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Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ. Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. THE ISME JOURNAL 2011; 5:274-84. [PMID: 20703316 PMCID: PMC3105692 DOI: 10.1038/ismej.2010.103] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 05/21/2010] [Accepted: 06/13/2010] [Indexed: 11/09/2022]
Abstract
Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. In this study, the complete genome of deep-sea sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913 was less tolerant of H(2)O(2) than TAC125. SM9913 has gene clusters related to both polar and lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea bacteria and absent in the related surface bacteria, are important for the survival of SM9913 in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal resistance. Many signal transduction genes and a glycogen production operon were also present in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy in a deep-sea environment.
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Affiliation(s)
- Qi-Long Qin
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Yang Li
- State Key Lab of Microbial Technology, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yan-Jiao Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Zhe-Min Zhou
- State Key Lab of Microbial Technology, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Wei-Xin Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Xiu-Lan Chen
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Xi-Ying Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Bai-Cheng Zhou
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Lei Wang
- State Key Lab of Microbial Technology, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yu-Zhong Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
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Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci U S A 2010; 107:16420-7. [PMID: 20807744 DOI: 10.1073/pnas.1010732107] [Citation(s) in RCA: 263] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Marine dissolved organic matter (DOM) contains as much carbon as the Earth's atmosphere, and represents a critical component of the global carbon cycle. To better define microbial processes and activities associated with marine DOM cycling, we analyzed genomic and transcriptional responses of microbial communities to high-molecular-weight DOM (HMWDOM) addition. The cell density in the unamended control remained constant, with very few transcript categories exhibiting significant differences over time. In contrast, the DOM-amended microcosm doubled in cell numbers over 27 h, and a variety of HMWDOM-stimulated transcripts from different taxa were observed at all time points measured relative to the control. Transcripts significantly enriched in the HMWDOM treatment included those associated with two-component sensor systems, phosphate and nitrogen assimilation, chemotaxis, and motility. Transcripts from Idiomarina and Alteromonas spp., the most highly represented taxa at the early time points, included those encoding TonB-associated transporters, nitrogen assimilation genes, fatty acid catabolism genes, and TCA cycle enzymes. At the final time point, Methylophaga rRNA and non-rRNA transcripts dominated the HMWDOM-amended microcosm, and included gene transcripts associated with both assimilatory and dissimilatory single-carbon compound utilization. The data indicated specific resource partitioning of DOM by different bacterial species, which results in a temporal succession of taxa, metabolic pathways, and chemical transformations associated with HMWDOM turnover. These findings suggest that coordinated, cooperative activities of a variety of bacterial "specialists" may be critical in the cycling of marine DOM, emphasizing the importance of microbial community dynamics in the global carbon cycle.
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Galperin MY, Koonin EV. From complete genome sequence to 'complete' understanding? Trends Biotechnol 2010; 28:398-406. [PMID: 20647113 PMCID: PMC3065831 DOI: 10.1016/j.tibtech.2010.05.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 05/18/2010] [Accepted: 05/28/2010] [Indexed: 12/29/2022]
Abstract
The rapidly accumulating genome sequence data allow researchers to address fundamental biological questions that were not even asked just a few years ago. A major problem in genomics is the widening gap between the rapid progress in genome sequencing and the comparatively slow progress in the functional characterization of sequenced genomes. Here we discuss two key questions of genome biology: whether we need more genomes, and how deep is our understanding of biology based on genomic analysis. We argue that overly specific annotations of gene functions are often less useful than the more generic, but also more robust, functional assignments based on protein family classification. We also discuss problems in understanding the functions of the remaining 'conserved hypothetical' genes.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Qin QL, Zhang XY, Wang XM, Liu GM, Chen XL, Xie BB, Dang HY, Zhou BC, Yu J, Zhang YZ. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 2010; 11:247. [PMID: 20398413 PMCID: PMC2864250 DOI: 10.1186/1471-2164-11-247] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Accepted: 04/17/2010] [Indexed: 01/31/2023] Open
Abstract
Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.
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Affiliation(s)
- Qi-Long Qin
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
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van der Horst MA, Stalcup TP, Kaledhonkar S, Kumauchi M, Hara M, Xie A, Hellingwerf KJ, Hoff WD. Locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium Idiomarina loihiensis. J Am Chem Soc 2010; 131:17443-51. [PMID: 19891493 DOI: 10.1021/ja9057103] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Idiomarina loihiensis is a heterotrophic deep sea bacterium with no known photobiology. We show that light suppresses biofilm formation in this organism. The genome of I. loihiensis encodes a single photoreceptor protein: a homologue of photoactive yellow protein (PYP), a blue light receptor with photochemistry based on trans to cis isomerization of its p-coumaric acid (pCA) chromophore. The addition of trans-locked pCA to I. loihiensis increases biofilm formation, whereas cis-locked pCA decreases it. This demonstrates that the PYP homologue regulates biofilm formation in I. loihiensis, revealing an unexpected functional versatility in the PYP family of photoreceptors. These results imply that I. loihiensis thrives not only in the deep sea but also near the water surface and provide an example of genome-based discovery of photophysiological responses. The use of locked pCA analogs is a novel and generally applicable pharmacochemical tool to study the in vivo role of PYPs irrespective of genetic accessibility. Heterologously produced PYP from I. loihiensis (Il PYP) absorbs maximally at 446 nm and has a pCA pK(a) of 3.4. Photoexcitation triggers the formation of a pB signaling state that decays with a time constant of 0.3 s. FTIR difference signals at 1726 and 1497 cm(-1) reveal that active-site proton transfer during the photocycle is conserved in Il PYP. It has been proposed that a correlation exists between the lifetime of a photoreceptor signaling state and the time scale of the biological response that it regulates. The data presented here provide an example of a protein with a rapid photocycle that regulates a slow biological response.
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Affiliation(s)
- Michael A van der Horst
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
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Van Houdt R, Monchy S, Leys N, Mergeay M. New mobile genetic elements in Cupriavidus metallidurans CH34, their possible roles and occurrence in other bacteria. Antonie van Leeuwenhoek 2009; 96:205-26. [DOI: 10.1007/s10482-009-9345-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 03/18/2009] [Indexed: 10/20/2022]
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Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 2009; 5:e1000362. [PMID: 19197347 PMCID: PMC2628731 DOI: 10.1371/journal.pgen.1000362] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 12/31/2008] [Indexed: 11/19/2022] Open
Abstract
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment--some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20 degrees C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere--anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.
