Evidence ◽  
Phoca Vitulina ◽  
Halichoerus Grypus ◽  
Grey Seal ◽  
The North ◽  
Single Night ◽  
Considerable Size

1. In the course of three trips to the herring grounds in the vicinity of St. Ives five seals were sighted. Seven others were also seen at various other times and places in the course of five days spent in that locality.2. During a single night at sea in Port Isaac Bay eight seals were sighted.3. It was obvious from the movements of certain of the seals observed on the fishing grounds that they were attracted to the herring nets.4. Direct evidence that the seals actually remove fish from the nets was not obtained.5. Damage done to drift nets by seals is negligible.6. Grey Seals (Halichœrus grypus) are present in considerable numbers, and are probably the commonest seals in Cornish waters.7. Brown Seals (Phoca vitulina) appear to be few—they may even be rare—around Cornwall.8. There is at least one seal colony of considerable size in certain caves near Boscastle. This appears to consist of Grey Seals. Probably other such colonies exist on the Cornish coast.9. Clupeoid remains have been found in two out of the three Grey Seal stomachs which have been examined.10. Further and more exact knowledge of the habits and relative abundance of Grey and Brown Seals around the Cornish coast is desirable.

scholarly journals Transcriptional, Behavioral and Biochemical Profiling in the 3xTg-AD Mouse Model Reveals a Specific Signature of Amyloid Deposition and Functional Decline in Alzheimer’s Disease

2020 ◽  
Vol 14 ◽  
Author(s):  
Wencheng Yin ◽  
Navei Cerda-Hernández ◽  
Atahualpa Castillo-Morales ◽  
Mayra L. Ruiz-Tejada-Segura ◽  
Jimena Monzón-Sandoval ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Mechanisms ◽  
Transcriptional Profiling ◽  
Differential Expression Analysis ◽  
Functional Decline ◽  
Insular Cortex ◽  
Learning Performance ◽  
Significant Enrichment ◽  
Transcriptional Changes

Alzheimer’s disease (AD)-related degenerative decline is associated to the presence of amyloid beta (Aβ) plaque lesions and neuro fibrillary tangles (NFT). However, the precise molecular mechanisms linking Aβ deposition and neurological decline are still unclear. Here we combine genome-wide transcriptional profiling of the insular cortex of 3xTg-AD mice and control littermates from early through to late adulthood (2–14 months of age), with behavioral and biochemical profiling in the same animals to identify transcriptional determinants of functional decline specifically associated to build-up of Aβ deposits. Differential expression analysis revealed differentially expressed genes (DEGs) in the cortex long before observed onset of behavioral symptoms in this model. Using behavioral and biochemical data derived from the same mice and samples, we found that down but not up-regulated DEGs show a stronger average association with learning performance than random background genes in control not seen in AD mice. Conversely, these same genes were found to have a stronger association with Aβ deposition than background genes in AD but not in control mice, thereby identifying these genes as potential intermediaries between abnormal Aβ/NFT deposition and functional decline. Using a complementary approach, gene ontology analysis revealed a highly significant enrichment of learning and memory, associative, memory, and cognitive functions only among down-regulated, but not up-regulated, DEGs. Our results demonstrate wider transcriptional changes triggered by the abnormal deposition of Aβ/NFT occurring well before behavioral decline and identify a distinct set of genes specifically associated to abnormal Aβ protein deposition and cognitive decline.

scholarly journals Molecular Mechanism ofN,N-Dimethylformamide Degradation inMethylobacteriumsp. Strain DM1

2019 ◽  
Vol 85 (12) ◽  
Author(s):  
Xinyu Lu ◽  
Weiwei Wang ◽  
Lige Zhang ◽  
Haiyang Hu ◽  
Ping Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Gene Clusters ◽  
Sole Source ◽  
Human Beings ◽  
Sequencing Data ◽  
Carbon And Nitrogen ◽  
Redundant Genes ◽  
Evolutionary Advantage ◽  
Redundant Gene ◽  
Phenotype Identification

