scholarly journals The Capability of Utilizing Abiotic Enantiomers of Amino Acids by Halomonas sp. LMO_D1 Derived From the Mariana Trench

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiangyu Wang ◽  
Yi Yang ◽  
Yongxin Lv ◽  
Xiang Xiao ◽  
Weishu Zhao
Keyword(s):  
Amino Acids ◽  
Subduction Zones ◽  
Fosmid Library ◽  
Mariana Trench ◽  
Amino Acid Dehydrogenase ◽  
Degradation Activity ◽  
Essential Function ◽  
Microbial Potential ◽  
Trench Sediments ◽  
Library Method

D-amino acids (D-AAs) have been produced both in organisms and in environments via biotic or abiotic processes. However, the existence of these organic materials and associated microbial degradation activity has not been previously investigated in subduction zones where tectonic activities result in the release of hydrothermal organic matter. Here, we isolated the bacterium Halomonas sp. LMO_D1 from a sample obtained from the Mariana trench, and we determined that this isolate utilized 13 different D-AAs (D-Ala, D-Glu, D-Asp, D-Ser, D-Leu, D-Val, D-Tyr, D-Gln, D-Asn, D-Pro, D-Arg, D-Phe, and D-Ile) in the laboratory and could grow on D-AAs under high hydrostatic pressure (HHP). Moreover, the metabolism of L-AAs was more severely impaired under HHP conditions compared with that of their enantiomers. The essential function gene (Chr_2344) required for D-AA catabolism in strain LMO_D1 was identified and confirmed according to the fosmid library method used on the D-AAs plate. The encoded enzyme of this gene (DAADH_2344) was identified as D-amino acid dehydrogenase (DAADH), and this gene product supports the catabolism of a broad range of D-AAs. The ubiquitous distribution of DAADHs within the Mariana Trench sediments suggests that microorganisms that utilize D-AAs are common within these sediments. Our findings provide novel insights into the microbial potential for utilizing abiotic enantiomers of amino acids within the subduction zone of the Mariana trench under HHP, and our results provide an instructive significance for understanding these abiotic enantiomers and allow for insights regarding how organisms within extraterrestrial HHP environments can potentially cope with toxic D-AAs.

scholarly journals The Glycine-Phenylalanine-Rich Region Determines the Specificity of the Yeast Hsp40 Sis1

1999 ◽  
Vol 19 (11) ◽  
pp. 7751-7758 ◽  
Author(s):  
Wei Yan ◽  
Elizabeth A. Craig
Keyword(s):  
Amino Acids ◽  
Molecular Chaperones ◽  
Rich Region ◽  
Critical Determinant ◽  
Unique Region ◽  
Chimeric Genes ◽  
F Region ◽  
Initiation Of Translation ◽  
J Domain ◽  
Essential Function

ABSTRACT Hsp40s are ubiquitous, conserved proteins which function with molecular chaperones of the Hsp70 class. Sis1 is an essential Hsp40 of the cytosol of Saccharomyces cerevisiae, thought to be required for initiation of translation. We carried out a genetic analysis to determine the regions of Sis1 required to perform its key function(s). A C-terminal truncation of Sis1, removing 231 amino acids but retaining the N-terminal 121 amino acids encompassing the J domain and the glycine-phenylalanine-rich (G-F) region, was able to rescue the inviability of a Δsis1 strain. The yeast cytosol contains other Hsp40s, including Ydj1. To determine which regions carried the critical determinants of Sis1 function, we constructed chimeric genes containing portions of SIS1 and YDJ1. A chimera containing the J domain of Sis1 and the G-F region of Ydj1 could not rescue the lethality of the Δsis1 strain. However, a chimera with the J domain of Ydj1 and the G/F region of Sis1 could rescue the strain’s lethality, indicating that the G-F region is a unique region required for the essential function of Sis1. However, a J domain is also required, as mutants expected to cause a disruption of the interaction of the J domain with Hsp70 are inviable. We conclude that the G-F region, previously thought only to be a linker or spacer region between the J domain and C-terminal regions of Hsp40s, is a critical determinant of Sis1 function.