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Huang Y, Lai X, He X, Cao L, Zeng Z, Zhang J, Zhou S. Characterization of a deep-sea sediment metagenomic clone that produces water-soluble melanin in Escherichia coli. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2009; 11:124-131. [PMID: 18648877 DOI: 10.1007/s10126-008-9128-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 06/13/2008] [Indexed: 05/26/2023]
Abstract
To access to the microbial genetic resources of deep-sea sediment by a culture-independent approach, the sediment DNA was extracted and cloned into fosmid vector (pCC1FOS) generating a library of 39,600 clones with inserts of 24-45 kb. The clone fss6 producing red-brown pigment was isolated and characterized. The pigment was identified as melanin according to its physico-chemical characteristics. Subcloning and sequences analyses of fss6 demonstrated that one open reading frame (ORF2) was responsible for the pigment production. The deduced protein from ORF2 revealed significant amino acid similarity to the 4-hydroxyphenylpyruvate dioxygenase (HPPD) from deep-sea bacteria Idiomarina loihiensis. Further study demonstrated that the production of melanin was correlated with homogentistic acid (HGA). The p-hydroxyphenylpyruvate produced by the Escherichia coli host was converted to HGA through the oxidation reaction of introduced HPPD. The results demonstrate that expression of DNA extracted directly from the environment might generate applicable microbial gene products. The construction and analysis of the metagenomic library from deep-sea sediment contributed to our understanding for the reservoir of unexploited deep-sea microorganisms.
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Affiliation(s)
- Yali Huang
- State Key Laboratory for Biocontrol, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J, Tiedje JM. Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach. BMC Genomics 2008; 9:547. [PMID: 19019206 PMCID: PMC2615787 DOI: 10.1186/1471-2164-9-547] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 11/18/2008] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5 degrees C to 39 degrees C to study its thermal adaptation. RESULTS The E. sibiricum genome has one chromosome and two small plasmids with a total of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%. The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of 27%, 3.2%, and 5.2% of E. sibiricum CDS spotted on the DNA microarray detected differentially expressed genes in cells grown at -2.5 degrees C, 10 degrees C, and 39 degrees C, respectively, when compared to cells grown at 28 degrees C. The hypothetical and unknown genes represented 10.6%, 0.89%, and 2.3% of the CDS differentially expressed when grown at -2.5 degrees C, 10 degrees C, and 39 degrees C versus 28 degrees C, respectively. CONCLUSION The results show that E. sibiricum is constitutively adapted to cold temperatures stressful to mesophiles since little differential gene expression was observed between 4 degrees C and 28 degrees C, but at the extremities of its Arrhenius growth profile, namely -2.5 degrees C and 39 degrees C, several physiological and metabolic adaptations associated with stress responses were observed.
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Affiliation(s)
- Debora F Rodrigues
- Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1604, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Marianne Huebner
- Michigan State University, Department of Statistics and Probability, East Lansing, MI, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - James M Tiedje
- Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA
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Saw JH, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G, Wu J, Galperin MY, Koonin EV, Makarova KS, Wolf YI, Rigden DJ, Dunfield PF, Wang L, Alam M. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1. Genome Biol 2008; 9:R161. [PMID: 19014707 PMCID: PMC2614493 DOI: 10.1186/gb-2008-9-11-r161] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 10/08/2008] [Accepted: 11/17/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. RESULTS We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. CONCLUSIONS Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
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Affiliation(s)
- Jimmy H Saw
- Department of Microbiology, University of Hawai'i, 2538 The Mall, Honolulu, HI 96822, USA.
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Abstract
This review covers the 390 novel marine natural products described to date from deep-water (>50 m) marine fauna, with details on the source organism, its depth and country of origin, along with any reported biological activity of the metabolites. Relevant synthetic studies on the deep-sea natural products have also been included.
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Affiliation(s)
- Danielle Skropeta
- School of Chemistry, University of Wollongong, Wollongong, Australia.
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Lysogenic virus-host interactions predominate at deep-sea diffuse-flow hydrothermal vents. ISME JOURNAL 2008; 2:1112-21. [PMID: 18719614 DOI: 10.1038/ismej.2008.73] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The consequences of viral infection within microbial communities are dependent on the nature of the viral life cycle. Among the possible outcomes is the substantial influence of temperate viruses on the phenotypes of lysogenic prokaryotes through various forms of genetic exchange. To date, no marine microbial ecosystem has consistently shown a predisposition for containing significant numbers of inducible temperate viruses. Here, we show that deep-sea diffuse-flow hydrothermal vent waters display a consistently high incidence of lysogenic hosts and harbor substantial populations of temperate viruses. Genetic fingerprinting and initial metagenomic analyses indicate that temperate viruses in vent waters appear to be a less diverse subset of the larger virioplankton community and that these viral populations contain an extraordinarily high frequency of novel genes. Thus, it appears likely that temperate viruses are key players in the ecology of prokaryotes within the extreme geothermal ecosystems of the deep sea.
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Kumauchi M, Hara MT, Stalcup P, Xie A, Hoff WD. Identification of Six New Photoactive Yellow ProteinsDiversity and StructureFunction Relationships in a Bacterial Blue Light Photoreceptor. Photochem Photobiol 2008; 84:956-69. [DOI: 10.1111/j.1751-1097.2008.00335.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hou S, Makarova KS, Saw JHW, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 2008; 3:26. [PMID: 18593465 PMCID: PMC2474590 DOI: 10.1186/1745-6150-3-26] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 07/01/2008] [Indexed: 12/31/2022] Open
Abstract
Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. Results We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins. Conclusion The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria. Reviewers This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.
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Affiliation(s)
- Shaobin Hou
- Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii, Keller Hall #319, Honolulu, Hawaii, 96822, USA.
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Shapiro BJ, Alm EJ. Comparing patterns of natural selection across species using selective signatures. PLoS Genet 2008; 4:e23. [PMID: 18266472 PMCID: PMC2233676 DOI: 10.1371/journal.pgen.0040023] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Accepted: 12/18/2007] [Indexed: 12/04/2022] Open
Abstract
Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell. Natural selection promotes the survival of the fittest individuals within a species. Over many generations, this may result in the maintenance of ancestral traits (conservation through purifying selection), or the emergence of newly beneficial traits (adaptation through positive selection). At the genetic level, long-term purifying or positive selection can cause genes to evolve more slowly, or more rapidly, providing a way to identify these evolutionary forces. While some genes are subject to consistent purifying or positive selection in most species, other genes show unexpected levels of selection in a particular species or group of species—a pattern we refer to as the “selective signature” of the gene. In this work, we demonstrate that these patterns of natural selection can be mined for information about gene function and species ecology. In the future, this method could be applied to any set of related species with fully sequenced genomes to better understand the genetic basis of ecological divergence.
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Affiliation(s)
- B. Jesse Shapiro
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Eric J Alm
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Virtual institute of Microbial Stress and Survival, Berkeley, California, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Riley M, Staley JT, Danchin A, Wang TZ, Brettin TS, Hauser LJ, Land ML, Thompson LS. Genomics of an extreme psychrophile, Psychromonas ingrahamii. BMC Genomics 2008; 9:210. [PMID: 18460197 PMCID: PMC2405808 DOI: 10.1186/1471-2164-9-210] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Accepted: 05/06/2008] [Indexed: 11/10/2022] Open
Abstract
Background The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Results Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. Conclusion The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.