ABSTRACTN,N-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings. Herein, an efficient DMF-degrading strain, DM1, was isolated and identified asMethylobacteriumsp. This strain can use DMF as the sole source of carbon and nitrogen. Whole-genome sequencing of strain DM1 revealed that it has a 5.66-Mbp chromosome and a 200-kbp megaplasmid. The plasmid pLVM1 specifically harbors the genes essential for the initial steps of DMF degradation, and the chromosome carries the genes facilitating subsequent methylotrophic metabolism. Through analysis of the transcriptome sequencing data, the complete mineralization pathway and redundant gene clusters of DMF degradation were elucidated. The dimethylformamidase (DMFase) gene was heterologously expressed, and DMFase was purified and characterized. Plasmid pLVM1 is catabolically crucial for DMF utilization, as evidenced by the phenotype identification of the plasmid-free strain. This study systematically elucidates the molecular mechanisms of DMF degradation byMethylobacterium.IMPORTANCEDMF is a hazardous pollutant that has been used in the chemical industry, pharmaceutical manufacturing, and agriculture. Biodegradation as a method for removing DMF has received increasing attention. Here, we identified an efficient DMF degrader,Methylobacteriumsp. strain DM1, and characterized the complete DMF mineralization pathway and enzymatic properties of DMFase in this strain. This study provides insights into the molecular mechanisms and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting the emergence of new ecotypes ofMethylobacterium.

Spatial and temporal variability of the phytoplankton community structure in the North Water Polynya, investigated using pigment biomarkers

2004 ◽  
Vol 61 (11) ◽  
pp. 2038-2052 ◽  
Author(s):  
Francesca Vidussi ◽  
Suzanne Roy ◽  
Connie Lovejoy ◽  
Marie Gammelgaard ◽  
Helge Abildhauge Thomsen ◽  
...  
Keyword(s):  
Community Structure ◽  
Phytoplankton Community ◽  
Phytoplankton Bloom ◽  
Circulation Pattern ◽  
Spatial And Temporal Variability ◽  
Phytoplankton Community Structure ◽  
Southeastern Part ◽  
Chl A ◽  
The North ◽  
North Water

Phytoplankton taxonomic pigments were measured by high-performance liquid chromatography (HPLC) during a 3-month survey (April–June 1998) in the North Water (NOW) Polynya (Canadian Arctic) to investigate changes in phytoplankton biomass and composition and the physical–chemical factors that influence these changes. A phytoplankton bloom with high chlorophyll a (Chl a) concentrations (up to 17.45 mg·m–3 at 15 m) occurred in mid-May along the Greenland coast in the southeastern part of the NOW Polynya. The initiation of the phytoplankton bloom was linked to shallow mixed-layer depths. The contribution of the different phytoplankton groups to Chl a inferred using a factorization program (CHEMTAX) indicated that the bloom was diatom-dominated (maximum 94% diatoms). The phytoplankton community structure was influenced by the water mass characteristics and the surface circulation pattern. Autotrophic flagellates dominated in April and May along the Canadian coast, where cold Arctic waters with relatively deep mixed layers were found. In contrast, diatoms dominated in May along the Greenland coast in warmer water masses of Atlantic origin and during June in the whole polynya, except in the southernmost part.

scholarly journals Anomalous wind triggered the largest phytoplankton bloom in the oligotrophic North Pacific Subtropical Gyre

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chun Hoe Chow ◽  
Wee Cheah ◽  
Jen-Hua Tai ◽  
Sin-Fu Liu
Keyword(s):  
North Pacific ◽  
Phytoplankton Bloom ◽  
Subtropical Gyre ◽  
Velocity Shear ◽  
North Pacific Subtropical Gyre ◽  
The North ◽  
Large Eddy ◽  
Anomalous Wind ◽  
Anticyclonic Eddies

Abstract In summer 2010, a massive bloom appeared in the middle (16–25°N, 160–200°E) of the North Pacific Subtropical Gyre (NPSG) creating a spectacular oasis in the middle of the largest oceanic desert on Earth. Peaked in June 2010 covering over two million km2 in space, this phytoplankton bloom is the largest ever recorded by ocean color satellites in the NPSG over the period from 1997 to 2013. The initiation and mechanisms sustaining the massive bloom were due to atmospheric and oceanic anomalies. Over the north (25–30°N) of the bloom, strong anticyclonic winds warmed sea surface temperature (SST) via Ekman convergence. Subsequently, anomalous westward ocean currents were generated by SST meridional gradients between 19°N and 25°N, producing strong velocity shear that caused large number of mesoscale (100-km in order) cyclonic eddies in the bloom region. The ratio of cyclonic to anticyclonic eddies of 2.7 in summer 2010 is the highest over the 16-year study period. As a result of the large eddy-number differences, eddy-eddy interactions were strong and induced submesoscale (smaller than 100 km) vertical pumping as observed in the in-situ ocean profiles. The signature of vertical pumping was also presented in the in-situ measurements of chlorophyll and nutrients, which show higher concentrations in 2010 than other years.

scholarly journals Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Yuki Saito ◽  
Akira Shigehisa ◽  
Yohei Watanabe ◽  
Naoki Tsukuda ◽  
Kaoru Moriyama-Ohara ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Utilization ◽  
Bifidobacterium Adolescentis ◽  
Content Type

ABSTRACT Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut. IMPORTANCE Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.

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