scholarly journals The single CCA-adding enzyme of T. brucei has distinct functions in the cytosol and in mitochondria

2020 ◽  
Vol 295 (18) ◽  
pp. 6138-6150 ◽  
Author(s):  
Shikha Shikha ◽  
André Schneider
Keyword(s):  
Amino Acids ◽  
Growth Arrest ◽  
Trna Genes ◽  
Potential Candidate ◽  
Mitochondrial Localization ◽  
Putative Protein ◽  
Blast Search ◽  
Genes Encoding ◽  
Essential Function ◽  
Nucleotide Triplet

tRNAs universally carry a CCA nucleotide triplet at their 3′-ends. In eukaryotes, the CCA is added post-transcriptionally by the CCA-adding enzyme (CAE). The mitochondrion of the parasitic protozoan Trypanosoma brucei lacks tRNA genes and therefore imports all of its tRNAs from the cytosol. This has generated interest in the tRNA modifications and their distribution in this organism, including how CCA is added to tRNAs. Here, using a BLAST search for genes encoding putative CAE proteins in T. brucei, we identified a single ORF, Tb927.9.8780, as a potential candidate. Knockdown of this putative protein, termed TbCAE, resulted in the accumulation of truncated tRNAs, abolished translation, and inhibited both total and mitochondrial CCA-adding activities, indicating that TbCAE is located both in the cytosol and mitochondrion. However, mitochondrially localized tRNAs were much less affected by the TbCAE ablation than the other tRNAs. Complementation assays revealed that the N-terminal 10 amino acids of TbCAE are dispensable for its activity and mitochondrial localization and that deletion of 10 further amino acids abolishes both. A growth arrest caused by the TbCAE knockdown was rescued by the expression of the cytosolic isoform of yeast CAE, even though it was not imported into mitochondria. This finding indicated that the yeast enzyme complements the essential function of TbCAE by adding CCA to the primary tRNA transcripts. Of note, ablation of the mitochondrial TbCAE activity, which likely has a repair function, only marginally affected growth.

scholarly journals Creation of a Broad-Range and Highly Stereoselectived-Amino Acid Dehydrogenase for the One-Step Synthesis ofd-Amino Acids

2006 ◽  
Vol 128 (33) ◽  
pp. 10923-10929 ◽  
Author(s):  
Kavitha Vedha-Peters ◽  
Manjula Gunawardana ◽  
J. David Rozzell ◽  
Scott J. Novick
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Acid Dehydrogenase ◽  
Amino Acid Dehydrogenase ◽  
One Step ◽  
The One

scholarly journals The cmaR gene of Corynebacterium ammoniagenes performs a novel regulatory role in the metabolism of sulfur-containing amino acids

Microbiology ◽  
2009 ◽  
Vol 155 (6) ◽  
pp. 1878-1889 ◽  
Author(s):  
Seok-Myung Lee ◽  
Byung-Joon Hwang ◽  
Younhee Kim ◽  
Heung-Shick Lee
Keyword(s):  
Amino Acids ◽  
Target Genes ◽  
Sulfur Metabolism ◽  
Regulatory Gene ◽  
Positive Control ◽  
Negative Control ◽  
Biosynthetic Genes ◽  
Corynebacterium Ammoniagenes ◽  
Essential Function