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Affiliation(s)
- Monica Riley
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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Wang F, Wang J, Jian H, Zhang B, Li S, Wang F, Zeng X, Gao L, Bartlett DH, Yu J, Hu S, Xiao X. Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3. PLoS One 2008; 3:e1937. [PMID: 18398463 PMCID: PMC2276687 DOI: 10.1371/journal.pone.0001937] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 02/28/2008] [Indexed: 01/01/2023] Open
Abstract
Shewanella species are widespread in various environments. Here, the genome sequence of Shewanella piezotolerans WP3, a piezotolerant and psychrotolerant iron reducing bacterium from deep-sea sediment was determined with related functional analysis to study its environmental adaptation mechanisms. The genome of WP3 consists of 5,396,476 base pairs (bp) with 4,944 open reading frames (ORFs). It possesses numerous genes or gene clusters which help it to cope with extreme living conditions such as genes for two sets of flagellum systems, structural RNA modification, eicosapentaenoic acid (EPA) biosynthesis and osmolyte transport and synthesis. And WP3 contains 55 open reading frames encoding putative c-type cytochromes which are substantial to its wide environmental adaptation ability. The mtr-omc gene cluster involved in the insoluble metal reduction in the Shewanella genus was identified and compared. The two sets of flagellum systems were found to be differentially regulated under low temperature and high pressure; the lateral flagellum system was found essential for its motility and living at low temperature.
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Affiliation(s)
- Fengping Wang
- Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, Xiamen, People's Republic of China
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
| | - Jianbin Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Huahua Jian
- Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, Xiamen, People's Republic of China
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
| | - Bing Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Shengkang Li
- Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, Xiamen, People's Republic of China
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
| | - Feng Wang
- Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, Xiamen, People's Republic of China
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
| | - Xiaowei Zeng
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Lei Gao
- The T-Life Research Center, Fudan University, Shanghai, People's Republic of China
| | - Douglas Hoyt Bartlett
- Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, United States of America
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, People's Republic of China
- * E-mail: (SH); (XX)
| | - Xiang Xiao
- Key Laboratory of Marine Biogenetic Resources, State Oceanic Administration, Xiamen, People's Republic of China
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, People's Republic of China
- * E-mail: (SH); (XX)
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Bertin PN, Médigue C, Normand P. Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems. MICROBIOLOGY-SGM 2008; 154:347-359. [PMID: 18227239 DOI: 10.1099/mic.0.2007/011791-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Microbial genome sequencing has, for the first time, made accessible all the components needed for both the elaboration and the functioning of a cell. Associated with other global methods such as protein and mRNA profiling, genomics has considerably extended our knowledge of physiological processes and their diversity not only in human, animal and plant pathogens but also in environmental isolates. At a higher level of complexity, the so-called meta approaches have recently shown great promise in investigating microbial communities, including uncultured micro-organisms. Combined with classical methods of physico-chemistry and microbiology, these endeavours should provide us with an integrated view of how micro-organisms adapt to particular ecological niches and participate in the dynamics of ecosystems.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, Université Louis Pasteur, UMR7156 CNRS, Strasbourg, France
| | | | - Philippe Normand
- Ecologie Microbienne, Université Claude Bernard - Lyon 1, UMR5557 CNRS, Villeurbanne, France
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69
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SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 2008; 452:741-4. [PMID: 18337719 DOI: 10.1038/nature06776] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 01/30/2008] [Indexed: 11/08/2022]
Abstract
Sulphur is a universally required cell nutrient found in two amino acids and other small organic molecules. All aerobic marine bacteria are known to use assimilatory sulphate reduction to supply sulphur for biosynthesis, although many can assimilate sulphur from organic compounds that contain reduced sulphur atoms. An analysis of three complete 'Candidatus Pelagibacter ubique' genomes, and public ocean metagenomic data sets, suggested that members of the ubiquitous and abundant SAR11 alphaproteobacterial clade are deficient in assimilatory sulphate reduction genes. Here we show that SAR11 requires exogenous sources of reduced sulphur, such as methionine or 3-dimethylsulphoniopropionate (DMSP) for growth. Titrations of the algal osmolyte DMSP in seawater medium containing all other macronutrients in excess showed that 1.5 x 10(8) SAR11 cells are produced per nanomole of DMSP. Although it has been shown that other marine alphaproteobacteria use sulphur from DMSP in preference to sulphate, our results indicate that 'Cand. P. ubique' relies exclusively on reduced sulphur compounds that originate from other plankton.
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71
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Arp DJ, Chain PSG, Klotz MG. The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annu Rev Microbiol 2007; 61:503-28. [PMID: 17506671 DOI: 10.1146/annurev.micro.61.080706.093449] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The availability of whole-genome sequences for ammonia-oxidizing bacteria (AOB) has led to dramatic increases in our understanding of these environmentally important microorganisms. Their genomes are smaller than many other members of the proteobacteria and may indicate genome reductions consistent with their limited lifestyle. The genomes have a surprising level of gene repetition including genes for ammonia catabolism, iron acquisition, and insertion sequences. The gene profiles reveal limited genes for catabolism and transport of complex organic compounds, but complete pathways for some other compounds. This led to the observation of chemolithoheterotrophic growth of Nitrosomonas europaea. Genes for sucrose synthesis/degradation were identified. The core metabolic module of aerobic ammonia oxidation, the extraction of electrons from hydroxylamine to generate proton-motive force and reductant, has evolutionary roots in the denitrification inventory of anaerobic sulfur-dependent bacteria. The extension by ammonia monooxygenase provides a mechanism to feed this module using ammonia and O(2).
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Affiliation(s)
- Daniel J Arp
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.
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72
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Kim EJ, Angell S, Janes J, Watanabe CMH. Estimating P-coverage of biosynthetic pathways in DNA libraries and screening by genetic selection: biotin biosynthesis in the marine microorganism Chromohalobacter. MOLECULAR BIOSYSTEMS 2007; 4:606-13. [PMID: 18493659 DOI: 10.1039/b712770g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Traditional approaches to natural product discovery involve cell-based screening of natural product extracts followed by compound isolation and characterization. Their importance notwithstanding, continued mining leads to depletion of natural resources and the reisolation of previously identified metabolites. Metagenomic strategies aimed at localizing the biosynthetic cluster genes and expressing them in surrogate hosts offers one possible alternative. A fundamental question that naturally arises when pursuing such a strategy is, how large must the genomic library be to effectively represent the genome of an organism(s) and the biosynthetic gene clusters they harbor? Such an issue is certainly augmented in the absence of expensive robotics to expedite colony picking and/or screening of clones. We have developed an algorism, named BPC (biosynthetic pathway coverage), supported by molecular simulations to deduce the number of BAC clones required to achieve proper coverage of the genome and their respective biosynthetic pathways. The strategy has been applied to the construction of a large-insert BAC library from a marine microorganism, Hon6 (isolated from Honokohau, Maui) thought to represent a new species. The genomic library is constructed with a BAC yeast shuttle vector pClasper lacZ paving the way for the culturing of libraries in both prokaryotic and eukaryotic hosts. Flow cytometric methods are utilized to estimate the genome size of the organism and BPC implemented to assess P-coverage or percent coverage. A genetic selection strategy is illustrated, applications of which could expedite screening efforts in the identification and localization of biosynthetic pathways from marine microbial consortia, offering a powerful complement to genome sequencing and degenerate probe strategies. Implementing this approach, we report on the biotin biosynthetic pathway from the marine microorganism Hon6.
