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Publications (9 of 9) Show all publications
Arias, C., Obudulu, O., Zhao, X., Ansolia, P., Zhang, X., Paul, S., . . . Bajhaiya, A. K. (2020). Nuclear proteome analysis of Chlamydomonas with response to CO2 limitation. Algal Research, 46, Article ID 101765.
Open this publication in new window or tab >>Nuclear proteome analysis of Chlamydomonas with response to CO2 limitation
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2020 (English)In: Algal Research, ISSN 2211-9264, Vol. 46, article id 101765Article in journal (Refereed) Published
Abstract [en]

Chlamydomonas reinhardtii is a unicellular green alga that can survive at a wide range of inorganic carbon (Ci) concentrations by regulating the activity of a CO2-concentrating mechanism (CCM) as well as other cellular functions. Under CO2 limited conditions, C. reinhardtii cells display a wide range of adaptive responses including changes in photosynthetic electron transport, mitochondria localization in the cells, the structure of the pyrenoid starch sheath, and primary metabolism. In addition to these functional and structural changes, gene and protein expression are also affected. Several physiological aspects of the CO2 response mechanism have been studied in detail. However, the regulatory components (transcription factors and transcriptional regulators) involved in this process are not fully characterized. Here we report a comprehensive analysis of the C. reinhardtii nuclear proteome using liquid chromatography electrospray ionization spectrometry (LC-ESI-MS). The study aims to identify the proteins that govern adaptation to varying CO2 concentrations in Chlamydomonas. The nuclear proteome of C. reinhardtii cells grown in the air at high (5%) and low (0.04%) CO2 concentrations were analyzed. Using this approach, we identified 1378 proteins in total, including 90 putative transcription factors and 27 transcriptional regulators. Characterization of these new regulatory components could shed light on the molecular mechanisms underlying acclimation to CO2 stress.

Place, publisher, year, edition, pages
Elsevier, 2020
Keywords
Chlamydomonas, CO2-concentrating mechanism, Nucleus proteome, Ribosomes, Spliceosome, Transcription factors and regulators
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-168841 (URN)10.1016/j.algal.2019.101765 (DOI)000512364900033 ()
Available from: 2020-03-18 Created: 2020-03-18 Last updated: 2020-03-18Bibliographically approved
Obudulu, O., Mähler, N., Skotare, T., Bygdell, J., Abreu, I. N., Ahnlund, M., . . . Tuominen, H. (2018). A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees. BMC Genomics, 19, Article ID 11.
Open this publication in new window or tab >>A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees
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2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 11Article in journal (Refereed) Published
Abstract [en]

Background: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3;Potri.019G104000).

Results: The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with a tendency towards increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. Multivariate OnPLS (orthogonal projections to latent structures) modeling of five different omics datasets (the transcriptome, proteome, GC-MS metabolome, LC-MS metabolome and pyrolysis-GC/MS metabolome) collected from the secondary xylem tissues of the stem revealed systemic variation in the different variables in the transgenic lines, including changes that correlated with the changes in the secondary cell wall composition. The OnPLS model also identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis.

Conclusions: Populus SCAMP proteins were shown to influence accumulation of secondary cell wall components, including polysaccharides and phenolic compounds, in the woody tissues of Populus tree stems. Our multi-omics analyses combined with the OnPLS modelling suggest that this function is mediated by changes in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.

Place, publisher, year, edition, pages
Springer Publishing Company, 2018
Keywords
Secretory Carrier-Associated Membrane Protein (SCAMP), Populus, Wood chemistry, Wood density, Biomass, Bioprocessing, Cork, Multi-omics
National Category
Cell Biology
Identifiers
urn:nbn:se:umu:diva-143890 (URN)10.1186/s12864-017-4411-1 (DOI)000419232000004 ()
Projects
Bio4Energy
Funder
Swedish Research Council Formas, 232-2009-1698
Available from: 2018-01-12 Created: 2018-01-12 Last updated: 2020-01-30Bibliographically approved
Piltti, J., Bygdell, J., Qu, C. & Lammi, M. (2018). Effects of long-term hypoxia in human chondrosarcoma cells. Journal of Cellular Biochemistry, 119(2), 2320-2332
Open this publication in new window or tab >>Effects of long-term hypoxia in human chondrosarcoma cells
2018 (English)In: Journal of Cellular Biochemistry, ISSN 0730-2312, E-ISSN 1097-4644, Vol. 119, no 2, p. 2320-2332Article in journal (Refereed) Published
Abstract [en]

