| 1. |
- Agervald, Åsa, et al.
(författare)
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Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120
- 2008
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 8, s. 69-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The maturation of hydrogenases into active enzymes is a complex process and e. g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hypgenes in Nostoc sp. strain PCC 7120. Results: RTPCRs demonstrated that the six hypgenes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hypoperon, and two downstream ORFs from the hypgenes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifUlike protein. Orthologues of the four ORFs asr0689alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2fixing cyanobacteria, but are absent in non N2fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hypoperon, appearing between 11 and 79 times in the genome. Conclusion: This study demonstrated that five ORFs upstream of the hypgene cluster are cotranscribed with the hypgenes, and identified three TSPs in the extended hypgene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme.
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| 2. |
- Devine, Ellenor, et al.
(författare)
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Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120
- 2009
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 9, s. 53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively. Results: In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW) and LexA (hoxW). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for[NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase. Conclusion: Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co-evolution could be the result of a close interaction between the protease and the large subunit of the[NiFe]-hydrogenases, a theory supported by protein-protein docking experiments performed with 3D-models. Finally we present data that may explain the specificity seen among hydrogenase specific proteases, the so called "HOXBOX"; an amino acid sequence specific for proteases of Hox-type. This opens the door for more detailed studies of the specificity found among hydrogenase specific proteases and the structural properties behind it.
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| 3. |
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| 4. |
- Holmqvist, Marie, et al.
(författare)
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Characterization of the hupSL promoter activity in Nostoc punctiforme ATCC 29133
- 2009
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 9, s. 54-
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Tidskriftsartikel (refereegranskat)abstract
- Background: In cyanobacteria three enzymes are directly involved in the hydrogen metabolism; a nitrogenase that produces molecular hydrogen, H-2, as a by-product of nitrogen fixation, an uptake hydrogenase that recaptures H-2 and oxidize it, and a bidirectional hydrogenase that can both oxidize and produce H-2. Nostoc punctiforme ATCC 29133 is a filamentous dinitrogen fixing cyanobacterium containing a nitrogenase and an uptake hydrogenase but no bidirectional hydrogenase. Generally, little is known about the transcriptional regulation of the cyanobacterial uptake hydrogenases. In this study gel shift assays showed that NtcA has a specific affinity to a region of the hupSL promoter containing a predicted NtcA binding site. The predicted NtcA binding site is centred at 258.5 bp upstream the transcription start point (tsp). To further investigate the hupSL promoter, truncated versions of the hupSL promoter were fused to either gfp or luxAB, encoding the reporter proteins Green Fluorescent Protein and Luciferase, respectively. Results: Interestingly, all hupsSL promoter deletion constructs showed heterocyst specific expression. Unexpectedly the shortest promoter fragment, a fragment covering 57 bp upstream and 258 bp downstream the tsp, exhibited the highest promoter activity. Deletion of the NtcA binding site neither affected the expression to any larger extent nor the heterocyst specificity. Conclusion: Obtained data suggest that the hupSL promoter in N. punctiforme is not strictly dependent on the upstream NtcA cis element and that the shortest promoter fragment (- 57 to tsp) is enough for a high and heterocyst specific expression of hupSL. This is highly interesting because it indicates that the information that determines heterocyst specific gene expression might be confined to this short sequence or in the downstream untranslated leader sequence.
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| 5. |
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| 6. |
- Pipkorn, Bengt, 1963, et al.
(författare)
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Mathematical human body models in side impacts- A validation study with particular emphasis on the torso and shoulder and their influence on head and neck motion
- 2008
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Ingår i: Int. Res. Counc. Biomech. Inj. - Int. IRCOBI Conf. Biomech. Inj., Proc.. - 9783033015807 ; , s. 99-114, s. 99-114
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Konferensbidrag (refereegranskat)abstract
- The ability of three mathematical human body models to predict previously published human responses in two different side impact loading configurations was evaluated using an objective rating method. In particular the kinematics of the shoulder, T1 and head were evaluated. The human body models evaluated were THUMS, HUMOS 2 and the GM model. The impact loading configurations used were pendulum impact tests and sled tests. In the pendulum configurations, the closest correlation to the published responses was shown by THUMS followed by the GM model. In the sled configuration, closest correlation to the published responses was shown by HUMOS 2 followed by THUMS. According to the objective rating method the published responses in the pendulum configuration were predicted by all human body models. The published responses in the sled configuration were predicted by HUMOS 2 and THUMS.
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| 7. |
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| 8. |
- Thorn, Colin E., et al.
(författare)
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Comparison of radiocarbon dating of buried paleosols using arbuscular mycorrhizae spores and bulk soil samples
- 2009
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 19:7, s. 1031-1037
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Tidskriftsartikel (refereegranskat)abstract
- Ten paleosols from four separate soil pits located in Karkevagge, a glaciated trough in Swedish Lapland, were dated using radiocarbon. Each soil was dated using both conventional bulk soil organic material (SOM) and a pure sample of arbuscular mycorrhizae (AM) fungal spores. The latter are produced by ubiquitous mycorrhizal fungi associated with the roots of many plant genera and may be viewed as a fossil material that has not interacted with any soil constituent subsequent to its emplacement in the soil - at a time presumed to mark the cessation of a favorable soil-forming environment. Regional deglaciation is presumed to have been about 10 000 BP, while a cosmogenic exposure date obtained from the valley floor in Karkevagge dated at 13 100 +/- 1638 BP. The youngest paleosol, buried at similar to 6 cm in soil pit M3, produced a spore date of 0-281 cal. yr BP (1 sigma). However, bulk SOM dates of the same paleosol A horizon gave widely divergent dates and varied with the sample pretreatment, ie, the combustion temperature and the acid-base treatment. For example, the bulk SOM dates for that paleosol ranged from a post-bomb date of 0-314 cal. yr BP (1 sigma) to 2366-2710 cal. yr BP (1 sigma) when subjected to different pretreatments (acid only, acid-base-acid) and the ignition temperatures (400, 800, or 900 degrees C). The oldest paleosol in the set, buried at similar to 61 cm in soil pit M6, dated at 5479-5698 cal. yr BP (1 sigma) using spores, but beyond calibration using bulk SOM. The spore dates were all within the range to be expected of postglacial paleosols, but the bulk SOM dates were frequently beyond the generally accepted time of deglaciation. In addition, all of the spore dates followed a conventional age/depth pattern while the bulk SOM dates did not. There are known possible sources of geogenic carbon contamination in Karkevagge which may well account for the obviously invalid older bulk SOM dates. An additional complication is that the spore dates vary somewhat with their density and diameter. However, where other types of fossil or charcoal are unavailable it appears that the enormously broad distribution of spores and their lack of interaction within the soil and persistence may well offer the prospect of an unusually useful radiocarbon dating medium within paleosols.
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