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Affiliation(s)
- Eun Jin Kim
- Department of Chemistry, Texas A&M University, College Station, MS 3255, TX 77843, USA
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73
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Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y, Wang J, Mountain BW, Crowe MA, Weatherby TM, Bodelier PLE, Liesack W, Feng L, Wang L, Alam M. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 2007; 450:879-82. [DOI: 10.1038/nature06411] [Citation(s) in RCA: 423] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 10/24/2007] [Indexed: 11/09/2022]
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Lombardot T, Kottmann R, Giuliani G, de Bono A, Addor N, Glöckner FO. MetaLook: a 3D visualisation software for marine ecological genomics. BMC Bioinformatics 2007; 8:406. [PMID: 17953757 PMCID: PMC2134934 DOI: 10.1186/1471-2105-8-406] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 10/22/2007] [Indexed: 11/12/2022] Open
Abstract
Background Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenomes of environmental relevance must take into account the corresponding habitat (contextual) data, e.g. water depth, physical and chemical parameters. The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis. Results We implemented the MetaLook software for visualisation and analysis of marine ecological genomic and metagenomic data with respect to habitat parameters. MetaLook offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a centralised georeferenced database. The user can define environmental containers to organise the sequences according to different habitat criteria. To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported sequences, using the BLAST algorithm. This allows an interactive assessment of the distribution of gene functions in the environment. Conclusion MetaLook allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. This software is a step towards the creation of specialised tools to study constrained distributions and habitat specificity of genes correlated with specific processes. MetaLook is available at:
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Affiliation(s)
- Thierry Lombardot
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany.
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75
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Elsaied H, Stokes HW, Nakamura T, Kitamura K, Fuse H, Maruyama A. Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents. Environ Microbiol 2007; 9:2298-312. [PMID: 17686026 DOI: 10.1111/j.1462-2920.2007.01344.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lack of information about mobile DNA in deep-sea hydrothermal vents limits our understanding of the phylogenetic diversity of the mobile genome of bacteria in these environments. We used culture-independent techniques to explore the diversity of the integron/mobile gene cassette system in a variety of hydrothermal vent communities. Three samples, which included two different hydrothermal vent fluids and a mussel species that contained essentially monophyletic sulfur-oxidizing bacterial endosymbionts, were collected from Suiyo Seamount, Izu-Bonin, Japan, and Pika site, Mariana arc. First, using degenerate polymerase chain reaction (PCR) primers, we amplified integron integrase genes from metagenomic DNA from each sample. From vent fluids, we discovered 74 new integrase genes that were classified into 11 previously undescribed integron classes. One integrase gene was recorded in the mussel symbiont and was phylogenetically distant from those recovered from vent fluids. Second, using PCR primers targeting the gene cassette recombination site (59-be), we amplified and subsequently identified 60 diverse gene cassettes. In multicassette amplicons, a total of 13 59-be sites were identified. Most of these sites displayed features that were atypical of the features previously well conserved in this family. The Suiyo vent fluid was characterized by gene cassette open reading frames (ORFs) that had significant homologies with transferases, DNA-binding proteins and metal transporter proteins, while the majority of Pika vent fluid gene cassettes contained novel ORFs with no identifiable homologues in databases. The symbiont gene cassette ORFs were found to be matched with DNA repair proteins, methionine aminopeptidase, aminopeptidase N, O-sialoglycoprotein endopeptidase and glutamate synthase, which are proteins expected to play a role in animal/symbiont metabolism. The success of this study indicates that the integron/gene cassette system is common in deep-sea hydrothermal vents, an environment type well removed from anthropogenic disturbance.
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Affiliation(s)
- Hosam Elsaied
- Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi Tsukuba, Ibaraki 305-8566, Japan
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76
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Xu K, Ma BG. Comparative analysis of predicted gene expression among deep-sea genomes. Gene 2007; 397:136-42. [PMID: 17544603 DOI: 10.1016/j.gene.2007.04.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 04/08/2007] [Accepted: 04/20/2007] [Indexed: 11/18/2022]
Abstract
Deep-sea species live in an environment that is specifically characterized by extreme temperature and hydrostatic pressure. In this work, predicted highly expressed (PHX) genes are comparatively analyzed for six deep-sea microbes, which allows us to pinpoint the common highly expressed genes shared by them. The relationships between gene expression level and some basic properties such as genomic G + C content, optimal growth temperature (OGT), and environmental hydrostatic pressure of the six deep-sea species are also investigated. We find that the percentage of PHX genes out of a whole genome positively correlates to OGT for the deep-sea genomes, whereas such positive correlation seems not to exist between environmental hydrostatic pressure and percentage of PHX genes. Moreover, there exists a negative correlation between genomic G + C content and diversity of gene expression level for the deep-sea genomes, which is in sharp contrast to land-living microbes. We report the top 20 PHX genes for the six deep-sea genomes and find no common highly expressed genes shared by them except for ribosomal proteins, transcription factors, and translation factors. Our present work proffers a paradigm for studying the relationship between environmental factors and microbes' predicted gene expression level.
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Affiliation(s)
- Ke Xu
- College of Mathematics and Information Science, Shandong University of Technology, Zibo, PR China
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Donadio S, Monciardini P, Sosio M. Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics. Nat Prod Rep 2007; 24:1073-109. [PMID: 17898898 DOI: 10.1039/b514050c] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A total of 223 complete bacterial genomes are analyzed, with 281 citations, for the presence of genes encoding modular polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS). We report on the distribution of these systems in different bacterial taxa and, whenever known, the metabolites they synthesize. We also highlight, in the different bacterial lineages, the PKS and NRPS genes and, whenever known, the corresponding products.
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78
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Qin G, Zhu L, Chen X, Wang PG, Zhang Y. Structural characterization and ecological roles of a novel exopolysaccharide from the deep-sea psychrotolerant bacterium Pseudoalteromonas sp. SM9913. Microbiology (Reading) 2007; 153:1566-1572. [PMID: 17464071 DOI: 10.1099/mic.0.2006/003327-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudoalteromonas sp. SM9913 is a psychrotolerant bacterium isolated from deep-sea sediment. The structural characterization and ecological roles of the exopolysaccharide (EPS) secreted by this strain were studied in this work. The yield of the EPS increased as the culture temperature decreased in the range 30-10 degrees C, and it reached 5.25 g l(-1) (dry weight) under optimal growth conditions (15 degrees C, 52 h). EPS fraction was purified and its structure was identified by the combination of NMR spectra, high-resolution mass spectrometry (HRMS) analysis and methylation analysis. The ratio of the sugar units, the acetyl group and the ethoxyl group was close to 4 : 5 : 1. The major sugar unit of the EPS was 6-linked glucose (61.8 %); other sugar units present included terminal arabinofuranosyl (11.0 %) and glucopyranosyl (11.2 %) residues and a small amount of other sugar derivatives. Its structure was different from EPSs reported for other marine bacteria. Besides the structural elucidation of the EPS, its ecological roles were studied. This EPS could enhance the stability of the cold-adapted protease MCP-01 secreted by the same strain through preventing its autolysis. It could bind many metal ions, including Fe(2+), Zn(2+), Cu(2+), Co(2+). It was also a very good flocculating agent and could conglomerate colloidal and suspended particles. These results indicated that the EPS secreted by strain SM9913 might help this strain enrich the proteinaceous particles and the trace metals in the deep-sea environment, stabilize the secreted cold-adapted proteases and avoid its diffusion. This is believed to be the first report on the structure of the EPS secreted by a deep-sea psychrotolerant bacterium and its ecological roles. According to these results and other studies, a schematic diagram of the lifestyle of the deep-sea psychrotolerant strain SM9913 is suggested.