The cell-based therapies could be potential methods to treat damaged cartilage tissues. Instead of native hyaline cartilage, the current therapies generate mainly weaker fibrocartilage-type of repair tissue. A correct microenvironment influences the cellular phenotype, and together with external factors it can be used, e.g., to aid the differentiation of mesenchymal stem cells to defined types of differentiated adult cells. In this study, we investigated the effect of long-term exposure to 5% low oxygen atmosphere on human chondrosarcoma HCS-2/8 cells. This atmosphere is close to normal oxygen tension of cartilage tissue. The proteome was analyzed with label-free mass spectrometric method and further bioinformatic analysis. The qRT-PCR method was used to gene expression analysis, and ELISA and dimethylmethylene blue assays for type II collagen and sulfated glycosaminoglycan measurements. The hypoxic atmosphere did not influence cell proliferation, but enhanced slightly ACAN and COL2A1 gene expression. Proteomic screening revealed a number of hypoxia-induced protein level responses. Increased ones included NDUFA4L2, P4HA1, NDRG1, MIF, LDHA, PYGL, while TXNRD1, BAG2, TXN2, AQSTM1, TNFRSF1B and EPHX1 decreased during the long-term hypoxia. Also a number of proteins previously not related to hypoxia changed during the treatment. Of those S100P, RPSS26, NDUFB11, CDV3 and TUBB8 had elevated levels, while ALCAM, HLA-B, EIF1, and ACOT9 were lower in the hypoxia samples. In conclusion, low oxygen condition causes changes in the cellular amounts of several proteins.

Place, publisher, year, edition, pages
John Wiley & Sons, 2018
Keywords
chondrosarcoma, extracellular matrix, hypoxia, label-free quantitative proteomics, S100 proteins
National Category
Cell Biology Cell and Molecular Biology
Research subject
Biochemistry; cell research; Medical Cell Biology
Identifiers
urn:nbn:se:umu:diva-138929 (URN)10.1002/jcb.26394 (DOI)000418708300098 ()28865129 (PubMedID)
Funder
Swedish Rheumatism Association, R-567071
Available from: 2017-09-04 Created: 2017-09-04 Last updated: 2018-12-18Bibliographically approved
Bollhöner, B., Jokipii-Lukkari, S., Bygdell, J., Stael, S., Adriasola, M., Muñiz, L., . . . Tuominen, H. (2018). The function of two type II metacaspases in woody tissues of Populus trees. New Phytologist, 217(4), 1551-1565
Open this publication in new window or tab >>The function of two type II metacaspases in woody tissues of Populus trees
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2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 4, p. 1551-1565Article in journal (Refereed) Published
Abstract [en]

Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populustremulaxtremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2018
Keywords
aspartic protease, cellular autolysis, cysteine protease, metacaspase, Populus, programmed cell ath, wood formation, xylem differentiation
National Category
Plant Biotechnology
Identifiers
urn:nbn:se:umu:diva-145132 (URN)10.1111/nph.14945 (DOI)000424284400017 ()29243818 (PubMedID)
Projects
Bio4Energy
Available from: 2018-03-05 Created: 2018-03-05 Last updated: 2019-08-30Bibliographically approved
Bygdell, J., Srivastava, V., Obudulu, O., Srivastava, M. K., Nilsson, R., Sundberg, B., . . . Wingsle, G. (2017). Protein expression in tension wood formation monitored at high tissue resolution in Populus. Journal of Experimental Botany, 68(13), 3405-3417
Open this publication in new window or tab >>Protein expression in tension wood formation monitored at high tissue resolution in Populus
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2017 (English)In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, p. 3405-3417Article in journal (Refereed) Published
Abstract [en]

Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

Place, publisher, year, edition, pages
Oxford University Press, 2017
Keywords
cell wall, cellulose, lignin, Populus, proteomics, tension wood, tissue resolution, xylogenesis
National Category
Plant Biotechnology Botany
Identifiers
urn:nbn:se:umu:diva-139165 (URN)10.1093/jxb/erx186 (DOI)000408119100011 ()
Projects
Bio4Energy
Available from: 2017-09-08 Created: 2017-09-08 Last updated: 2019-09-06Bibliographically approved
Piltti, J., Bygdell, J., Fernández-Echevarría, C., Marcellino, D. & Lammi, M. (2017). Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and change the S100 protein profile in human chondrosarcoma cells. Scientific Reports, 7, Article ID 3708.
Open this publication in new window or tab >>Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and change the S100 protein profile in human chondrosarcoma cells
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2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 3708Article in journal (Refereed) Published
Abstract [en]

Articular chondrocytes are slowly dividing cells that tend to lose their cell type-specific phenotype and ability to produce structurally and functionally correct cartilage tissue when cultured. Thus, culture conditions, which enhance the maintenance of chondrocyte phenotype would be very useful for cartilage research. Here we show that Rho-kinase inhibition by Y-27632 under hypoxic conditions efficiently maintains and even enhances chondrocyte-specific extracellular matrix production by chondrocytic cells. The effects of long-term Y-27632 exposure to human chondrosarcoma 2/8 cell phenotype maintenance and extracellular matrix production were studied at normoxia and at a 5% low oxygen atmosphere. Y-27632 treatment at normoxia induced ACAN and COL2A1 gene up-regulation and a minor increase of sulfated glycosaminoglycans (sGAGs), while type II collagen expression was not significantly up-regulated. A further increase in expression of ACAN and COL2A1 was achieved with Y-27632 treatment and hypoxia. The production of sGAGs increased by 65.8%, and ELISA analysis revealed a 6-fold up-regulation of type II collagen. Y-27632 also induced the up-regulation of S100-A1 and S100-B proteins and modified the expression of several other S100 protein family members, such as S100-A4, S100-A6, S100-A13 and S100-A16. The up-regulation of S100-A1 and S100-B proteins is suggested to enhance the chondrocytic phenotype of these cells.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
Keywords
ROCK inhibitor, chondrocyte, extracellullar matrix, S100 proteins
National Category
Cell and Molecular Biology
Research subject
Biochemistry; cell research; Molecular Biology
Identifiers
urn:nbn:se:umu:diva-133850 (URN)10.1038/s41598-017-03958-5 (DOI)
Available from: 2017-04-19 Created: 2017-04-19 Last updated: 2020-03-18Bibliographically approved
Piltti, J., Bygdell, J., Fernández-Echevarría, C., Marcellino, D. & Lammi, M. (2017). Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells. Scientific Reports, 7, Article ID 3708.
Open this publication in new window or tab >>Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells
Show others...
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 3708Article in journal (Refereed) Published
Abstract [en]

Articular chondrocytes are slowly dividing cells that tend to lose their cell type-specific phenotype and ability to produce structurally and functionally correct cartilage tissue when cultured. Thus, culture conditions, which enhance the maintenance of chondrocyte phenotype would be very useful for cartilage research. Here we show that Rho-kinase inhibition by Y-27632 under hypoxic conditions efficiently maintains and even enhances chondrocyte-specific extracellular matrix production by chondrocytic cells. The effects of long-term Y-27632 exposure to human chondrosarcoma 2/8 cell phenotype maintenance and extracellular matrix production were studied at normoxia and at a 5% low oxygen atmosphere. Y-27632 treatment at normoxia induced ACAN and COL2A1 gene up-regulation and a minor increase of sulfated glycosaminoglycans (sGAGs), while type II collagen expression was not significantly up-regulated. A further increase in expression of ACAN and COL2A1 was achieved with Y-27632 treatment and hypoxia. The production of sGAGs increased by 65.8%, and ELISA analysis revealed a 6-fold up-regulation of type II collagen. Y-27632 also induced the up-regulation of S100-A1 and S100-B proteins and modified the expression of several other S100 protein family members, such as S100-A4, S100-A6, S100-A13 and S100-A16. The up-regulation of S100-A1 and S100-B proteins is suggested to enhance the chondrocytic phenotype of these cells.