A novel regulatory gene, which performs an essential function in sulfur metabolism, has been identified in Corynebacterium ammoniagenes and was designated cmaR (cysteine and methionine regulator in C. ammoniagenes). The cmaR-disrupted strain (ΔcmaR) lost the ability to grow on minimal medium, and was identified as a methionine and cysteine double auxotroph. The mutant strain proved unable to convert cysteine to methionine (and vice versa), and lost the ability to assimilate and reduce sulfate to sulfide. In the ΔcmaR strain, the mRNAs of the methionine biosynthetic genes metYX, metB and metFE were significantly reduced, and the activities of the methionine biosynthetic enzymes cystathionine γ-synthase, O-acetylhomoserine sulfhydrylase, and cystathionine β-lyase were relatively low, thereby suggesting that the cmaR gene exerts a positive regulatory effect on methionine biosynthetic genes. In addition, with the exception of cysK, reduced transcription levels of the sulfur-assimilatory genes cysIXYZ and cysHDN were noted in the cmaR-disrupted strain, which suggests that sulfur assimilation is also under the positive control of the cmaR gene. Furthermore, the expression of the cmaR gene itself was strongly induced via the addition of cysteine or methionine alone, but not the introduction of both amino acids together to the growth medium. In addition, the expression of the cmaR gene was enhanced in an mcbR-disrupted strain, which suggests that cmaR is under the negative control of McbR, which has been identified as a global regulator of sulfur metabolism. DNA binding of the purified CmaR protein to the promoter region of its target genes could be demonstrated in vitro. No metabolite effector was required for the protein to bind DNA. These results demonstrated that the cmaR gene of C. ammoniagenes plays a role similar to but distinct from that of the functional homologue cysR of Corynebacterium glutamicum.

scholarly journals Regulation of the dauBAR operon and characterization of d-amino acid dehydrogenase DauA in arginine and lysine catabolism of Pseudomonas aeruginosa PAO1

Microbiology ◽  
2010 ◽  
Vol 156 (1) ◽  
pp. 60-71 ◽  
Author(s):  
Congran Li ◽  
Xiangyu Yao ◽  
Chung-Dar Lu
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Mutation Analysis ◽  
Regulatory Region ◽  
Mobility Shift ◽  
Signal Molecule ◽  
Acid Dehydrogenase ◽  
Amino Acid Dehydrogenase ◽  
Activity Measurements

A unique d-to-l racemization of arginine by coupled arginine dehydrogenases DauA and DauB encoded by the dauBAR operon has been recently reported as a prerequisite for d-arginine utilization as the sole source of carbon and nitrogen through l-arginine catabolic pathways in P. aeruginosa. In this study, enzymic properties of the catabolic FAD-dependent d-amino acid dehydrogenase DauA and the physiological functions of the dauBAR operon were further characterized with other d-amino acids. These results establish DauA as a d-amino acid dehydrogenase of broad substrate specificity, with d-Arg and d-Lys as the two most effective substrates, based on the kinetic parameters. In addition, expression of dauBAR is specifically induced by exogenous d-Arg and d-Lys, and mutations in the dauBAR operon affect utilization of these two amino acids alone. The function of DauR as a repressor in the control of the dauBAR operon was demonstrated by dauB promoter activity measurements in vivo and mobility shift assays with purified His-tagged protein in vitro. The potential effect of 2-ketoarginine (2-KA) derived from d-Arg deamination by DauA as a signal molecule in dauBAR induction was first revealed by mutation analysis and further supported by its in vitro effect on alleviation of DauR–DNA interactions. Through sequence analysis, putative DauR operators were identified and confirmed by mutation analysis. Induction of the dauBAR operon to the maximal level was found to require the l-arginine-responsive regulator ArgR, as supported by the loss of inductive effect by l-Arg on dauBAR expression in the argR mutant and binding of purified ArgR to the dauB regulatory region in vitro. In summary, this study establishes that optimal induction of the dauBAR operon requires relief of DauR repression by 2-KA and activation of ArgR by l-Arg as a result of d-Arg racemization by the encoded DauA and DauB.

Dermacozines H–J Isolated from a Deep-Sea Strain of Dermacoccus abyssi from Mariana Trench Sediments

2014 ◽  
Vol 77 (2) ◽  
pp. 416-420 ◽  
Author(s):  
Marcell Wagner ◽  
Wael M. Abdel-Mageed ◽  
Rainer Ebel ◽  
Alan T. Bull ◽  
Michael Goodfellow ◽  
...  
Keyword(s):  
Deep Sea ◽  
Mariana Trench ◽  
Trench Sediments

scholarly journals Periodic and Spatial Spreading of Alkanes andAlcanivoraxBacteria in Deep Waters of the Mariana Trench