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Affiliation(s)
- Guokui Qin
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, P. R. China
| | - Lizhi Zhu
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Xiulan Chen
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, P. R. China
| | - Peng George Wang
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, P. R. China
| | - Yuzhong Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, 250100, P. R. China
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Su J, Yang J, Zhao D, Kawula TH, Banas JA, Zhang JR. Genome-wide identification of Francisella tularensis virulence determinants. Infect Immun 2007; 75:3089-101. [PMID: 17420240 PMCID: PMC1932872 DOI: 10.1128/iai.01865-06] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a gram-negative pathogen that causes life-threatening infections in humans and has potential for use as a biological weapon. The genetic basis of the F. tularensis virulence is poorly understood. This study screened a total of 3,936 transposon mutants of the live vaccine strain for infection in a mouse model of respiratory tularemia by signature-tagged mutagenesis. We identified 341 mutants attenuated for infection in the lungs. The transposon disruptions were mapped to 95 different genes, virtually all of which are also present in the genomes of other F. tularensis strains, including human pathogenic F. tularensis strain Schu S4. A small subset of these attenuated mutants carried insertions in the genes encoding previously known virulence factors, but the majority of the identified genes have not been previously linked to F. tularensis virulence. Among these are genes encoding putative membrane proteins, proteins associated with stress responses, metabolic proteins, transporter proteins, and proteins with unknown functions. Several attenuated mutants contained disruptions in a putative capsule locus which partially resembles the poly-gamma-glutamate capsule biosynthesis locus of Bacillus anthracis, the anthrax agent. Deletional mutation analysis confirmed that this locus is essential for F. tularensis virulence.
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Affiliation(s)
- Jingliang Su
- Center for Immunology and Microbial Disease, Albany Medical College, 47 New Scotland Avenue, Albany, NY 12208, USA
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80
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Xu Y, Labedan B, Glansdorff N. Surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms. Microbiol Mol Biol Rev 2007; 71:36-47. [PMID: 17347518 PMCID: PMC1847373 DOI: 10.1128/mmbr.00032-06] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major aspects of the pathway of de novo arginine biosynthesis via acetylated intermediates in microorganisms must be revised in light of recent enzymatic and genomic investigations. The enzyme N-acetylglutamate synthase (NAGS), which used to be considered responsible for the first committed step of the pathway, is present in a limited number of bacterial phyla only and is absent from Archaea. In many Bacteria, shorter proteins related to the Gcn5-related N-acetyltransferase family appear to acetylate l-glutamate; some are clearly similar to the C-terminal, acetyl-coenzyme A (CoA) binding domain of classical NAGS, while others are more distantly related. Short NAGSs can be single gene products, as in Mycobacterium spp. and Thermus spp., or fused to the enzyme catalyzing the last step of the pathway (argininosuccinase), as in members of the Alteromonas-Vibrio group. How these proteins bind glutamate remains to be determined. In some Bacteria, a bifunctional ornithine acetyltransferase (i.e., using both acetylornithine and acetyl-CoA as donors of the acetyl group) accounts for glutamate acetylation. In many Archaea, the enzyme responsible for glutamate acetylation remains elusive, but possible connections with a novel lysine biosynthetic pathway arose recently from genomic investigations. In some Proteobacteria (notably Xanthomonadaceae) and Bacteroidetes, the carbamoylation step of the pathway appears to involve N-acetylornithine or N-succinylornithine rather than ornithine. The product N-acetylcitrulline is deacetylated by an enzyme that is also involved in the provision of ornithine from acetylornithine; this is an important metabolic function, as ornithine itself can become essential as a source of other metabolites. This review insists on the biochemical and evolutionary implications of these findings.
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Affiliation(s)
- Ying Xu
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris Sud, Bâtiment 400, 91405 Orsay Cedex, France
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81
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Lauro FM, Bartlett DH. Prokaryotic lifestyles in deep sea habitats. Extremophiles 2007; 12:15-25. [PMID: 17225926 DOI: 10.1007/s00792-006-0059-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 12/10/2006] [Indexed: 11/25/2022]
Abstract
Gradients of physicochemical factors influence the growth and survival of life in deep-sea environments. Insights into the characteristics of deep marine prokaryotes has greatly benefited from recent progress in whole genome and metagenome sequence analyses. Here we review the current state-of-the-art of deep-sea microbial genomics. Ongoing and future genome-enabled studies will allow for a better understanding of deep-sea evolution, physiology, biochemistry, community structure and nutrient cycling.
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Affiliation(s)
- Federico M Lauro
- Scripps Institution of Oceanography, Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, University of California, 8750 Biological Grade, San Diego, La Jolla, CA 92093-0202, USA
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82
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Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Würdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann RI, Glöckner FO. Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ Microbiol 2007; 8:2201-13. [PMID: 17107561 DOI: 10.1111/j.1462-2920.2006.01152.x] [Citation(s) in RCA: 245] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Members of the Bacteroidetes, formerly known as the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum, are among the major taxa of marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part of free-living microbial assemblages in nutrient-rich microenvironments. Their abundance and distribution pattern in combination with enzymatic activity studies has led to the notion that organisms of this group are specialists for degradation of high molecular weight compounds in both the dissolved and particulate fraction of the marine organic matter pool, implying a major role of Bacteroidetes in the marine carbon cycle. Despite their ecological importance, comprehensive molecular data on organisms of this group have been scarce so far. Here we report on the first whole genome analysis of a marine Bacteroidetes representative, 'Gramella forsetii' KT0803. Functional analysis of the predicted proteome disclosed several traits which in joint consideration suggest a clear adaptation of this marine Bacteroidetes representative to the degradation of high molecular weight organic matter, such as a substantial suite of genes encoding hydrolytic enzymes, a predicted preference for polymeric carbon sources and a distinct capability for surface adhesion.
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Affiliation(s)
- Margarete Bauer
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany.