Place, publisher, year, edition, pages
London: Nature Publishing Group, 2017
Keywords
Chondrocyte, S-100 proteins, Rho-kinase inhibition, extracellular matrix
National Category
Cell and Molecular Biology Orthopaedics Cell Biology
Research subject
Biochemistry; cell research; molecular medicine (genetics and pathology)
Identifiers
urn:nbn:se:umu:diva-136633 (URN)10.1038/s41598-017-03958-5 (DOI)000403413700070 ()28623370 (PubMedID)
Available from: 2017-06-20 Created: 2017-06-20 Last updated: 2018-06-09Bibliographically approved
Obudulu, O., Bygdell, J., Sundberg, B., Moritz, T., Hvidsten, T. R., Trygg, J. & Wingsle, G. (2016). Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. BMC Genomics, 17, Article ID 119.
Open this publication in new window or tab >>Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development
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2016 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 17, article id 119Article in journal (Refereed) Published
Abstract [en]

Background: Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numerous aspects of both pure and applied plant science) have been made using transcriptomic analyses and/or low-resolution sampling. However, transcriptomic data do not correlate perfectly with levels of expressed proteins due to effects of post-translational modifications and variations in turnover rates. In addition, high-resolution analysis is needed to characterize key transitions. In order to identify protein profiles across the developmental region of wood formation, an in-depth and tissue specific sampling was performed. Results: We examined protein profiles, using an ultra-performance liquid chromatography/quadrupole time of flight mass spectrometry system, in high-resolution tangential sections spanning all wood development zones in Populus tremula from undifferentiated cambium to mature phloem and xylem, including cell expansion and cell death zones. In total, we analyzed 482 sections, 20-160 mu m thick, from four 47-year-old trees growing wild in Sweden. We obtained high quality expression profiles for 3,082 proteins exhibiting consistency across the replicates, considering that the trees were growing in an uncontrolled environment. A combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS) modeling and an enhanced stepwise linear modeling approach identified several major transitions in global protein expression profiles, pinpointing (for example) locations of the cambial division leading to phloem and xylem cells, and secondary cell wall formation zones. We also identified key proteins and associated pathways underlying these developmental landmarks. For example, many of the lignocellulosic related proteins were upregulated in the expansion to the early developmental xylem zone, and for laccases with a rapid decrease in early xylem zones. We observed upregulation of two forms of xylem cysteine protease (Potri.002G005700.1 and Potri.005G256000.2; Pt-XCP2.1) in early xylem and their downregulation in late maturing xylem. Our data also show that Pt-KOR1.3 (Potri.003G151700.2) exhibits an expression pattern that supports the hypothesis put forward in previous studies that this is a key xyloglucanase involved in cellulose biosynthesis in primary cell walls and reduction of cellulose crystallinity in secondary walls. Conclusion: Our novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development.

Keywords
Quantitative proteomics, Stepwise linear modelling, Aspen wood formation
National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-117810 (URN)10.1186/s12864-016-2458-z (DOI)000370225400001 ()
Available from: 2016-04-08 Created: 2016-03-04 Last updated: 2018-06-07Bibliographically approved
Piltti, J., Bygdell, J. & Lammi, M.Effects of long-term hypoxia in human chondrosarcoma cells.
Open this publication in new window or tab >>Effects of long-term hypoxia in human chondrosarcoma cells
(English)Manuscript (preprint) (Other academic)
Abstract
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-133849 (URN)
Available from: 2017-04-19 Created: 2017-04-19 Last updated: 2020-03-18
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-9833-4628

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