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Wen-Li Li ◽  
Jiao-Mei Huang ◽  
Pei-Wei Zhang ◽  
Guo-Jie Cui ◽  
Zhan-Fei Wei ◽  
...  
Keyword(s):  
Water Samples ◽  
Deep Sea ◽  
Subduction Zones ◽  
Deep Ocean ◽  
Nitrogen Sources ◽  
Alkane Degradation ◽  
Mariana Trench ◽  
Content Type ◽  
Deep Waters ◽  
Degrading Bacteria

ABSTRACTIn subduction zones, serpentinization and biological processes may release alkanes to the deep waters, which would probably result in the rapid spread ofAlcanivorax. However, the timing and area of the alkane distribution and associated enrichment of alkane-degrading microbes in the dark world of the deep ocean have not been explored. In this study, we report the richness (up to 17.8%) of alkane-degrading bacteria, represented byAlcanivorax jadensis, in deep water samples obtained at 3,000 to 6,000 m in the Mariana Trench in two cruises. The relative abundance ofA. jadensiscorrelated with copy numbers of functionalalmAandalkBgenes, which are involved in alkane degradation. In these water samples, we detected a high flux of alkanes, which probably resulted in the prevalence ofA. jadensisin the deep waters. Contigs ofA. jadensiswere binned from the metagenomes for examination of alkane degradation pathways and deep sea-specific pathways, which revealed a lack of nitrate and nitrite dissimilatory reduction in ourA. jadensisstrains. Comparing the results for the two cruises conducted close to each other, we suggest periodic release of alkanes that may spread widely but periodically in the trench. Distribution of alkane-degrading bacteria in the world’s oceans suggests the periodic and remarkable contributions ofAlcanivoraxto the deep sea organic carbon and nitrogen sources.IMPORTANCEIn the oligotrophic environment of the Mariana Trench, alkanes as carbohydrates are important for the ecosystem, but their spatial and periodic spreading in deep waters has never been reported. Alkane-degrading bacteria such asAlcanivoraxspp. are biological signals of the alkane distribution. In the present study,Alcanivoraxwas abundant in some waters, at depths of up to 6,000 m, in the Mariana Trench. Genomic, transcriptomic, and chemical analyses provide evidence for the presence and activities ofAlcanivorax jadensisin deep sea zones. The periodic spreading of alkanes, probably from the subductive plates, might have fundamentally modified the local microbial communities, as well as perhaps the deep sea microenvironment.

Palaeoclimate, sedimentation and continental accretion

1981 ◽  
Vol 301 (1461) ◽  
pp. 253-264 ◽  
Keyword(s):  
South America ◽  
Subduction Zones ◽  
Heated Surface ◽  
Climatic Zones ◽  
Run Off ◽  
Tectonic Erosion ◽  
Opposite Process ◽  
North And South ◽  
Trench Sediments ◽  
Continental Accretion

Climate has a pervasive effect on sedimentation today, and the same climatic patterns are reflected in the distribution of lithofacies through the Palaeozoic, as the continents migrate beneath the climatic zones. The low-latitude hot wet zone is represented by thick elastics, coals and carbonates and is best developed along east coasts where prevailing winds bring moisture and heated surface waters toward the continent. The desert zones occur on the west sides of continents centred at 20° north and south, and these dry belts are represented in the geological record by evaporites. Tillites, thick elastics and coals occur in the temperate rainy belts, especially on the windward, west sides of continents above 40° latitude. Continental accretion occurs where subduction zones coincide with rainy zones, such that the products of erosion are transported to the trench, and thus thrust back, extending the margin of the continent. The opposite process of ‘tectonic erosion’, wherein the descending oceanic slab continually ‘rasps’ away the margin of the continental crust, may occur in areas where rainfall and surface run-off is insufficient to provide trench sediments. This process has been operating adjacent to the Atacama Desert in South America during the past 200 Ma. To judge by the eastward migration of the calc-alkaline intrusive foci, about 250 km of the margin of South America have been transported down the subduction zone during this period.

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