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83
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Parks AR, Peters JE. Transposon Tn7 is widespread in diverse bacteria and forms genomic islands. J Bacteriol 2006; 189:2170-3. [PMID: 17194796 PMCID: PMC1855776 DOI: 10.1128/jb.01536-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We find that relatives of the bacterial transposon Tn7 are widespread in disparate environments and phylogenetically diverse species. These elements form functionally diverse genomic islands at the specific site of Tn7 insertion adjacent to glmS. This work presents the first example of genomic island formation by a DDE type transposon.
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Affiliation(s)
- Adam R Parks
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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84
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Cho EA, Lee DW, Cha YH, Lee SJ, Jung HC, Pan JG, Pyun YR. Characterization of a novel D-lyxose isomerase from Cohnella laevoribosii RI-39 sp. nov. J Bacteriol 2006; 189:1655-63. [PMID: 17189362 PMCID: PMC1855708 DOI: 10.1128/jb.01568-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A newly isolated bacterium, Cohnella laevoribosii RI-39, could grow in a defined medium with L-ribose as the sole carbon source. A 21-kDa protein isomerizing L-ribose to L-ribulose, as well as D-lyxose to D-xylulose, was purified to homogeneity from this bacterium. Based on the N-terminal and internal amino acid sequences of the purified enzyme obtained by N-terminal sequencing and quantitative time of flight mass spectrometry-mass spectrometry analyses, a 549-bp gene (lyxA) encoding D-lyxose (L-ribose) isomerase was cloned and expressed in Escherichia coli. The purified endogenous enzyme and the recombinant enzyme formed homodimers that were activated by Mn(2+). C. laevoribosii D-lyxose (L-ribose) isomerase (CLLI) exhibits maximal activity at pH 6.5 and 70 degrees C in the presence of Mn(2+) for D-lyxose and L-ribose, and its isoelectric point (pI) is 4.2 (calculated pI, 4.9). The enzyme is specific for D-lyxose, L-ribose, and D-mannose, with apparent K(m) values of 22.4 +/- 1.5 mM, 121.7 +/- 10.8 mM, and 34.0 +/- 1.1 mM, respectively. The catalytic efficiencies (k(cat)/K(m)) of CLLI were 84.9 +/- 5.8 mM(-1) s(-1) for D-lyxose (V(max), 5,434.8 U mg(-1)), 0.2 mM(-1) s(-1) for L-ribose (V(max), 75.5 +/- 6.0 U mg(-1)), and 1.4 +/- 0.1 mM(-1) s(-1) for D-mannose (V(max), 131.8 +/- 7.4 U mg(-1)). The ability of lyxA to permit E. coli cells to grow on D-lyxose and L-ribose and homology searches of other sugar-related enzymes, as well as previously described sugar isomerases, suggest that CLLI is a novel type of rare sugar isomerase.
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Affiliation(s)
- Eun-Ah Cho
- Department of Biotechnology, Yonsei University, Seoul 120-749, Korea
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85
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Scott KM, Sievert SM, Abril FN, Ball LA, Barrett CJ, Blake RA, Boller AJ, Chain PSG, Clark JA, Davis CR, Detter C, Do KF, Dobrinski KP, Faza BI, Fitzpatrick KA, Freyermuth SK, Harmer TL, Hauser LJ, Hügler M, Kerfeld CA, Klotz MG, Kong WW, Land M, Lapidus A, Larimer FW, Longo DL, Lucas S, Malfatti SA, Massey SE, Martin DD, McCuddin Z, Meyer F, Moore JL, Ocampo LH, Paul JH, Paulsen IT, Reep DK, Ren Q, Ross RL, Sato PY, Thomas P, Tinkham LE, Zeruth GT. The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS Biol 2006; 4:e383. [PMID: 17105352 PMCID: PMC1635747 DOI: 10.1371/journal.pbio.0040383] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 09/14/2006] [Indexed: 12/25/2022] Open
Abstract
Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
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Affiliation(s)
- Kathleen M Scott
- Biology Department, University of South Florida, Tampa, Florida, United States of America.
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86
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Terashima H, Fukuoka H, Yakushi T, Kojima S, Homma M. The Vibrio motor proteins, MotX and MotY, are associated with the basal body of Na-driven flagella and required for stator formation. Mol Microbiol 2006; 62:1170-80. [PMID: 17038120 DOI: 10.1111/j.1365-2958.2006.05435.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The four motor proteins PomA, PomB, MotX and MotY, which are believed to be stator proteins, are essential for motility by the Na(+)-driven flagella of Vibrio alginolyticus. When we purified the flagellar basal bodies, MotX and MotY were detected in the basal body, which is the supramolecular complex comprised of the rotor and the bushing, but PomA and PomB were not. By antibody labelling, MotX and MotY were detected around the LP ring. These results indicate that MotX and MotY associate with the basal body. The basal body had a new ring structure beneath the LP ring, which was named the T ring. This structure was changed or lost in the basal body from a DeltamotX or DeltamotY strain. The T ring probably comprises MotX and MotY. In the absence of MotX or MotY, we demonstrated that PomA and PomB were not localized to a cell pole. From the above results, we suggest that MotX and MotY of the T ring are involved in the incorporation and/or stabilization of the PomA/PomB complex in the motor.
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Affiliation(s)
- Hiroyuki Terashima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-Ku, Nagoya 464-8602, Japan
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87
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Schneiker S, dos Santos VAPM, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol 2006; 24:997-1004. [PMID: 16878126 PMCID: PMC7416663 DOI: 10.1038/nbt1232] [Citation(s) in RCA: 276] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 06/19/2006] [Indexed: 11/25/2022]
Abstract
Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. A. borkumensis SK2 has a streamlined genome with a paucity of mobile genetic elements and energy generation–related genes, but with a plethora of genes accounting for its wide hydrocarbon substrate range and efficient oil-degradation capabilities. The genome further specifies systems for scavenging of nutrients, particularly organic and inorganic nitrogen and oligo-elements, biofilm formation at the oil-water interface, biosurfactant production and niche-specific stress responses. The unique combination of these features provides A. borkumensis SK2 with a competitive edge in oil-polluted environments. This genome sequence provides the basis for the future design of strategies to mitigate the ecological damage caused by oil spills.
