scholarly journals Genomic and morphologic characterization of a planktonic Thiovulum (Campylobacterota) dominating the surface waters of the sulfidic Movile Cave, Romania

2020 ◽  
Author(s):  
Mina Bizic ◽  
Traian Brad ◽  
Lucian Barbu-Tudoran ◽  
Joost Aerts ◽  
Danny Ionescu ◽  
...  
Keyword(s):  
Surface Waters ◽  
Aquatic Ecosystems ◽  
Elemental Sulfur ◽  
Carbon Fixation ◽  
Ferric Iron ◽  
Hydroxylamine Oxidoreductase ◽  
Type Iv ◽  
Sulfur Globules ◽  
Movile Cave

ABSTRACTLife in Movile Cave (Romania) relies entirely on primary carbon fixation by bacteria oxidizing sulfide, methane and ammonia with oxygen, nitrate, sulfate, and ferric iron. There, large spherical-ovoid bacteria (12-16 μm diameter), rich in intracellular sulfur globules, dominate the stable microbial community in the surface water of a hypoxic Air Bell. These were identified as Thiovulum sp. (Campylobacterota). We obtained a closed genome of this Thiovulum and compared it to that of Thiovulum ES. The genes for oxidizing sulfide to sulfate are absent, therefore, Thiovulum likely avoids constant accumulation of elemental sulfur either by oxidizing sulfide to sulfite which is then excreted, or via dissimilatory nitrate reduction to ammonia using the formate-dependent nitrite reductase or hydroxylamine oxidoreductase. Thus, Thiovulum, found also in other caves, is likely important to both S and N cycles in subterranean aquatic ecosystems. Additionally, using electron microscopy, we suggest that in absence of motor-like structures along the membrane, the peritrichous flagella-like structures are type IV pili, for which genes were found in both Thiovulum genomes. These pili may play a role in veil formation, connecting adjacent cells. The force exerted by coordinated movement of such pili may partly explain the exceptionally fast swimming of these bacteria.

scholarly journals Isolation and Polyphasic Characterization of Desulfuromonas versatilis sp. Nov., an Electrogenic Bacteria Capable of Versatile Metabolism Isolated from a Graphene Oxide-Reducing Enrichment Culture

2021 ◽  
Vol 9 (9) ◽  
pp. 1953
Author(s):  
Li Xie ◽  
Naoko Yoshida ◽  
Shun’ichi Ishii ◽  
Lingyu Meng
Keyword(s):  
Graphene Oxide ◽  
Elemental Sulfur ◽  
Ferric Iron ◽  
Enrichment Culture ◽  
Electron Donors ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Metabolic Capability ◽  
Polyphasic Characterization

In this study, a novel electrogenic bacterium denoted as strain NIT-T3 of the genus Desulfuromonas was isolated from a graphene-oxide-reducing enrichment culture that was originally obtained from a mixture of seawater and coastal sand. Strain NIT-T3 utilized hydrogen and various organic acids as electron donors and exhibited respiration using electrodes, ferric iron, nitrate, and elemental sulfur. The strain contained C16:1ω7c, C16:0, and C15:0 as major fatty acids and MK-8, 9, and 7 as the major respiratory quinones. Strain NIT-T3 contained four 16S rRNA genes and showed 95.7% similarity to Desulfuromonasmichiganensis BB1T, the closest relative. The genome was 4.7 Mbp in size and encoded 76 putative c-type cytochromes, which included 6 unique c-type cytochromes (<40% identity) compared to those in the database. Based on the physiological and genetic uniqueness, and wide metabolic capability, strain NIT-T3 is proposed as a type strain of ‘Desulfuromonas versatilis’ sp. nov.

scholarly journals Characterization of full-length transcriptome in Saccharum officinarum and molecular insights into tiller development

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haifeng Yan ◽  
Huiwen Zhou ◽  
Hanmin Luo ◽  
Yegeng Fan ◽  
Zhongfeng Zhou ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Developmental Stages ◽  
Genomic Data ◽  
Saccharum Officinarum ◽  
Full Length ◽  
Rna Seq ◽  
Pyruvate Phosphate Dikinase ◽  
Sugarcane Yield ◽  
Tiller Bud

Abstract Background Although extensive breeding efforts are ongoing in sugarcane (Saccharum officinarum L.), the average yield is far below the theoretical potential. Tillering is an important component of sugarcane yield, however, the molecular mechanism underlying tiller development is still elusive. The limited genomic data in sugarcane, particularly due to its complex and large genome, has hindered in-depth molecular studies. Results Herein, we generated full-length (FL) transcriptome from developing leaf and tiller bud samples based on PacBio Iso-Seq. In addition, we performed RNA-seq from tiller bud samples at three developmental stages (T0, T1 and T2) to uncover key genes and biological pathways involved in sugarcane tiller development. In total, 30,360 and 20,088 high-quality non-redundant isoforms were identified in leaf and tiller bud samples, respectively, representing 41,109 unique isoforms in sugarcane. Likewise, we identified 1063 and 1037 alternative splicing events identified in leaf and tiller bud samples, respectively. We predicted the presence of coding sequence for 40,343 isoforms, 98% of which was successfully annotated. Comparison with previous FL transcriptomes in sugarcane revealed 2963 unreported isoforms. In addition, we characterized 14,946 SSRs from 11,700 transcripts and 310 lncRNAs. By integrating RNA-seq with the FL transcriptome, 468 and 57 differentially expressed genes (DEG) were identified in T1vsT0 and T2vsT0, respectively. Strong up-regulation of several pyruvate phosphate dikinase and phosphoenolpyruvate carboxylase genes suggests enhanced carbon fixation and protein synthesis to facilitate tiller growth. Similarly, up-regulation of linoleate 9S-lipoxygenase and lipoxygenase genes in the linoleic acid metabolism pathway suggests high synthesis of key oxylipins involved in tiller growth and development. Conclusions Collectively, we have enriched the genomic data available in sugarcane and provided candidate genes for manipulating tiller formation and development, towards productivity enhancement in sugarcane.