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Affiliation(s)
- Susanne Schneiker
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | | | - Daniela Bartels
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Thomas Bekel
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Martina Brecht
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Jens Buhrmester
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Tatyana N Chernikova
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Renata Denaro
- Istituto per l'Ambiente Marino Costiero (CNR), Messina, I-98122 Italy
| | - Manuel Ferrer
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute of Catalysis, Campus UAM, E-28049 Madrid, Spain (M.F.), Bioinformatics & Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, 10598 USA
- Division Biogeochemistry, Research Centre Rossendorf, Dresden, D-01314 Germany
| | - Christoph Gertler
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Alexander Goesmann
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Olga V Golyshina
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Filip Kaminski
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
| | - Amit N Khachane
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
| | - Siegmund Lang
- Institute of Biochemistry and Biotechnology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Burkhard Linke
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Alice C McHardy
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
- Institute of Catalysis, Campus UAM, E-28049 Madrid, Spain (M.F.), Bioinformatics & Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, 10598 USA
- Division Biogeochemistry, Research Centre Rossendorf, Dresden, D-01314 Germany
| | - Folker Meyer
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Taras Nechitaylo
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Daniela Regenhardt
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute of Catalysis, Campus UAM, E-28049 Madrid, Spain (M.F.), Bioinformatics & Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, 10598 USA
- Division Biogeochemistry, Research Centre Rossendorf, Dresden, D-01314 Germany
| | - Oliver Rupp
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Julia S Sabirova
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Werner Selbitschka
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Michail M Yakimov
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Istituto per l'Ambiente Marino Costiero (CNR), Messina, I-98122 Italy
| | - Kenneth N Timmis
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, D-38106 Germany
| | - Frank-Jörg Vorhölter
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Stefan Weidner
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Olaf Kaiser
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Bielefeld, D-33594 Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, D-33594 Germany
| | - Peter N Golyshin
- Division of Microbiology, German Research Center for Biotechnology, Braunschweig, D-38124 Germany
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88
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Worden AZ, Cuvelier ML, Bartlett DH. In-depth analyses of marine microbial community genomics. Trends Microbiol 2006; 14:331-6. [PMID: 16820296 DOI: 10.1016/j.tim.2006.06.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Revised: 05/18/2006] [Accepted: 06/19/2006] [Indexed: 11/21/2022]
Abstract
Marine microbes have evolved to live along extreme environmental gradients, whether at the microscale, in proximity to particles or over the entire water column. Using community genomics, DeLong et al. highlight deduced biological differences that result from open-ocean depth gradients. The power of the large-insert libraries used is that both phylogeny and function can be inferred from the genetic material obtained--even for uncultured microbes. Together with complete genomes of marine isolates and advances in physiology and ecology, this study paves the way for ecosystems biology approaches to dynamics and controls of marine microbial populations.
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Affiliation(s)
- Alexandra Z Worden
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, FL 33149, USA.
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89
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Moreira D, Rodríguez-Valera F, López-García P. Metagenomic analysis of mesopelagic Antarctic plankton reveals a novel deltaproteobacterial group. MICROBIOLOGY-SGM 2006; 152:505-517. [PMID: 16436438 DOI: 10.1099/mic.0.28254-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Phylogenetic screening of 3200 clones from a metagenomic library of Antarctic mesopelagic picoplankton allowed the identification of two bacterial 16S-rDNA-containing clones belonging to the Deltaproteobacteria, DeepAnt-1F12 and DeepAnt-32C6. These clones were very divergent, forming a monophyletic cluster with the environmental sequence GR-WP33-58 that branched at the base of the myxobacteria. Except for the possession of complete rrn operons without associated tRNA genes, DeepAnt-1F12 and DeepAnt-32C6 were very different in gene content and organization. Gene density was much higher in DeepAnt-32C6, whereas nearly one-third of DeepAnt-1F12 corresponded to intergenic regions. Many of the predicted genes encoded by these metagenomic clones were informational (i.e. involved in replication, transcription, translation and related processes). Despite this, a few putative cases of horizontal gene transfer were detected, including a transposase. DeepAnt-1F12 contained one putative gene encoding a long cysteine-rich protein, probably membrane-bound and Ca2+-binding, with only eukaryotic homologues. DeepAnt-32C6 carried some predicted genes involved in metabolic pathways that suggested this organism may be anaerobic and able to ferment and to degrade complex compounds extracellularly.
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Affiliation(s)
- David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405 Orsay Cedex, France
| | - Francisco Rodríguez-Valera
- División de Microbiología and Evolutionary Genomics Group, Universidad Miguel Hernández, Campus de San Juan, 03550 San Juan de Alicante, Spain
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405 Orsay Cedex, France
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90
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Ma BG, Song QS, Zhang HY. CvP-bias as an index to predict the life style of last common ancestor. J Biomol Struct Dyn 2006; 23:555-8. [PMID: 16494505 DOI: 10.1080/07391102.2006.10507080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
CvP-bias (difference between proportions of charged and polar non-charged amino acids) has been recognized as an efficient criterion to distinguish hyperthermophiles from mesothermophiles. By analyzing the CvP-biases of seven barophiles's proteomes, we reveal that this criterion still works for barophiles. As a result, CvP-bias criterion is applicable to disclosing some secrets in the lifestyles of the last common ancestor (LCA), no matter the LCA lived in deep sea or not, which is helpful to building a self-consistent model for the LCA.
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Affiliation(s)
- Bin-Guang Ma
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, P. R. China
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91
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Xu Y, Glansdorff N, Labedan B. Bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of N-acetylated intermediates in prokaryotes. BMC Genomics 2006; 7:4. [PMID: 16409639 PMCID: PMC1382215 DOI: 10.1186/1471-2164-7-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 01/12/2006] [Indexed: 12/04/2022] Open
Abstract
Background The N-acetylation of L-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. Until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical N-acetylglutamate synthase (NAGS, gene argA) first characterized in Escherichia coli and Pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (OAT, gene argJ) present in Bacteria, Archaea and many Eukaryotes. This paper focuses on a new and surprising aspect of glutamate acetylation. We recently showed that in Moritella abyssi and M. profunda, two marine gamma proteobacteria, the gene for the last enzyme in arginine biosynthesis (argH) is fused to a short sequence that corresponds to the C-terminal, N-acetyltransferase-encoding domain of NAGS and is able to complement an argA mutant of E. coli. Very recently, other authors identified in Mycobacterium tuberculosis an independent gene corresponding to this short C-terminal domain and coding for a new type of NAGS. We have investigated the two prokaryotic Domains for patterns of gene-enzyme relationships in the first committed step of arginine biosynthesis. Results The argH-A fusion, designated argH(A), and discovered in Moritella was found to be present in (and confined to) marine gamma proteobacteria of the Alteromonas- and Vibrio-like group. Most of them have a classical NAGS with the exception of Idiomarina loihiensis and Pseudoalteromonas haloplanktis which nevertheless can grow in the absence of arginine and therefore appear to rely on the arg(A) sequence for arginine biosynthesis. Screening prokaryotic genomes for virtual argH-X 'fusions' where X stands for a homologue of arg(A), we retrieved a large number of Bacteria and several Archaea, all of them devoid of a classical NAGS. In the case of Thermus thermophilus and Deinococcus radiodurans, the arg(A)-like sequence clusters with argH in an operon-like fashion. In this group of sequences, we find the short novel NAGS of the type identified in M. tuberculosis. Among these organisms, at least Thermus, Mycobacterium and Streptomyces species appear to rely on this short NAGS version for arginine biosynthesis. Conclusion The gene-enzyme relationship for the first committed step of arginine biosynthesis should now be considered in a new perspective. In addition to bifunctional OAT, nature appears to implement at least three alternatives for the acetylation of glutamate. It is possible to propose evolutionary relationships between them starting from the same ancestral N-acetyltransferase domain. In M. tuberculosis and many other bacteria, this domain evolved as an independent enzyme, whereas it fused either with a carbamate kinase fold to give the classical NAGS (as in E. coli) or with argH as in marine gamma proteobacteria. Moreover, there is an urgent need to clarify the current nomenclature since the same gene name argA has been used to designate structurally different entities. Clarifying the confusion would help to prevent erroneous genomic annotation.