scholarly journals Cryo-ET Characterization of Novel Cellular Extrusions in Escherichia coli Induced by the Major Subunit Protein of Type IV Pili, PilA, from Pseudomonas aeruginosa

2021 ◽  
Vol 27 (S1) ◽  
pp. 280-282
Author(s):  
Juan Sanchez ◽  
Daniel Parrell ◽  
Alba Gonzalez-Rivera ◽  
Nicoleta Ploscariu ◽  
Katrina Forest ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Type Iv Pili ◽  
Subunit Protein ◽  
Type Iv

Isolation and characterization of pepsin-solubilized human basement membrane (type IV) collagen peptides

Biochemistry ◽  
1983 ◽  
Vol 22 (21) ◽  
pp. 4940-4948 ◽  
Author(s):  
Robert S. MacWright ◽  
Virginia A. Benson ◽  
Katherine T. Lovello ◽  
Michel Van der Rest ◽  
Peter P. Fietzek
Keyword(s):  
Basement Membrane ◽  
Type Iv Collagen ◽  
Collagen Peptides ◽  
Type Iv ◽  
Isolation And Characterization ◽  
Membrane Type

viking: identification and characterization of a second type IV collagen in Drosophila

Gene ◽  
1997 ◽  
Vol 198 (1-2) ◽  
pp. 17-25 ◽  
Author(s):  
Sukkid Yasothornsrikul ◽  
Wendy J Davis ◽  
Gabrielle Cramer ◽  
Deborah A Kimbrell ◽  
Charles R Dearolf
Keyword(s):  
Type Iv Collagen ◽  
Type Iv ◽  
Identification And Characterization

Synthesis and Redox Reactions of Binuclear Zinc(II)-thiolate Complexes with Elemental Sulfur

2021 ◽  
Author(s):  
Tilak Naskar ◽  
Nabhendu Pal ◽  
Amit Majumdar
Keyword(s):  
Redox Reactions ◽  
Elemental Sulfur ◽  
Synthesis And Characterization ◽  
Thiolate Complexes

Synthesis and characterization of a series of new binuclear Zn(II) complexes bearing (i) terminal H2O/OH, (ii) bridging thiolates, (iii) bridging thiocarboxylates, (iv) bridging carboxylates, and (v) bridging carboxylate bearing free...

Identification and initial characterization of a new pair of sibling sRNAs of Neisseria gonorrhoeae involved in type IV pilus biogenesis

Microbiology ◽  
2021 ◽  
Vol 167 (9) ◽  
Author(s):  
Marie Zachary ◽  
Susanne Bauer ◽  
Maximilian Klepsch ◽  
Katharina Wagler ◽  
Bruno Hüttel ◽  
...  
Keyword(s):  
Target Genes ◽  
Target Prediction ◽  
Type Iv Pilus ◽  
Content Type ◽  
Type Iv ◽  
Gene Expression Control ◽  
Initial Characterization ◽  
Pilus Biogenesis ◽  
Regulatory Rnas

Non-coding regulatory RNAs mediate post-transcriptional gene expression control by a variety of mechanisms relying mostly on base-pairing interactions with a target mRNA. Though a plethora of putative non-coding regulatory RNAs have been identified by global transcriptome analysis, knowledge about riboregulation in the pathogenic Neisseriae is still limited. Here we report the initial characterization of a pair of sRNAs of N. gonorrhoeae , TfpR1 and TfpR2, which exhibit a similar secondary structure and identical single-stranded seed regions, and therefore might be considered as sibling sRNAs. By combination of in silico target prediction and sRNA pulse expression followed by differential RNA sequencing we identified target genes of TfpR1 which are involved in type IV pilus biogenesis and DNA damage repair. We provide evidence that members of the TfpR1 regulon can also be targeted by the sibling TfpR2.

Activation of Bis(guanidinate)lanthanide Alkyl and Aryl Complexes on Elemental Sulfur: Synthesis and Characterization of Bis(guanidinate)lanthanide Thiolates and Disulfides

2010 ◽  
Vol 49 (12) ◽  
pp. 5715-5722 ◽  
Author(s):  
Zhengxing Zhang ◽  
Lixin Zhang ◽  
Yanrong Li ◽  
Longcheng Hong ◽  
Zhenxia Chen ◽  
...  
Keyword(s):  
Elemental Sulfur ◽  
Synthesis And Characterization ◽  
Aryl Complexes
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