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Affiliation(s)
- Ying Xu
- Marine Sciences Research Center, State University of New York at Stony Brook, Stony Brook, New York 11794-5000, USA
| | - Nicolas Glansdorff
- Microbiology and Genetics, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Bernard Labedan
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris Sud, Bâtiment 400, 91405 Orsay Cedex, France
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92
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Cianciotto NP. Type II secretion: a protein secretion system for all seasons. Trends Microbiol 2005; 13:581-8. [PMID: 16216510 DOI: 10.1016/j.tim.2005.09.005] [Citation(s) in RCA: 258] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 09/06/2005] [Accepted: 09/22/2005] [Indexed: 01/20/2023]
Abstract
In Gram-negative bacteria, type II secretion (T2S) is one of five protein secretion systems that permit the export of proteins from within the bacterial cell to the extracellular milieu and/or into target host cells. An analysis of numerous sequenced genomes now reveals that T2S genes are common, but by no means universal, in Gram-negative bacteria. Recent functional studies indicate that T2S can promote the virulence of human, animal and plant pathogens, as well as the physiology of various environmental bacteria. Thus, it is an opportune time to highlight the new and different ways in which T2S serves bacterial function.
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Affiliation(s)
- Nicholas P Cianciotto
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, IL 60611, USA.
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93
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Abstract
The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.
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Affiliation(s)
- Edward F DeLong
- Department of Civil and Environmental Engineering & Division of Biological Engineering, 48-427 Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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94
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Shibata S, Alam M, Aizawa SI. Flagellar Filaments of the Deep-sea Bacteria Idiomarina loihiensis Belong to a Family Different from those of Salmonella typhimurium. J Mol Biol 2005; 352:510-6. [PMID: 16120444 DOI: 10.1016/j.jmb.2005.07.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 06/27/2005] [Accepted: 07/08/2005] [Indexed: 11/17/2022]
Abstract
The helical filaments of the bacterial flagella so far studied seem to be universal in the bacterial kingdom. Despite the variation in flagellin molecular masses, which range from 24 kDa to 62 kDa in different species, there are only two forms: either the so-called Normal (left-handed) or the Curly (right-handed). The Normal and Curly helical forms are asymmetric; the two characteristic helical parameters, which are the pitch and diameter, of Normal filaments are twice those of Curly filaments. Both the universality of these two helical forms and their asymmetry are biological puzzles. We found that the marine bacteria Idiomarina loihiensis have flagella with left-handed Curly-like filaments. Analysis of the polymorphic forms under different pH conditions showed that the Curly-like filaments are actually Normal filaments having a smaller pitch and diameter than those of Salmonella typhimurium. A minor modification of Calladine's model for a filament lattice can explain the variant helical forms. Pseudomonas aeruginosa filaments also belong to the family of I.loihiensis filaments. Thus, there are at least two families of flagella filaments.
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Affiliation(s)
- Satoshi Shibata
- Soft Nano-Machine Project, JST, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
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95
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Patrauchan MA, Sarkisova S, Sauer K, Franklin MJ. Calcium influences cellular and extracellular product formation during biofilm-associated growth of a marine Pseudoalteromonas sp. Microbiology (Reading) 2005; 151:2885-2897. [PMID: 16151201 DOI: 10.1099/mic.0.28041-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria undergo a variety of physiological changes following a switch from planktonic growth to surface-associated biofilm growth. Here, it is shown that biofilm development of a marine isolate, Pseudoalteromonas sp. 1398, results in global changes in its cytosolic and extracellular proteomes. Calcium influences these proteome responses, and affects the amount of surface-associated biomass and extracellular matrix material produced by Pseudoalteromonas sp. 1398. Four extracellular proteins, characterized by N-terminal sequencing, showed increased abundances, while one protein, flagellin, showed reduced abundance at higher [Ca2+]. Immunoblotting and transmission-electron-microscopy analysis confirmed that higher [Ca2+] and surface-associated growth results in the repression of flagella production. Two-dimensional gel electrophoresis (2DGE) studies combined with cluster analysis of global proteome responses demonstrated that Ca2+ had a greater regulatory influence on Pseudoalteromonas sp. growing in biofilms than on planktonic cultures. Approximately 22 % of the total cytosolic proteins resolved by 2DGE had differing abundances in response to a switch from planktonic growth to surface-associated growth when the cells were cultivated in 1 mM Ca2+. At higher [Ca2+] this number increased to 38 %. Fifteen cellular proteins that were differentially expressed in response to biofilm growth and/or Ca2+ were analysed by N-terminal sequencing and/or MS/MS. These proteins were identified as factors involved in cellular metabolic functions, putative proteases and transport proteins, although there were several proteins that had not been previously characterized. These results indicate that Ca2+ causes global changes in matrix material, as well as in cellular and extracellular protein profiles of Pseudoalteromonas sp. 1398. These changes are more pronounced when the bacterium grows in biofilms than when it grows in planktonic culture.
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Affiliation(s)
- M A Patrauchan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - S Sarkisova
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA
| | - K Sauer
- Department of Biological Sciences, State University of New York at Binghamton, Binghamton, NY 13902, USA
| | - M J Franklin
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA
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96
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Naganuma T, Hua PN, Okamoto T, Ban S, Imura S, Kanda H. Depth distribution of euryhaline halophilic bacteria in Suribati Ike, a meromictic lake in East Antarctica. Polar Biol 2005. [DOI: 10.1007/s00300-005-0026-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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97
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Abstract
Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.
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Affiliation(s)
- Edward F DeLong
- Division of Biological Engineering and Department of Civil and Environmental Engineering, Room 48-427, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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98
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Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW. Genome update: base skews in 200+ bacterial chromosomes. MICROBIOLOGY-SGM 2005; 151:633-637. [PMID: 15758208 DOI: 10.1099/mic.0.27889-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Peter F Hallin
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Natasja Nielsen
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kevin M Devine
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tim T Binnewies
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Hanni Willenbrock
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - David W Ussery
- Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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99
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Galperin MY. A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC Microbiol 2005; 5:35. [PMID: 15955239 PMCID: PMC1183210 DOI: 10.1186/1471-2180-5-35] [Citation(s) in RCA: 320] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Accepted: 06/14/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. RESULTS This paper presents results of a comprehensive census of signal transduction proteins--histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases--encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others. CONCLUSION The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set) can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the highest IQ, including the current leader Wolinella succinogenes, are found among the poorly studied beta-, delta- and epsilon-proteobacteria. Among all bacterial phyla, only cyanobacteria appear to be true introverts, probably due to their capacity to conduct oxygenic photosynthesis, using a complex system of intracellular membranes. The census data, available at http://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html, can be used to get an insight into metabolic and behavioral propensities of each given organism and improve prediction of the organism's properties based solely on its genome sequence.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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100
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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